1. Genomics and Evolutionary Biology
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The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa

  1. Paul HGM Dirks Is a corresponding author
  2. Eric M Roberts
  3. Hannah Hilbert-Wolf
  4. Jan D Kramers
  5. John Hawks
  6. Anthony Dosseto
  7. Mathieu Duval
  8. Marina Elliott
  9. Mary Evans
  10. Rainer Grün
  11. John Hellstrom
  12. Andy IR Herries
  13. Renaud Joannes-Boyau
  14. Tebogo V Makhubela
  15. Christa J Placzek
  16. Jessie Robbins
  17. Carl Spandler
  18. Jelle Wiersma
  19. Jon Woodhead
  20. Lee R Berger
  1. James Cook University, Australia
  2. University of the Witwatersrand, South Africa
  3. University of Johannesburg, South Africa
  4. University of Wisconsin-Madison, United States
  5. University of Wollongong, Australia
  6. Environmental Futures Research Institute, Griffith University, Australia
  7. Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Spain
  8. The Australian National University, Australia
  9. The University of Melbourne, Australia
  10. La Trobe University, Australia
  11. Southern Cross University, Australia
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Cite as: eLife 2017;6:e24231 doi: 10.7554/eLife.24231

Abstract

New ages for flowstone, sediments and fossil bones from the Dinaledi Chamber are presented. We combined optically stimulated luminescence dating of sediments with U-Th and palaeomagnetic analyses of flowstones to establish that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity (sub-unit 3b), interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested by varying the assumed levels of 222Rn loss in the encasing sediments: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils. By combining the US-ESR maximum age estimate obtained from the teeth, with the U-Th age for the oldest flowstone overlying Homo naledi fossils, we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology.

https://doi.org/10.7554/eLife.24231.001

eLife digest

Species of ancient humans and the extinct relatives of our ancestors are typically described from a limited number of fossils. However, this was not the case with Homo naledi. More than 1500 fossils representing at least 15 individuals of this species were unearthed from the Rising Star cave system in South Africa between 2013 and 2014. Found deep underground in the Dinaledi Chamber, the H. naledi fossils are the largest collection of a single species of an ancient human-relative discovered in Africa.

After the discovery was reported, a number of questions still remained. Not least among these questions was: how old were the fossils? The material was undated, and predictions ranged from anywhere between 2 million years old and 100,000 years old. H. naledi shared several traits with the most primitive of our ancient relatives, including its small brain. As a result, many scientists guessed that H. naledi was an old species in our family tree, and possibly one of the earliest species to evolve in the genus Homo.

Now, Dirks et al. – who include many of the researchers who were involved in the discovery of H. naledi – report that the fossils are most likely between 236,000 and 335,000 years old. These dates are based on measuring the concentration of radioactive elements, and the damage caused by these elements (which accumulates over time), in three fossilized teeth, plus surrounding rock and sediments from the cave chamber. Importantly, the most crucial tests were carried out at independent laboratories around the world, and the scientists conducted the tests without knowing the results of the other laboratories. Dirks et al. took these extra steps to make sure that the results obtained were reproducible and unbiased.

The estimated dates are much more recent than many had predicted, and mean that H. naledi was alive at the same time as the earliest members of our own species – which most likely evolved between 300,000 and 200,000 years ago. These new findings demonstrate why it can be unwise to try to predict the age of a fossil based only on its appearance, and emphasize the importance of dating specimens via independent tests. Finally in two related reports, Berger et al. suggest how a primitive-looking species like H. naledi survived more recently than many would have predicted, while Hawks et al. describe the discovery of more H. naledi fossils from a separate chamber in the same cave system.

https://doi.org/10.7554/eLife.24231.002

Introduction

The fossil assemblage attributed to Homo naledi from the Rising Star Cave in the Cradle of Humankind, UNESCO World Heritage Area, South Africa (CoH) (Berger et al., 2015), represents one of the richest and most unusual taphonomic assemblages yet discovered in the hominin fossil record (Dirks et al., 2015). The remains are exceptionally well preserved and represent the largest collection of fossils from a single primitive hominin species ever discovered in Africa. The H. naledi fossils occur without a direct association with non-hominin macrofossil remains, and are found deep inside the difficult to access U.W.101-Dinaledi Chamber (Dirks et al., 2015). The Dinaledi Chamber is characterised by a sedimentary environment that is geochemically and sedimentologically distinct from the rest of the Rising Star Cave (Dirks et al., 2015), and the fossiliferous deposit it contains is profoundly different from other known hominin-bearing cave assemblages in the CoH (e.g., Reynolds and Kibii, 2011; Dirks et al., 2010; Pickering et al., 2011a; Dirks and Berger, 2013; Bruxelles et al., 2014). The fossils occur as a dense bone accumulation in mostly unconsolidated muddy sediment that largely originated from within the cave through weathering of the dolomite host rock (Dirks et al., 2015). The fossils have not been dated until now.

In this paper we present results of uranium-thorium (U-Th) disequilibrium, electron spin resonance (ESR), radiocarbon, and optically stimulated luminescence (OSL) dating in combination with palaeomagnetic analyses, to provide ages for the fossils and surrounding deposits in the Dinaledi Chamber, and build upon the geological context described in Dirks et al. (2015). Dates acquired via U-Th and ESR techniques were obtained using a double blind approach for each technique to ensure robust, reproducible results, with each laboratory using their own analytical and computational approach. Approaches taken by each laboratory that contributed to this paper are described in detail in the methodology section.

The age of the hominins in the Dinaledi Chamber has implications for our understanding of the mode and tempo of the morphological evolution of hominins (Hawks and Berger, 2016), raising questions about evolutionary stasis and the role of refugia. The results challenge our ability to associate given hominin species to specific cultures and behaviours in the past. These issues are discussed in greater detail in an accompanying paper (Berger et al., 2017).

Geological setting

The caves in the Cradle of Humankind (CoH), South Africa have yielded rich fossil assemblages of late Pliocene to early Pleistocene age, which include a range of hominin species (A. africanus, A. prometheus, A. sediba, P. robustus, H. ergaster, H. naledi and early Homo) and associated mammals, reptiles, and birds (e.g., Vrba, 1975, 1995; Brain, 1993; Tobias, 2000; Berger et al., 2010, 2015). For the past 3 million years, hominin-bearing deposits in caves formed in broadly similar settings, involving debris cone accumulations near cave openings (Partridge, 1973; Wilkinson, 1985; Brain, 1993; Pickering et al., 2007; de Ruiter et al., 2009; Dirks and Berger, 2013; Herries and Adams, 2013; Dirks et al., 2010, 2016b; Bruxelles et al., 2014; Stratford et al., 2014), with deposits cemented by carbonate-rich waters dripping from cave ceilings (e.g., Wilkinson, 1985; Pickering et al., 2011b). In contrast to all other hominin deposits in the CoH, the deposits that host H. naledi in Rising Star Cave are composed of largely unconsolidated, mud-clast breccia in a mud matrix with no evidence of coarse clastic sediment being carried in by water flow. This suggests a different depositional regime and timing for the sediments and the fossils (Dirks et al., 2015, Dirks et al., 2016a).

Rising Star Cave is situated in the Bloubank River valley, 2.2 km W of Sterkfontein Cave. The cave system comprises several kilometres of mapped passageways (Figure 1a) that are stratigraphically bound to a 20–30 m-thick, chert-poor dolomite horizon capped by a 1–1.3 m-thick chert unit that forms the roof to the cave system (Dirks et al., 2015). Geological mapping and laser-theodolite surveys indicate that this roof is intact and not penetrated by significant shafts that open to surface (Dirks et al., 2015; Kruger et al., 2016). The broader geological setting of the cave is discussed in Dirks et al. (2015), (Dirks et al., 2016a).

Location of Rising Star Cave and the Dinaledi Chamber.

(a) Simplified geological map showing the position of the Rising Star Cave (in grey); (b) close-up map of the Dinaledi Chamber showing the distribution of the dating samples, including: U-Th flowstone samples (yellow dots, black text); ESR samples (purple dots, orange text); and OSL samples (red dots, blue text). Age estimates for the different samples are shown, with cross reference to Tables 1, 7 and 8.

https://doi.org/10.7554/eLife.24231.003

The Dinaledi Chamber, which contains most of the fossils of H. naledi, is ~30 m below surface and ~80 m in a straight line from the nearest present-day opening to the surface (Figure 1a). The main cavity forming the Dinaledi Chamber is ~15 m long with variable widths not exceeding 2.5 meters (Figure 1b), and expands near the intersection with a crosscutting passage, which is the location of the main excavation site to date (Figure 1b). There is no evidence that the present entrance into the Dinaledi Chamber has significantly changed since the deposition of the fossil hominins, with sediment accumulating mostly near the current access point (Dirks et al., 2015, Dirks et al., 2016a; Figure 2). Samples for dating were collected from the various flowstone horizons and stratigraphic units exposed in the Dinaledi Chamber (Figures 1b, 2, 3, 4 and 5) as well as from fossil material itself (Figures 4, 6 and 7).

Geological face map and cross-sections through the sediment pile at different locations in the Dinaledi Chamber, illustrating the relationships between the flowstone groups and sedimentary units.

The positions of the section lines are shown in (a); a face map of the entry zone of the Dinaledi Chamber (looking NE) is shown in (b); geological cross-sections through the central part of the Dinaledi Chamber near the excavation pit are shown in (c) and (d).

https://doi.org/10.7554/eLife.24231.004

Lithologic and stratigraphic context for dating

The Dinaledi Chamber contains deposits of fine-grained, muddy sediments intercalated with flowstone drapes. The sediments include various types of orange, laminated mudstone and mud clast breccia distributed across three broad lithostratigraphic units (Units 1, 2 and 3; Dirks et al., 2015) that filled parts of the chamber over time. Based on variations in sediment composition, fossil content and/or stratigraphic position of each unit, we have divided Unit 1 into sub-units 1a, 1b and 1c, and Unit 3 into sub-units 3a and 3b, to more precisely define the stratigraphic packages targeted for dating (Figure 2). The units are separated by erosional unconformities or flowstone intercalations, but do not all necessarily occur in direct contact with one another due to the complex nature of caves as depositional systems (e.g., Brain, 1993; Martini et al., 2003). In addition, apart from sediments accumulating along the floor of the cave chamber, sediment in the form of orange mud deposits also accumulated inside fractures and along ledges higher up in the Dinaledi Chamber (Figure 2b), where it formed as a result of the combined effect of in situ weathering and deposition from water flowing down fractures and side walls. All units and sub-units are time-transgressive, meaning that they are lithostratigraphic units and not chronostratigraphic units that occur in strict temporal order. Periods of sedimentation alternated with periods of erosion, during which sediments were either redeposited or removed from the chamber via floor drains, resulting in erosional remnants of all units occurring in a variety of stratigraphic positions (Dirks et al., 2015).

Stalactites have formed at drip points along the roof and associated stalagmites formed below these points. In one area below the entrance to the chamber, these drip points repeatedly formed flowstone aprons over cave sediments that dip towards the deeper part of the chamber. Flowstone also formed as cascades and curtains that developed where water seeped down fractures and ran along the walls to locally spread out, horizontally, across the sediments comprising the cave floor (Dirks et al., 2015). The flowstones have preliminarily been sub-divided into three groups demarcating semi-contemporaneous generations of formation, which we named Flowstone Groups 1, 2 and 3 based on their appearance and relationships with each other, and with the floor sediments and other litho-stratigraphic units in the chamber. In making this subdivision it was realised that each group of flowstones will probably comprise a range of ages representing separate flowstone forming events (Dirks et al., 2015), a fact borne out by the ages presented below (Table 1).

Flowstone Group 1 (FS1 in Table 1; Figures 1b, 2 and 3) includes remnants of what are interpreted to be generally older flowstone units that were partly dissolved and resorbed to leave behind rims or aprons along the side walls of the cave chamber, some with sediment attached below them. Flowstone remnants interpreted as Flowstone Group 1 are mostly restricted to five staggered remnants (Flowstones 1a-e), one above the other in reverse stratigraphic order (oldest on top, youngest at the bottom), near the entry shaft into the Dinaledi Chamber (Figure 2b). Flowstone Group 2, the most extensive group of flowstones in the chamber (FS2 in Table 1, and Figures 1b, 2 and 3), comprises wall aprons and sheets that have spread out across the floor of the Dinaledi Chamber together with drip pools, cascades, curtains, stalactites and stalagmites that connect to these sheets, and, therefore, formed in conjunction with them. Flowstone Group 3 (FS3 in Table 1 and Figures 1b, 2 and 3) comprises the flowstone deposits that are actively forming below existing drip points, and include fresh growth of delicate crystals of aragonite and calcite in floor sediments and along cave walls.

Sedimentary deposits within the Dinaledi Chamber can be organized into three primary stratigraphic units (Dirks et al., 2015). Unit 1 consists of deposits of non-lithified, laminated, orange mud interpreted as suspension deposits in standing water (Facies 1a of Dirks et al., 2015), and laminated mud with fine sand containing small-scale ripple cross laminations and rodent remains (Facies 1b of Dirks et al., 2015), reflecting deposition by shallow, flowing water along the cave floor, with additional sandy material accumulating near local entry points, where fractures higher in the chamber act as sediment conduits (Dirks et al., 2015, Dirks et al., 2016a).

Within the Dinaledi Chamber Unit 1 deposits can be divided into three sub-units provisionally called sub-units 1a, 1b and 1c. It is assumed that Unit 1 is time-transgressive and future work may reveal additional sub-units. Sub-unit 1a is composed of laminated orange mudstone with isolated lenses of sandy material, occurs as erosion remnants along the cave floor, and is possibly more extensive beneath younger deposits in the chamber. Sub-unit 1b is dominated by sandy orange mud deposits that are rich in micro-faunal remain, stratigraphically overlies deposits of sub-unit 1a (Figure 2c and d), and may have formed through the partial erosion and re-deposition of sub-unit 1a. Deposits of sub-unit 1c are similar in appearance and composition to the laminated, muddy sediments of sub-unit 1a, but they occur along chert ledges, solution pockets and fractures in the chamber walls and along the entry shaft, higher up in the cave chamber (Figure 2). The orange mud is mostly the product of the cave formation process, representing the insoluble residue left over when cavities develop via dissolution of dolomite (Dirks et al., 2015). Some of the mud-bearing waters seeping out of the fractures would have flowed as water films along the cave walls to deposit mud on ledges and in fractures to form sub-unit 1c, whilst elsewhere this water would have dripped to the floor to contribute to the deposition of sub-unit 1a and 1b.

Unit 2 is composed of largely lithified mud clast breccia consisting of angular to sub-angular clasts of laminated orange mudstone (similar to that found in Unit 1), embedded in a brown mud matrix (Facies 2 of Dirks et al., 2015). The mud clasts are interpreted to be derived locally due to wetting and drying of orange mud deposits, which led to auto-brecciation, and subsequent erosion and re-deposition of angular mud clasts (Dirks et al., 2015). We hypothesize that the mud clasts forming Unit 2 are partly derived from erosion of deposits of sub-unit 1c, and partly from a yet unidentified unit that was likely deposited in fractures within and above the chamber entry zone. Two macro-fossils (partial shafts of long bones) that are non-specific, but not hominin, have been found in Unit 2.

Unit 2 sediments are only exposed as hanging remnants attached below the remains of a composite flowstone sheet (Flowstone 1a) near the entrance shaft into the chamber (Figure 2b; Dirks et al., 2015). Note that in Dirks et al. (2015) Unit 2 was originally defined to also include sediments below Flowstones 1b-e; however, based on our new dating results, the revised definition of Unit 2 has been narrowed to only include the more indurated and distinctly darker coloured erosional remnants of mud clast breccia under Flowstone 1a, which are notable for their absence of hominin fossils. Unit 2 sediments accumulated as a sloping debris cone of mud clast breccia below a vertical fracture system before being covered by flowstone (Flowstone 1a). The debris cone of mud clast breccia was subsequently eroded leaving behind hanging erosion remnants of Unit 2 below a flowstone apron (Figures 2b and 3l). The processes that caused erosion of the Unit 2 debris cone led to the deposition of Unit 3 sediment along the floor of the Dinaledi Chamber as shown in Figure 8.

Unit 3 is composed of largely unlithified, clast-supported, mud clast breccia (Facies 2 of Dirks et al., 2015), dominated by reworked angular to sub-angular mud clasts, which are interpreted as being locally derived from the reworking of Units 1 and 2. Unit 3 accumulated below the hanging remnants of the Unit 2 debris cone near the entry shaft, and also extends along the current, sloping cave floor to the SW end of the chamber (Figures 2c and 8). Unit 3 sediments are dynamic in the sense that they are poorly lithified in most places and actively slump towards, and erode into, floor drains that occur in parts of the chamber where sediment is being washed down to deeper levels in the cave (likely as a result of fluctuations in the ground water level). Remains of Unit 3 sediment are attached to apron-like erosional remnants of Flowstones 1b-e near the entrance shaft (Figure 2a and 3l). Erosional remnants of Unit 3 under Flowstone 1c contain in situ long bones consistent with H. naledi, which are actively eroding out and accumulating along the present cave floor. Note that Dirks et al. (2015) originally included these erosional remnants as part of Unit 2. Everywhere else, Unit 3 deposits are spread across the cave floor as loosely packed, semi-moist, orange mud clasts of varying sizes in which bone material of H. naledi is distributed. Unit 3 is partly covered by sheets of Flowstone Groups 1, 2 and 3.

Unit 3 has been divided into a lower and an upper sub-unit, termed sub-unit 3a and 3b (Figure 2), based on the respective absence or presence of hominin fossils. Sediments belonging to sub-unit 3a are not directly exposed in the chamber, but their presence has been confirmed in the deepest part of the excavation area (Figure 2d). In contrast sub-unit 3b is exposed within the talus cone near the entry shaft and along the cave floor, and contains all of the known H. naledi fossils in the chamber (Figure 2c and d). The thickness of sub-unit 3b is thought to be no more than 20–30 cm (see below).

The distribution of fossils, units, and flowstones

All hominin bones identified in the Dinaledi Chamber are contained in deposits of sub-unit 3b. Bones attributed to H. naledi have been recovered as: (a) isolated elements that weathered out from erosion remnants of sub-unit 3b below Flowstones 1b-e; (b) as fragmented remains scattered across the cave floor; and (c) as partly articulated remains from a single excavation pit down to a depth of ~20 cm below the current floor level (Dirks et al., 2015).

Preliminary ground penetrating radar work (Naidoo, 2016) suggests that Unit 3 deposits along the floor of the Dinaledi Chamber could be up to 1.5 m thick. A 50 cm-deep sondage was dug in the centre of the excavation pit, which itself is 20 cm deep, to indicate a minimum depth of 70 cm for the mud clast breccia pile of Unit 3. The top 20 cm of this sediment contains H. naledi remains and is part of sub-unit 3b (Figure 2d). A discrete contact occurs at 15–20 cm depth, below which no more fossils were encountered with the exception of a single juvenile baboon tooth (sample 1841; Figure 7) that was recovered from a depth of 55–60 cm below the original cave floor surface in sediment of sub-unit 3a (Figures 2 and 8).

Staining patterns on bone fragments, skeletal element representation, and the fact that bones can be seen to weather out from erosional remnants of sub-unit 3b, indicate that part of the fossil assemblage has been reworked (Dirks et al., 2015). The presence of well-articulated remains in the excavation pit away from the chamber entrance indicates that some of the remains entered the cave intact. The mixed taphonomic signature suggests that fossils entered the cave over a period of time, which is minimally assumed to be during deposition of sub-unit 3b, and before deposition of Flowstone 1c. Fossil entry may have continued as sediment accumulations of sub-unit 3b near the entry shaft were reworked and redistributed along the cave floor (Figure 8).

The stratigraphic relationships in the Dinaledi Chamber suggest that Unit 1 sediments were deposited over a long period, which both predates and spans the more limited depositional timeframes of Units 2 and 3. Hence, Unit 1 is time-transgressive, meaning that these sediments were (and are) constantly forming in different parts of the chamber due to weathering of the dolomitic cave walls (i.e., wad formation sensu Martini et al., 2003), and that their age is dependent upon where in the cave the material is located. At present, we can only divide Unit 1 into three sub-units, but we hypothesize that an older sub-unit consisting of laminated orange mudstone exists (or existed) higher up in the chamber as well (possibly only on ledges and in fractures), which was eroded to provide some of the sediment that formed Unit 2 and parts of Unit 3, near the entry shaft.

Flowstone 1a, which overlies remnants of Unit 2, is the oldest flowstone unit in the chamber, and displays evidence of multiple phases of flowstone formation followed by partial dissolution (Figure 2b). Flowstone dissolution occurred during time periods when the water table was elevated and the chamber was filled with standing water. The erosion remnants of Flowstone 1a dip towards the deeper part of the chamber, indicating that at the time of its formation, a sloping debris cone of Unit 2 sediment was present. Erosion of Unit 2 sediments from underneath Flowstone 1a only occurred after the flowstone had formed and lithified the top of Unit 2. Following erosion of Unit 2, deposition of Unit 3 began, as sediment and mud clasts spread out over the cave floor and also filled much of the space underneath Flowstone 1a. This has led to an inverted stratigraphy near the cave entrance, although a normal stratigraphy is documented at the bottom of the chamber, where the cave floor is flat lying and sediment of Unit 3 progressively built up (Figures 2b and 8). At some point during these processes remains of H. naledi entered the cave chamber, marking the start of deposition of sub-unit 3b. Following deposition of sub-unit 3b and the hominin remains, Flowstones 1b-e were deposited over sub-unit 3b in the entry zone. These flowstones have been interpreted as younger than Flowstone 1a, but older than the Flowstone Group 2 sheets along the cave floor. In other words, after deposition of Unit 3 commenced to form the talus cone near the entrance of the chamber, parts of the cone slumped and eroded down towards deeper parts of the chamber after Flowstones 1b-e were deposited, but before Flowstone Group 2 was deposited. This slumping motion was probably driven by sediment being removed from the base of the stratigraphic pile through floor drains.

Flowstone Group 2 covers erosion remnants of Flowstones 1a-e as coatings and stalactites along drip rims. In places, Flowstone Group 2 also covers erosion remnants of Unit 1 and Unit 3 along the floor and displays variable relationships with Unit 3 (Figure 2). Where parts of Unit 3 have been eroded via floor drains, hanging remnants of Flowstone Group 2 can be found attached to the walls as fringing aprons, up to 10 cm above the current floor level, establishing the fact that parts of the floor are currently in a state of erosion. In other places, Flowstone Group 2 sheets directly overlie Unit 3 and the H. naledi fossils it contains. These varying relationships indicate that Flowstone Group 2 sheets were deposited over an extended period of time, post-dating deposition and partial reworking of sub-unit 3b.

In summary, the stratigraphic context indicates that the H. naledi fossils entered the cave during deposition (and possibly during partial reworking) of sub-unit 3b, after deposition of the older sediments of Unit 1 (sub-unit 1a) and Unit 2. Several isolated, non-hominin bone fragments in hanging erosion remnants of Unit 2 and a single baboon tooth in floor sediments in sub-unit 3a were deposited prior to the entry of the hominin remains. The accumulation of Unit 3 along the cave floor involved a dynamic interplay between the accumulation of mud clast breccia below sediment entry points or in situ sediment sources (Unit 1 and Unit 2) in the chamber, and erosion through floor drains resulting in contrasting stratigraphic relationships across the chamber (Figures 2 and 8).

Dating the H. naledi fossils

Most fossil deposits in the Cradle of Humankind that have been dated are between 0.5 and 3.7 Ma old and consist of bone material encased in well-cemented hard clastic rocks commonly referred to as cave breccia (e.g., Wilkinson, 1985; O'Regan and Reynolds, 2009; Herries et al., 2009; Pickering et al., 2011b; Granger et al., 2015). In the absence of volcanic deposits, it is generally difficult to obtain accurate ages for the fossils, not just because reliable techniques are few, but mostly because the stratigraphic sequences in the caves are complex, discontinuous and frequently reworked (e.g., Brain, 1993; Pickering et al., 2011a; Bruxelles et al., 2014; Stratford et al., 2014). Workers have relied on a combination of biochronology of faunal remains, palaeomagnetic work and a range of radiometric methods, including U-Pb, U-Th and ESR dating targeting flowstones and fossil teeth (e.g., Vrba, 1975; Partridge et al., 1999; Berger et al., 2002; Walker et al., 2006; Herries et al., 2006, 2013, 2014; Herries and Shaw, 2011; Dirks et al., 2010; Pickering and Kramers, 2010; Pickering et al., 2011a; Herries and Adams, 2013), as well as limited cosmogenic (10Be, 16Al) dating (e.g., Partridge et al., 2003; Granger et al., 2015; Dirks et al., 2016b). Whilst some of these techniques are well established, others such as the application of cosmogenic isochrons (e.g., Granger et al., 2015) are relatively new and not without significant analytical (and interpretative) challenges (Kramers and Dirks, 2017), and all efforts are strongly dependent on the stratigraphic interpretation of the fossils or units that are being dated.

Unlike other fossil deposits in the Cradle of Humankind, the remains in the Dinaledi Chamber are largely restricted to hominins. This makes it impossible to use biochronology as a preliminary technique to assess the age of the fossils. In addition, the fossils are contained in mostly unconsolidated muddy sediment with clear evidence of a mixed taphonomic signature indicative of repeated cycles of reworking and more than one episode of primary deposition (Dirks et al., 2015). This indicates that caution is required when interpreting the stratigraphy and the age of the fossils they contain.

In preparation for this study, trial dating of the deposits in the Dinaledi Chamber was undertaken to obtain an indication of the age of the deposit and the best techniques to apply. Preliminary work was focussed on assessing the viability of U-series techniques for flowstone dating, using 14C for dating bone fragments, and using OSL to test samples of quartz-bearing Unit 1 (Dirks et al., 2015). Initial tests were carried out at the University of Johannesburg (UJ) to assess suitability for U-Pb dating, which allows for the dating of older (>500 ka) flowstone material (e.g., Walker et al., 2006; Pickering et al., 2010; Pickering and Kramers, 2010), on the assumption that the H. naledi material could be older than 1 Ma based on its primitive morphology (Berger et al., 2015; Dembo et al., 2016; Hawks and Berger, 2016; Thackeray, 2016; Hawks et al., 2017). It was found that the older flowstones in the Dinaledi Chamber contained excessive common Pb caused by the inclusion of detrital material (mainly clays) making them unsuitable for U-Pb dating (Dirks et al., 2015). In contrast, preliminary tests with U-Th disequilibrium dating at James Cook University (JCU) returned promising results. U-Th dating is more precise in the <500 ka range than U-Pb dating, and is much less critically affected by detrital material. The initial tests with U-Th disequilibrium dating revealed that the fossils may be much younger than originally anticipated (e.g., Dembo et al., 2016; Thackeray, 2016), and mostly well within the range of the U-Th technique. Therefore, U-Pb dating was not pursued further.

Preliminary tests with OSL were conducted at the University of the Witwatersrand (Wits) on samples from Unit 1, which were assumed to be older than the fossils of H. naledi. These preliminary studies, and the results contained in this paper, are the first OSL results for cave sediments from the CoH, and again indicated that the H. naledi fossils were probably relatively young (i.e.,<500 ka).

Tests with radiocarbon (14C) dating were undertaken through a commercial facility (Beta Analytic Inc. in Florida), to ensure a fast turn-around time for results. At the time these dating tests were done, it was already known from U-Th and OSL tests that the H. naledi fossils would be too old to be dated by 14C. Nevertheless, analyses were carried out as part of the due diligence process, and the results of these tests are presented here. Following this initial work, no further radiocarbon studies were carried out.

The preliminary results have guided the subsequent dating strategy and sampling approach reported here. The dating strategy was designed to achieve three objectives: (i) establish a detailed stratigraphy for the cave sediments in the Dinaledi Chamber; (ii) date sedimentary units that potentially bracket the fossil-bearing deposits; and (iii) date the fossils directly.

To obtain an upper age limit for the fossil-bearing deposits of Unit 3 (i.e. sub-unit 3b), we conducted U-Th dating of flowstones that directly overlie Unit 3. A large number of such flowstones were sampled with the aim of finding the oldest flowstone directly overlying H. naledi fossils. To obtain a lower age limit for sub-unit 3b, erosional remnants of Unit 1 sediments that were at least partially covered by fossil-bearing sub-unit 3b sediments, were sampled for OSL dating on the assumption that sub-units 1a and 1b in these areas are older than sub-unit 3b (Dirks et al., 2015). This was done in the full knowledge that OSL dating of cave sediments is complex and difficult to interpret (e.g., Roberts et al., 2009), and probably imprecise. As an internal control, we also sampled flowstones that cover the outcrops of sub-units 1a and 1b from which OSL samples were taken. These flowstones were dated with U-Th with the expectation that they are younger than the underlying Unit 1 sediments. In addition to OSL, Flowstone 1a, which overlies Unit 2 sediments, was sampled for palaeomagnetic analyses. This flowstone was targeted, because it was expected to be the oldest flowstone in the chamber and possibly older than 780 ka, and hence could potentially record reverse magnetic polarity (e.g., Singer, 2014). In this case, this would constrain the minimum age of Unit 2.

The best age estimates for H. naledi can be obtained by directly dating fossil material. It was clear from preliminary tests that this could not be achieved with 14C, and instead combined ESR and U-Th disequilibrium dating techniques (US-ESR; Grün et al., 1988) were applied to three H. naledi teeth that were freshly collected from near the site of the original excavation (Figures 1, 2, 4 and 6), as well as a single baboon tooth (cf. Papio) that had been recovered from sub-unit 3a below the hominin-bearing horizon (Figures 2d and 7).

Once results were obtained for ESR and U-Th dating, it became apparent that OSL dating would only provide general age constraints that confirmed the ESR results, but in their own right did not return additional age constraints for the fossils. OSL results were also difficult to interpret in the complex cave environment that was strongly affected by Rn loss (see Discussion). It was, therefore, decided not to pursue more detailed OSL studies at this stage, even though we did carry out preliminary tests for single grain and feldspar analyses at the University of Wollongong, to assess the suitability of these techniques. Pilot results are encouraging, and suggest that future, detailed OSL studies are worth pursuing.

Results

U-Th dating of flowstones

U-Th dating of 17 flowstone samples (Figure 3) has yielded minimum depositional age estimates for the sedimentary units they overlie, and has provided insights into the timing of flowstone formation events (Tables 1, 2 and 3). Three separate checks were built into the U-Th dating strategy to ensure robust results would be obtained. Independent dates for the same samples were obtained by laboratories at JCU and at the University of Melbourne (UoM), with results displaying a high degree of concordance. In instances where samples were obtained from the same flowstone layer, but at different stratigraphic levels (e.g., sample pairs RS13 and RS18, RS22 and RS23, RS16 and RS17, and RS11 and RS21) all ages are consistent with stratigraphic order, and blind duplicates of the same sample (RS1 and RS15) returned identical results within error, indicating that results are both accurate and precise. Double blind U-Th results from JCU and UoM are shown in Tables 2 and 3, respectively. The distribution of flowstone ages across the Dinaledi Chamber is shown in Figures 1b and 2.

Field and close-up photographs of all flowstone samples collected for U-Th dating.

The flowstone groups (i.e., Flowstone Groups 1, 2 or 3), sample numbers, and ages (2σ uncertainty), as listed in Table 1, are shown below each sample. Ages reported here are from JCU, unless otherwise stated.

https://doi.org/10.7554/eLife.24231.005
Table 1

Summary table of U-Th disequilibrium ages obtained for samples from the Dinaledi Chamber by James Cook University (JCU - 1) and the University of Melbourne (UoM - 2). The detailed analytical results are shown in Tables 2 and 3. Sample locations are shown in Figure 1b. The data are ranked by increasing age of the oldest flowstone horizon within the sample, based on the JCU ages. The grey shading highlights the different age groupings observed within the flowstones: 24–32 ka, ~50 ka, 88–105 ka, ~242 ka, ~290 ka and >440 ka. Ages are reported relative to 1950.

https://doi.org/10.7554/eLife.24231.006
Sample IDFlowstone groupUnderlying unitAge1 (ka)1 (ka)Age2 (ka)2 (ka)
 RS19FS2sub-unit 3b24.70.224.530.43
 RS11FS3 (top to RS21)FS29.050.069.9460.063
 RS21FS2 (base to RS11)sub-unit 3b28.40.428.620.29
 RS10FS2sub-unit 3b (and bone)30.10.3
 RS20FS2sub-unit 1a (Facies 1a; OSL5)30.40.232.120.38
 RS6FS2sub-unit 1a, sub-unit 3b49.80.350.820.43
 RS15FS2 (blind duplicate of RS1)sub-unit 3b92.61.091.400.65
 RS1FS2 (blind duplicate of RS15)sub-unit 3b91.040.72
 RS8FS2 (below FS1a-e)sub-unit 3b95.01.096.290.69
 RS14FS2in drain, along dolostone wall100.11.296.200.36
 RS17FS2 (top to RS16)in drain, along dolostone wall102.60.898.61.4
 RS16FS2 (base to RS17)in drain, along dolostone wall104.01.999.11.4
 RS13FS2 (rim to RS18)sub-unit 3b88.460.67
 RS18FS1c (core to RS13)sub-unit 3b2425242.96.6
 RS5FS1sub-unit 1b (Facies 1b; OSL4)2906
 RS22FS1a (top to RS23)Unit 2equilibrium478+107/−41
 RS23FS1a (base to RS22)Unit 2equilibrium502+181/−53
 RS9n/a (surface outcrop)n/aequilibriumequilibrium
  1. 1James Cook University (JCU), Advanced Analytical Centre.

  2. 2University of Melbourne (UoM), paleochronology laboratory.

Table 2

U-Th data table for James Cook University. Uncertainties include: analytical error, decay constant uncertainty, and uncertainty on initial 230Th/232Th. Ages are reported relative to 1950 and assume an initial 230Th/232Th activity of 0.83 ± 0.5, and the equation given in Placzek et al. (2006). Decay constants for 234U and 230Th are from Cheng et al. (2013).

https://doi.org/10.7554/eLife.24231.007
Sample IDU (ppm)234U/238U230Th/238U232Th/238UAge (ka BP)2σ (ka)234U/238Uinitial
(activity)(activity)(corrected)(activity)
 RS112.3141.7720.0500.1440.0010.00010880.00000059.050.061.81840.0003
 RS190.6521.8550.0010.3870.0020.0021760.00000824.70.21.9890.001
 RS210.4211.9460.0010.4600.0040.0019200.00001528.40.42.1090.002
 RS100.8461.8850.0010.4660.0030.0007920.00000330.10.32.0530.001
 RS200.7951.8550.0010.4630.0030.0013630.00000530.40.22.0220.001
 RS60.5601.9660.0010.7470.0030.0009740.00000249.80.32.2630.002
 RS150.4001.9120.0011.1640.0080.004720.0000192.61.02.4840.007
 RS80.3281.8130.0031.1200.0080.003160.0000295.01.02.3730.007
 RS140.7341.6390.0951.0390.0080.002980.00002100.11.22.1750.008
 RS170.6801.6090.0011.0320.0050.0006790.000001102.60.82.1500.005
 RS160.9731.5830.0001.0240.0110.0004030.000006104.01.92.120.01
 RS180.1521.8480.0011.8560.0130.011750.0000524253.660.05
 RS50.0901.7280.0011.8180.0090.017320.0000529063.920.07
 RS230.3141.1870.0021.3150.0110.003460.00002>400
 RS220.3671.2090.0011.3220.0080.0001250.000001>400
 RS90.7371.0070.0021.0290.0040.0004620.000001>400
Table 3

U-Th data table for the University of Melbourne. Activity ratios are determined after Hellstrom (2003) and Drysdale et al. (2012). Ages are corrected for initial 230Th using Equation 1 of Hellstrom (2006), the decay constants of Cheng et al. (2013), and an initial 230Th/232Th activity of 1.5 ± 1.5. The initial 234U/238U ratios are calculated using corrected ages, which are reported relative to 1950.

https://doi.org/10.7554/eLife.24231.008
Sample IDU (ppm)234U/238U230Th/238U232Th/238UAge (ka BP)2σ (ka)234U/238Uinitial
(activity)(activity)(corrected)(activity)
 RS111.5181.8080.0030.15970.00090.00008750.00000049.9460.0631.8310.004
 RS190.5011.8840.0110.39160.00260.0043220.00001024.530.431.9470.011
 RS210.3611.9680.0110.46540.00300.00113420.000001928.620.292.0490.011
 RS200.6261.8780.0110.49250.00320.00238370.000004032.120.381.9610.011
 RS60.2762.0230.0040.78560.00210.004960.0001050.820.432.1810.004
 RS130.0762.0060.0041.18370.00470.0047860.00005888.460.672.2910.005
 RS150.3811.9340.0041.16610.00290.006390.0001291.370.652.2090.005
 RS140.6651.6260.0031.00100.00150.0012620.00001496.240.361.8220.003
 RS80.2571.8310.0041.13970.00340.0057460.00006096.290.692.0910.004
 RS170.5171.6370.0091.02480.00660.00239630.000003798.61.41.8410.010
 RS160.9051.5900.0100.99630.00670.00170990.000003799.11.41.7800.011
 RS180.1042.0010.0112.03200.01400.0205570.000041242.96.62.9870.027
 RS220.3241.2280.0071.30170.00830.00012010.0000008478+107/–41
 RS230.2061.2250.0071.30160.00930.0078180.000016502+181/–53
 RS90.8961.0100.0021.02040.00180.0009160.000012

The oldest dated flowstone in the assemblage is Flowstone 1a overlying Unit 2, which yields age estimates of 502 +181/–53 ka (RS 23) and 478 +107/–41 ka (RS 22) (Table 1). The next oldest age comes from a flowstone interpreted as Flowstone Group 1 overlying sediment of sub-unit 1b to the W of the excavation pit (Figure 1b) with an age of 290 ± 6 ka (RS5; Table 1). This age is younger than the OSL age derived from sub-unit 1a (OSL5), but is slightly older than OSL ages derived from sub-unit 1b in this location (OSL4; Figure 2c). This suggests that sub-unit 1a was deposited prior to precipitation of this flowstone and that sub-unit 1b formed out of stratigraphic order due to erosion and redeposition of the top of sub-unit 1a beneath this flowstone. However, the U-Th date for RS5 should be interpreted with caution as the flowstone has a porous texture (Figure 3a), which probably indicates some degree of dissolution and/or recrystallization of the primary calcite, and may have affected the U-Th systematics (see Discussion).

Flowstone samples that overlie sub-unit 3b, which contains the H. naledi fossils, yield age estimates that fall within four distinct time periods: ~242 ka (RS18 = 242 ± 5 ka [JCU] and 242.9 ± 6.6 ka [UoM]) for Flowstone 1c; 88–106 ka (RS1, RS8, RS13-17); 50 ka (RS6); and 24–32 ka (RS10, RS19-21) for Flowstone Group 2 deposits. The results for RS18 provide a minimum age for the H. naledi fossils in this part of the cave.

An actively forming (i.e., dripping) stalagmite of Flowstone Group 3 (RS11) on top of an older base of Flowstone Group 2 returned a younger age of 9–10 ka (RS11 = 9.05 ± 0.06 [JCU] and 9.95 ± 0.06 ka [UoM]). The final flowstone sample that was dated in this study was collected on the land surface above the cave system. It was sampled from a ~14 cm wide vertical flowstone-filled fracture exposed on the surface above the southern end of the Dinaledi Chamber itself. This is the only possible alternative entry-way into the Dinaledi Chamber that we have observed. The replicate samples (RS9) analysed at JCU and UoM both indicated secular equilibrium, which confirms that the flowstone sealed this fracture sometime before ~600 ka, eliminating this thin flowstone-filled fracture as a possible alternative entrance for H. naledi into the Dinaledi Chamber. It should also be noted that no evidence of a talus cone or any other evidence of sediment entry into the chamber below this point has been observed.

The spatial distribution of the flowstones belonging to the different age groups (Figure 1b) indicates that the oldest flowstones (Flowstone Group 1) occur near the entry zone into the chamber and as an erosional remnant (RS 5) near the back of a WNW-trending fracture W of the excavation pit. The 88–106 ka flowstones formed in three separate parts of the chamber (Figure 1b): (a) on top of older flowstones near the entry; (b) as wall drapes above a drain 6 m SW of the entry; and (c) deep within a N-trending fracture, 8 m N of the excavation pit. The ~ 50 ka flowstones originate from a W-trending fracture, 6 m W of the entry shaft where it overlies sub-unit 1a and sub-unit 3b sediments. The 24–32 ka flowstones all originate from around the area where the excavation pit is located at the intersection point of three fracture sets (Figure 1b). The youngest flowstone sample comes from below an active drip point, 1.5 m E of the excavation pit, and similar actively forming flowstones can be seen in other parts of the chamber. The flowstone age groupings indicate that episodic wet periods in the Dinaledi Chamber alternated with periods during which no flowstone was deposited.

U-Th analyses on teeth

U-Th disequilibrium analyses of four tooth samples were conducted to constrain U uptake models into dental tissues used in ESR dating. The analyses were also used to provide apparent U-Th age estimates (Tables 4 and 5). Analyses of all four teeth (samples 1767, 1788 and1810 from H. naledi, and sample 1841 from Papio sp.) were performed at the University of Wollongong (UoW), in collaboration with Southern Cross University (SCU). Duplicate analyses of two of the tooth samples (samples 1788 and 1810) were conducted at Griffith University (GU) in collaboration with the Australian National University (ANU).

Table 4

Summary table of U-Th disequilibrium ages obtained for the three H. naledi teeth (samples 1767, 1788 and 1810) and the baboon tooth (sample 1841) from the Dinaledi Chamber obtained by SCU-UoW. No age calculations were carried out for U concentrations of ≤0.5 ppm or U/Th ≤250 (indicated in red and underlined). Mean values in this table only incorporate values from which meaningful ages could be calculated (indicated in black), however all values (i.e., red and black) were averaged to obtain the relevant mean values reported in Table 4. All uncertainties are given as 2σ.

https://doi.org/10.7554/eLife.24231.009
Sample1767U (ppm)U/Th230Th/238U234U/238UAge (ka)2s (ka)(234U/238U)i
1767-1 D7.226852.1670.0246.2590.00943.51.16.9490.026
1767-2 D7.759962.2610.0236.2820.01045.51.17.0090.030
1767-3 D8.031962.2250.8256.2760.012
1767-4 D8.559512.2090.0316.3010.00944.11.47.0070.030
1767-5* E3.6912382.2590.0316.1970.05546.21.86.9240.126
1767-6* E1.761082.2391.1336.1650.038
1767-7* E2.151092.3370.9476.2310.024
1767-8* E2.465182.2760.0216.2530.01946.11.16.9860.048
Mean:
1767 D7.848772.2120.0266.2810.00944.51.26.9880.029
1767 E3.088782.2680.0266.2250.03746.21.46.9550.087
Sample1788U (ppm)U/Th230Th/238U234U/238UAge (ka)2s (ka)(234U/238U)i
1788-1 D6.673902.9670.0266.4230.01161.41.57.4530.054
1788-2 D7.081763.3700.8336.4410.010
1788-3 D7.17603.2063.1266.3940.049
1788-4 D7.4513913.3130.0236.4450.01070.31.47.6450.056
1788-5 D5.5244233.2690.0236.3490.01070.41.47.5310.052
1788-6 D5.0740903.4160.0146.3780.01474.11.17.6340.054
1788-7 D5.3947293.3850.0206.4000.01472.91.47.6400.054
1788-8 D5.9332093.4270.0156.3930.01374.21.17.6540.054
1788-9 D5.2443293.4490.0146.4130.01474.51.07.6850.052
1788-10 D4.8931613.3900.0106.4030.01173.00.97.6450.052
1788-11 D4.825563.3940.0146.4160.01472.91.07.6590.052
1788-12 D5.4816063.3560.0176.3840.01472.31.17.6090.052
1788-13 D5.048383.3170.0256.4200.01470.71.57.6230.058
1788-14 D5.69933.2812.4266.4080.013
1788-15 D5.03723.3153.7316.4270.014
1788-16 E0.1331.78618.1493.8340.267
1788-17 E0.68250.7529.1496.2480.273
1788-18 E0.4160.80113.0536.2360.050
1788-19 E0.0831.78336.2314.3010.288
1788-20 E1.023062.9900.1175.5410.15475.19.36.6170.394
1788-21* E0.33502.04127.1355.7930.141
1788-22* E0.12301.51324.8015.9750.098
1788-23* E0.25341.36817.0715.9880.079
1788-24* E0.36901.23713.5556.1670.055
1788-25* E0.411071.0848.6726.2060.033
1788-26* E0.481021.30211.3336.3840.081
1788-27* E0.491650.6867.7336.3670.037
1788-28* E0.311671.6156.9755.6020.246
1788-29* E0.4462.31111.8985.5760.306
1788-30 E0.44620.9885.3106.0890.075
1788-31 E0.2981.06619.2566.1510.056
1788-32 E0.23950.99417.4516.3520.064
1788-33 E0.4161.10321.6516.3440.049
1788-34 E0.28511.34011.4506.3820.061
1788-35 E0.3541.28621.0886.3210.062
1788-36 E0.41151.21612.8966.3720.041
1788-37 E0.3611.10617.0596.3130.073
1788-38 E0.542792.8100.2376.3000.06458.912.27.2620.270
Mean:
1788 D5.5927933.3350.0186.4020.01371.51.27.6160.054
1788 E0.782932.9000.1775.9200.10967.010.86.9360.332
Sample1810U (ppm)U/Th230Th/238U234U/238UAge (ka)2s (ka)(234U/238U)i
1810-1 D7.073483.2310.0215.8140.01777.91.67.0030.056
1810-2 D8.294113.1120.0305.8630.01073.42.16.9860.062
1810-3 D8.889793.1060.0275.9290.01072.11.87.0460.060
1810-4 D9.198333.0490.0445.9930.01169.42.67.0790.066
1810-5 D9.175082.9370.0475.9900.00766.22.87.0200.066
1810-6 D9.12553.1436.9195.9810.012
1810-7 D7.954323.0990.0185.9770.01371.11.37.0890.054
1810-8 D8.844892.9860.0746.0350.060674.17.0880.084
1810-9 D9.39159053.1220.0135.8700.00673.61.16.9990.052
1810-10 D9.7878393.1650.0175.8730.01174.81.37.0240.054
1810-11 D9.0372423.1740.0305.8880.01574.82.07.0430.058
1810-12 D9.5396263.1570.0195.8890.00974.31.47.0360.054
1810-13 D10.19102403.0940.0185.9040.00872.21.37.0160.052
1810-14 D10.64144633.1550.0305.9580.01073.11.97.0990.058
1810-15 E0.0051−0.384146.0361.9650.186
1810-16 E0.0022−1.06048.1681.0140.108
1810-17 E0.00415.40317.5732.3570.194
1810-18 E0.24553.1959.1094.0540.062
1810-19 E0.544264.0090.1865.0540.109130.821.86.8720.466
1810-20 E0.853283.6250.1194.2870.137146.822.75.9840.524
1810-21 E0.41485.0094.4744.4940.186
1810-22 E0.1577.6908.2254.3490.351
1810-23 E0.0329.9121.8435.1530.599
1810-24 E0.0100.661166.0561.8770.144
1810-25 E0.0227.4089.3864.9640.557
1810-26* E0.7333.7624.1004.7350.100
1810-27* E0.1435.2714.5104.2550.112
1810-28* E0.1853.5418.0794.5620.081
1810-29* E0.2593.5117.0954.5620.058
1810-30* E0.2134.0275.2914.0730.149
1810-31* E0.0913.87539.1364.0290.072
1810-32* E0.0522.4699.0994.1870.072
1810-33* E0.0612.60224.1694.4260.141
1810-34* E0.9120103.1310.0684.5610.032105.27.05.7980.128
1810-35 E1.0134.29115.5144.0850.025
1810-36 E0.04996.2978.8904.0600.242
1810-37 E0.145285.7533.9324.3850.234
1810-38 E0.02555.68728.4904.2110.437
1810-39 E0.01174.20331.0484.4740.314
1810-40 E2.0915863.9930.0494.9930.037132.56.26.8140.146
Mean:
1810 D9.0753323.1070.0305.9220.014572.31.97.0400.060
1810 E1.1010883.6900.1054.7240.0788128.814.46.5950.316
Sample1841U (ppm)U/Th230Th/238U234U/238UAge (ka)2s (ka)(234U/238U)i
1841-1 E2.51784.4153.2525.8510.035
1841-2 E1.96514.2687.6315.8420.044
1841-3 E2.372184.3190.0415.8710.021115.53.57.7580.090
1841-4 E1.883504.2610.0465.8910.016112.63.67.7300.082
1841-5 E2.52144.3780.0455.8460.032118.74.37.7840.124
1841-6 E2.5124.4282.7445.8810.044
1841-7 E2.4634.4841.7445.9460.044
1841-8 E2.14474.4992.4675.9620.037
Mean:
1841 E2.252614.3190.0445.8690.023115.63.87.7570.099
Table 5

Summary table of U-Th disequilibrium ages obtained for two H. naledi teeth (samples 1788 and 1810) from the Dinaledi Chamber obtained by GU-ANU. No age calculations were carried out for U concentrations of ≤0.5 ppm or U/Th ≤250 (indicated in red and underlined). Negative U/Th values are due to the Th background being higher than the measured values. Mean values in this table only incorporate values from which meaningful ages could be calculated (indicated in black). All uncertainties are given as 2σ. CS = Closed System; Diff = diffusion (i.e., calculated ages are based on the assumption of continuous diffusion after Sambridge et al. (2012).

https://doi.org/10.7554/eLife.24231.010
Sample 1810aU (ppm)U/Th230Th/238U234U/238UAge – CS (ka)2σ (ka)Age – Diff (ka)2σ (ka)(234U/238U)i*
 1 E0.03−273.71131.25084.43020.8881n/a
 2 E0.02−193.16480.93904.20830.4703n/a
 3 E0.04−333.02571.05315.12200.4988n/a
 4 E0.05−353.63521.38974.92240.4912n/a
 5 E0.19−2583.45040.19654.81060.1376n/a
 6 D6.07−29723.29090.06665.98010.055977.22.387.32.77.190.11
 7 D6.10−53543.26180.08245.97680.031276.32.686.23.37.170.08
 8 D6.39114363.31690.08005.98270.051477.92.688.33.37.210.11
 9 D6.4761933.33180.08995.94700.087379.03.289.73.87.180.17
 10 D6.65−50553.49850.10486.04620.040382.53.494.44.57.370.11
 11 D6.9551493.54650.09106.05310.040683.83.096.34.07.400.11
 12 D7.1532443.52380.09976.05010.042383.23.395.44.37.390.11
Mean:
1–5 E0.07 ± 0.063.43210.30034.79620.1504112.015.7137.125.5
6–12 D6.54 ± 0.313.40180.07496.00700.042880.12.591.13.27.270.11
Sample 1810bU (ppm)U/Th230Th/238U234U/238UAge – CS (ka)2σ (ka)Age – Diff (ka)2σ (ka)(234U/238U)i*
 1 E0.01176.844214.04350.02285.5626n/a
 2 E0.0039.233016.2333−2.28384.6085n/a
 3 E0.00–216.168827.6564−0.10337.6336n/a
 4 E0.00–314.9980967.0421−0.7695259.2590n/a
 5 E0.02−1827.1338296.11363.625048.0742n/a
 6 E0.86−24934.51760.17864.65880.0795189.116.7381.3137.97.240.44
 7 E0.98−6034.87970.14164.87370.0681201.414.00.00.07.840.40
 8 D4.49204233.57780.06705.93270.077387.12.7100.83.17.310.15
 9 D5.35−101283.30460.06595.91420.067778.72.489.22.87.140.13
 10 D5.67−41973.40770.07775.94800.045981.32.692.83.37.230.10
Mean:
1–5 E0.01 ± 0.018.7750204.69881.654793.9630n/a-----
6–7 E0.92 ± 0.124.71010.14654.77300.0602195.713.8471.0269.47.540.42
8–10 D5.17 ± 0.703.42140.07905.93190.052382.12.793.73.67.230.13
Sample 1788aU (ppm)U/Th230th/238U234U/238UAge – CS (ka)2σ (ka)Age – Diff (ka)2σ (ka)(234U/238U)i*
 1E0.0348772.10953.30583.57401.6107n/a
 2E0.01−213.78455.52711.35252.7713n/a
 3E0.00–110.503027.8940−2.490910.1171n/a
 4E0.00–19.0249113.8912−0.712032.3636n/a
 5E0.00–26.679566.27500.776918.7506n/a
 6E0.01–63.02310.98442.19040.4875n/a
 7E0.24−1052.81390.20766.37910.1624n/a
 8E0.24−2041.64951.58116.01230.2961n/a
 9E0.195792.40754.26206.33411.3187n/a
 10E0.481893.17172.28626.10060.1341n/a
 11E1.34138333.87920.28646.35210.102488.59.2102.912.67.870.32
 12E2.577554.17700.06096.32750.097298.63.0117.73.18.040.19
Mean:
1–6 E0.01 ± 0.013.51884.45312.34717.1463n/a---
7–10 E0.29 ± 0.132.64840.24696.18240.097856.26.561.07.7
11–12 E1.96 ± 1.234.07460.09416.33610.048295.13.2112.34.77.960.26
Sample 1788bU (ppm)U/Th230Th/238U234U/238UAge – CS (ka)2σ (ka)Age – Diff (ka)2σ (ka)(234U/238U)i*
 1E0.0242.39451.87743.50401.4368n/a
 2E0.02141.96561.32993.30990.9022n/a
 3E0.01–82.81562.10342.53590.8082n/a
 4E0.021602.102458.18543.23427.4009n/a
 5E0.03−312.38591.40844.12851.5222n/a
 6E0.03−202.895111.29114.10463.9747n/a
 7E0.02−102.84863.53834.93622.3343n/a
 8E0.03−182.83251.61135.70520.7139n/a
Mean:
1–8 E0.02 ± 0.012.55976.76184.13081.2209n/a
Sample 1788cU (ppm)U/Th230th/238U234U/238UAge – CS (ka)2σ (ka)Age – Diff (ka)2σ (ka)(234U/238U)i*
 1D5.44215783.92810.07076.42600.074088.62.6103.03.17.970.15
 2D5.391550373.89080.05656.44160.052487.22.0101.02.47.960.11
 3D4.9517083.89010.08286.40850.079287.83.0102.03.67.930.16
 4D3.8716533.80330.08596.37860.106885.83.399.03.67.850.20
 5D4.2511683.95690.08006.40510.095790.03.1105.03.67.970.19
 6D5.1214933.94330.05796.49510.096187.82.5102.02.58.040.17
 7D5.3426593.80200.05816.47130.058184.02.096.72.47.940.11
 8D5.0610933.99480.06726.44790.063090.32.4105.53.08.030.13
 9D4.7810184.04810.07186.44680.058692.02.5108.03.38.060.13
 10D5.228173.90110.05826.51870.081386.12.399.62.48.040.15
 11D5.254253.88720.08506.44150.062487.12.8101.03.67.960.14
 12D5.463453.95610.05846.46580.073388.82.3103.32.58.030.14
Mean:
1–12 D5.01 ± 0.283.91750.07966.44790.046187.92.6102.03.67.980.06

Summaries of the U-Th analytical data and ages are reported in Table 4 (SCU-UoW) and Table 5 (GU-ANU). In Table 4 only closed system dates are reported, while Table 5 also lists dates based on the continuous diffusion model of Sambridge et al. (2012). In both datasets, the U content in enamel is much lower than in dentine. Note that apparent U-Th ages for the teeth are likely to provide apparent age estimates, which will approach the age for U uptake events that affected the teeth during wet periods in the chamber, typically after deposition. These ages should, therefore, be regarded as minimum age estimates for the teeth, and do not represent depositional ages for the fossils.

Location of the three H. naledi tooth samples (samples 1767, 1788 and 1810) and one baboon (cf. Papio) tooth sample (sample 1841) used for combined U-series and ESR dating.

(a) Map of the Dinaledi Chamber showing the position of the excavation pit and the position of figures (b) and (c); (b) close-up of the SE corner of the excavation pit showing the sample site for sample 1810 and the 50 cm deep sondage from which sample 1841 was recovered; (c) the area to the W of the excavation pit from which samples 1767 and 1788 were collected.

https://doi.org/10.7554/eLife.24231.011
Samples of orange laminated mudstone of Unit 1 for OSL dating.

(a) sample OSL3 with an estimated MAM age of 231 ± 41 ka taken from sub-unit 1b; (b) sample OSL4 with an estimated MAM age of 241 ± 37 ka, taken from sub-unit 1b and covered by a flowstone sheet dated at 290 ± 6 ka (RS5); (c) sample OSL5 with an estimated MAM age of 353 ± 61 ka, taken from sub-unit 1a and covered by a flowstone sheet dated at 32.1 ± 0.4 ka (RS20). The scale bar in each of the photographs is 10 cm.

https://doi.org/10.7554/eLife.24231.012
Photographs of H. naledi teeth used for ESR dating.

(a) U.W.101–1767; (b) U.W.101–1788; (c) U.W.101–1810. The order of images for each panel is: buccal, distal, lingual, mesial, and occlusal views. The scale bar in each panel is 1 cm.

https://doi.org/10.7554/eLife.24231.013

Sample 1767: This extremely worn upper premolar crown (Figure 6a) is heavily weathered, and only a small fragment of enamel was left attached to the dentine. It could, therefore, only be dated once (at SCU-UoW). Both dentine and enamel yield consistent results with apparent U-Th ages of 44.5 ± 0.6 ka for dentine and 46.1 ± 0.7 ka for enamel, and initial 234U/238U activity ratios at 6.99 ± 0.01 and 6.99 ± 0.04 respectively. These results suggest that a single uptake event is dated. The tooth is characterised by an extremely high U content in the enamel when compared to the other teeth (Table 4). Uranium concentration gradients show the effects of diffusion into the enamel from all external surfaces, with enrichment at the Enamel Dentine Junction (EDJ).

Sample 1788: This lower right second molar was covered by a thin layer of sediment and is well-preserved (Figure 6b). Uranium concentrations in enamel and dentine vary across the surface, with minor hotspots and leaching zones near enamel cracks and along the dentine canal. The EDJ is enriched in U, showing a diffusion gradient into the enamel, and resulting in elevated U concentrations in spots located close to the EDJ (Figure 9). The U uptake history appears complex and heterogeneous, and probably involved several episodes. Most of the U concentrations in the enamel are too low to provide a meaningful age. However, parts of the enamel and the dentine yielded consistent measurements for which SCU-UoW provide ages with mean values of 71.5 ± 0.6 ka for dentine and 67.0 ± 5.4 ka for enamel with initial 234U/238U activity ratios of 7.62 ± 0.03 and 6.94 ± 0.17 respectively. GU-ANU obtained a combined age of 95.1 ± 3.2 ka for two enamel spots with higher U concentrations, with parts of the enamel with lower U-enrichment yielding a combined age of 56.2 ± 6.5 ka. GU-ANU also provide a consistent mean apparent age of 87.9 ± 2.6 ka, associated with initial 234U/238U activity ratios of 7.98 ± 0.06 (individual spots agreeing within error) for dentine which is interpreted as the age of an U uptake event.

Sample 1810: This lower left molar or premolar from the excavation pit (Figures 4 and 6c), is near complete and only moderately weathered. Uranium diffusion patterns show U accumulating at the EDJ with slow diffusion into the enamel tissue. The U concentrations in most of the enamel are too low to calculate a meaningful age. Areas of enamel with higher U concentrations return older ages (Tables 4 and 5). SCU-UoW provide a mean age for high-U spots in enamel of 128.8 ± 7.2 ka and an associated initial 234U/238U activity ratio of 7.60 ± 0.16. GU-ANU report a mean apparent U-Th age of 195.7 ± 13.8 ka, which is much higher than the adjacent dentine spots (at 81.1 ± 2.7 ka), but is coupled with realistic initial 234U/238U activity ratios of 7.24 and 7.84 with overlapping error limits. This indicates that a secondary overprint of the dentine took place for which the U source had a similar 234U/238U composition as the source of the initial U uptake event. Dentine measurements are consistent along the measured sections with small regions affected by leaching and enrichment near cracks and the pulp cavity. The dentine analyses done by SCU-UoW (Table 4) yield similar ages with consistent initial 234U/238U activity ratios of around 7.04 ± 0.03, and a mean apparent age of 72.3 ± 1.0 ka. The combined analytical data for dentine from GU-ANU in samples 1810A and 1810B yield apparent U-Th ages of 80.1 ± 2.5 ka and 82.1 ± 2.7 ka respectively, coupled with consistent initial 234U/238U activity ratios (Table 5).

Sample 1841 The baboon tooth consists of an enamel crown that is structurally intact, but the enamel is friable and weathered (Figure 7). The U distribution within the enamel appears homogenous, however, Th concentrations are low and the resolution of the elemental distribution is poor, which impairs the quality of the U-Th age estimates. A recent U uptake event may have occurred affecting enamel in contact with sediment, resulting in a mean apparent U-Th age estimate of 115.6 ± 1.9 ka with a mean initial 234U/238U activity ratio of 7.76 ± 0.05 (Table 4).

Photographs of the baboon (cf. Papio) tooth (sample 1841), recovered from the sondage in the excavation pit, and used for ESR dating.

Views are: (a) buccal, (b) occlusal, (c) lingual, and (d) internal.

https://doi.org/10.7554/eLife.24231.014

GU-ANU also provide age estimates in which the continuous diffusion assumptions of Sambridge et al. (2012) have been applied. The results obtained for samples 1788 and 1810 are about 20% older than the closed system ages (Table 5), but show much less consistency and are not further considered.

Collectively, the results show that the teeth are older than 70 ka, and considering sample 1810 with a minimum age of around 200 ka, that the H. naledi fossils are probably older than 200 ka (see Discussion).

US-ESR dating

Combined U-series and ESR dating (US-ESR; Grün et al., 1988) of three hominin teeth (samples 1767, 1788 and 1810) and a baboon tooth (sample 1841) was performed at SCU. Blind duplicate analyses of two of the hominin samples (samples 1788 and 1810) were performed at the ‘Centro Nacional de Investigación sobre la Evolución Humana’ (CENIEH), Spain in collaboration with GU (CENIEH-GU). In obtaining the ages, each laboratory carried out independent sample preparation, and ESR and U-series analyses of the fossil teeth. Estimates for the environmental dose rates used in the age calculations were standardized for both laboratories (Table 6) in order to produce comparable results (see discussion and methodology sections for details).

Table 6

Summary table of model parameters used in ESR dating separated by sample number and laboratory. See text for detailed discussion.

https://doi.org/10.7554/eLife.24231.015
Sample:1767178818101841
Laboratory:SCUSCUCenieh-guSCUCenieh-guSCU
Enamel:
De (Gy)194 ± 4231 ± 8159 ± 10296 ± 14232 ± 301676 ± 127
U (ppm)2.52 ± 0.530.38 ± 0.170.07 ± 0.070.32 ± 0.120.16 ± 0.162.28 ± 0.48
234U/238U6.21 ± 0.035.95 ± 0.326.258 ± 0.3494.04 ± 0.184.773 ± 0.0605.87 ± 0.03
230Th/234U0.37 ± 0.050.55 ± 0.520.598 ± 0.0380.92 ± 0.050.950 ± 0.0340.785 ± 0.038
Alpha efficiency*0.13 ± 0.020.13 ± 0.020.13 ± 0.020.13 ± 0.020.13 ± 0.020.13 ± 0.02
Initial thickness (μm)1027 ± 2101049 ± 2771486 ± 2481150 ± 2501527 ± 257650 ± 145
Water (%)000000
Dentine:
U (ppm)7.88 ± 0.665.76 ± 0.864.71 ± 0.279.08 ± 0.445.81 ± 0.37
234U/238U6.28 ± 0.096.40 ± 0.036.448 ± 0.0465.93 ± 0.035.969 ± 0.035
230Th/234U0.35 ± 0.110.62 ± 0.020.608 ± 0.0120.52 ± 0.090.572 ± 0.010
Water (%)10 ± 510 ± 510 ± 510 ± 510 ± 5
Sediment:
U (ppm)3.0 ± 0.32.9 ± 0.12.9 ± 0.13.2 ± 0.33.2 ± 0.30.64 ± 0.06
Th (ppm)7.9 ± 0.48.3 ± 0.68.3 ± 0.68.6 ± 0.48.6 ± 0.44.72 ± 0.47
K (%)1.17 ± 0.141.21 ± 0.141.21 ± 0.141.23 ± 0.141.23 ± 0.141.47 ± 0.15
Water (%)25 ± 1025 ± 1025 ± 1025 ± 1025 ± 1025 ± 10
Depth below ground surface (cm)0225555
Gamma Dose rate (μGy a−1)
25 ± 10% Water, 80% Rn degassing
25 ± 10% Water, no Rn degassing
534 ± 69
724 ± 116
534 ± 69
724 ± 116
534 ± 69
724 ± 116
534 ± 69
724 ± 116
534 ± 69
724 ± 116
534 ± 69
724 ± 116
Cosmic dose rate (μGy a−1)15 ± 115 ± 115 ± 115 ± 115 ± 115 ± 1
  1. A relative error of ± 10% was assumed.

Analyses and results from both labs are presented in Table 7 and Figures 10, 11 and 12. Results are presented for two scenarios: scenario 1 in which the teeth are fully covered in sediment that contains 25 ± 10% water and experienced 80% Rn loss; and scenario 2 in which the teeth are fully covered in sediment that contains 25 ± 10% water and experienced no Rn loss. Scenario 1 reflects the measured present-day situation and is interpreted as a maximum age estimate. Scenario 2 provides a minimum age estimate (Table 7). Together these scenarios provide our best estimate for the age range of the fossil teeth.

Table 7

Summary of ESR dating results (2σ uncertainties) for two end-member scenarios: (i) complete burial of the samples, 80% Rn loss in the sediment and post Th-230 equilibrium in dental tissue (i.e., maximum age scenario); (ii) complete burial of the samples and post-Rn equilibrium in sediment (i.e., minimum age scenario). See text for detailed discussion.

https://doi.org/10.7554/eLife.24231.016
Sample:1767178818101841
Laboratory:SCUSCUCenieh-guSCUCenieh-guSCU
 Scenario 1: 25 ± 10% Water, complete burial and 80% 222Rn degassing (maximum age scenario)
internal dose rate (μGy a−1)1142 ± 515190 ± 12947 ± 47323 ± 175176 ± 1761411 ± 596
alpha (μGy a−1)*008 ± 208 ± 20
beta dose rate, dentine (μGy a−1)73 ± 3391 ± 6264 ± 1675 ± 4151 ± 14
beta dose rate, sediment (μGy a−1)101 ± 24105 ± 3186 ± 1795 ± 2486 ± 18358 ± 74
gamma and cosmic (μGy a−1)549 ± 69549 ± 69549 ± 69549 ± 69549 ± 69549 ± 69
total dose rate (μGy a−1)1865 ± 521935 ± 162754 ± 871042 ± 194870 ± 1902318 ± 606
p enamel−0.030.49−0.02−0.70−0.770.91
p dentine0.080.13−0.061.020.54
Age (ka)104 ± 29247 ± 42211 ± 28284 ± 51267 ± 68723 ± 181
Combined SCU/CENIEH-GU age (ka)229 + 60/–46276 + 59/–77
Average age for 1788 & 1810 (ka)253 + 82/–70
 Scenario 2: 25 ± 10% Water, complete burial and no 222Rn degassing (minimum age scenario)
internal dose rate (μGy a−1)1277 ± 552216 ± 16551 ± 51335 ± 193184 ± 1841520 ± 630
alpha (μGy a−1)*008 ± 208 ± 20
beta dose rate, dentine (μGy a−1)82 ± 35102 ± 7869 ± 1887 ± 5059 ± 16--
beta dose rate, sediment (μGy a−1)132 ± 26134 ± 33111 ± 19126 ± 26112 ± 19380 ± 81
gamma and cosmic (μGy a−1)739 ± 116739 ± 116739 ± 116739 ± 116739 ± 116739 ± 116
total dose rate (μGy a−1)2230 ± 5861191 ± 219978 ± 1291287 ± 2321102 ± 2192639 ± 647
p enamel−0.310.06−0.37−0.83−0.910.67
p dentine−0.22−0.22−0.400.540.10
Age (ka)87 ± 22194 ± 34163 ± 24230 ± 40210 ± 50635 ± 148
Combined SCU/CENIEH-GU age (ka)179 + 49/–40220 + 50/–60
Average age for 1788 & 1810 (ka)200 + 70/–61
  1. *using alpha attenuation values of Grün (1987).

  2. considered as negligible given the low radioelement concentrations in the sediment and the high total dose rate value.

  3. for 1841, the beta dose rate on both sides of the enamel layer is derived from the sediment.

Combined US-ESR ages determined by SCU for samples 1810, 1788 and 1767 under scenario 1 conditions (i.e., the maximum age scenario) are 284 ± 51 ka, 247 ± 41 ka and 104 ± 29 ka (2σ uncertainty), respectively (Table 7). Combined US-ESR ages determined by CENIEH-GU for samples 1810 and 1788 under scenario 1 conditions are 267 ± 68 ka and 211 ± 28 ka (2σ uncertainty), respectively (Table 7).

Combined US-ESR ages determined by SCU for samples 1810, 1788 and 1767 under scenario 2 conditions (i.e., the minimum age scenario) are 230 ± 40 ka, 194 ± 34 ka and 87 ± 22 ka (2σ uncertainty), respectively (Table 7). Combined US-ESR ages determined by CENIEH-GU for samples 1810 and 1788 under this scenario are 210 ± 50 ka and 163 ± 24 ka (2σ uncertainty), respectively (Table 7).

Results for sample 1767 are based on anomalously high (~20 times) U concentrations in enamel, and probably yield anomalously low age estimates (Duval et al., 2012). This result is, therefore, considered to be unreliable and has been excluded from final age estimates (see Discussion).

The observed difference in age estimates obtained by SCU and CENIEH-GU for samples 1788 and 1810, are most likely explained by natural dose variations within the tested enamel layers (see Discussion and methodology sections), and we have no reason to prefer one age result over another. The optimal age estimate for the H. naledi fossils, therefore, combines the results from both laboratories with average maximum (i.e., scenario 1) age estimates for samples 1788 and 1810 of 229 + 60/–46 ka and 276 + 59/–77 ka (2 σ uncertainty) respectively, and average minimum (i.e., scenario 2) age estimates of 179 + 49/–40 ka and 220 + 50/–60 ka (2 σ uncertainty) respectively. Together these results provide an age range of 139–335 ka for the H. naledi remains, although dating of flowstone encasing H. naledi bones helps to better constrain this range (see Discussion).

Combined US-ESR ages for the baboon tooth (sample 1841) determined by SCU using scenario 1 and 2 conditions are 723 ± 181 ka and 635 ± 148 ka respectively. The tooth contained no inner dentine (Figure 7), and was filled with sediment. In calculating the age it was, therefore, assumed that sediment occurred on both sides of the enamel layer. Sample 1841 was recovered from sub-unit 3a directly below the occurrence of articulated H. naledi remains in the excavation pit (Dirks et al., 2015). The age results provide an upper age limit for the deposition of the H. naledi bearing layer, and mark an earlier stage of deposition of mud clast breccia in the cave assigned to sub-unit 3a, which predates the entry of H. naledi fossils into the cave.

OSL dating

Optically stimulated luminescence (OSL) dating of three samples of sediment from Unit 1 in the Dinaledi Chamber (samples OSL3 and OSL4 from sub-unit 1b, and sample OSL5 from sub-unit 1a; Figure 5) was performed at the University of the Witwatersrand (Wits). The measurements were carried out on small aliquots containing ~30 grains. Summaries of the OSL analytical data and ages are reported in Table 8.

Table 8

Summary of OSL results obtained by the University of the Witwatersrand for samples of Unit 1 from the Dinaledi Chamber (samples OSL3, 4 and 5). The ages were calculated using effective U concentration values (taking disequilibrium into account; see text for details). CAM = Central Age Model; MAM = Minimum Age Model.

https://doi.org/10.7554/eLife.24231.017
Sample IDH2O (%)Th (ppm)U (ppm) pre-RnU (ppm) post-RnK (%)Total dr (Gy/ka)Total de (Gy) CAMTotal de (Gy) MAMCAM
Age (ka)
CAM
MAM age (ka)MAM 2σOver dispersion
(%)
OSL318.9 ± 53.71 ± 1.600.75 ± 0.1770.193 ± 0.0440.45 ± 0.120.760.07428.5968.92176.427.75601032314163
OSL425.8 ± 53.38 ± 1.600.485 ± 0.1770.097 ± 0.0440.47 ± 0.120.700.06379.8943.58168.020.7546792413755
OSL522.7 ± 55.11 ± 1.600.692 ± 0.1770.138 ± 0.0440.56 ± 0.120.900.07759.54102.33315.6748.688491323536168

The reported dose rates for the samples range from 0.7 to 0.9 Gy ka−1 (Table 8), with significant within-sample scatter, resulting in uncertainties on age estimates of 15–18%. Overdispersion in De ranges from 50–70%, which is much higher than would be expected for a well-bleached sample, and indicates that it is most appropriate to apply a Minimum Age Model (MAM) to the dataset, in which the MAM age is likely to represent a maximum estimate for the age of the sediments (see Discussion). As with ESR, significant Rn loss was detected in the samples of Unit 1, and corrections to the measured U concentrations were applied (Table 8). The MAM calculations for the three samples yield maximum age estimates for the sediments of 231 ± 41 ka (OSL3), 241 ± 37 ka (OSL4), and 353 ± 61 ka (OSL5). The MAM apparent ages for OSL3 and OSL4 were obtained from the sandy facies of sub-unit 1b sediments and yield ages that are younger than the age of a Flowstone 1 sheet (sample RS5 at 290 ± 4 ka; Table 1) that covers the outcrop of sub-unit 1a from which sample OSL4 was taken (Figure 2c). This discrepancy can be attributed to inverted stratigraphy associated with erosion of the top of the older sub-unit 1a after the deposition of Flowstone 1 (RS5) by running water and subsequent deposition of sub-unit 1b between sub-unit 1a and the flowstone (Figure 2c). Sample OSL5 was obtained from muddy sediment of sub-unit 1a, and yields an older age than the covering flowstones (RS5 and RS20). Note that if a Central Age Model (CAM) is applied to the OSL data, results are significantly older at 560 ± 102 ka (OSL3), 546 ± 79 ka (OSL4), and 849 ± 132 ka (OSL5), however, this model is considered unrealistic within a cave environment (Galbraith et al., 1999).

Palaeomagnetic analysis of flowstone

Palaeomagnetic analysis of one composite sample of Flowstone 1a (Figure 13), covering erosional remnants of Unit 2 near the entry shaft into the Dinaledi Chamber, was performed at La trobe University, Melbourne (LTU). The palaeomagnetic results for Flowstone 1a are presented in Figure 13 and Table 9. The palaeomagnetic sample from Flowstone 1a comprises three distinct phases of flowstone formation (from base to top: A, B and C; Figure 13a,b) that have been analysed for their palaeomagnetic orientation (Figure 13c). Note that the palaeomagnetic sample of Flowstone 1a was taken up-dip from the position where the U-Th sample of Flowstone 1a was taken (i.e., RS22 and RS23). The basal, phase A flowstone observed in the palaeomagnetic sample tapers out down-dip (Figure 13a) and is not present in the U-Th sample; thus, RS23 at the base of the U-Th sample corresponds to phase B carbonate in the palaeomagnetic sample, and RS22 to phase C carbonate (Figure 2b).

Table 9

Final mean palaeomagnetic data for all subsamples analysed from each phase of Flowstone 1a as shown in Figure 13. MAD = mean maximum angular deviation for individual samples; K = precision/sample dispersal parameter; Plat = palaeolatitude).

https://doi.org/10.7554/eLife.24231.018
Flowstone 1aDeclination (O)Inclination (O)MADKPlat.Polarity
 Phase C15.5−39.7370.875.4N
 Phase B26−28.17.4156.263.3N
 Phase A156.415.95.730.2−60.0R

Phase A flowstone at the base of the sample records a consistent reversed magnetic polarity, with a clear overprint that is anti-parallel to the characteristic, reversed polarity remanence (ChRM) and is removed by ~10 mT. The reversed polarity ChRM is then stable between 10 and 40 mT, although within this range there are two reversed polarity components that can be identified in some samples (between 10 and 19 mT and then between 20 and 40 mT; Figure 13c). Both components have almost identical declination values, but the lower field component has a shallower inclination. This is not uncommon within speleothems (Herries and Shaw, 2011) because a single subsample of 2.5 cm depth is measuring the remanence recorded in multiple layers of speleothem as well as multiple layers of detrital contamination. Phase B flowstone records a weak, normal polarity ChRM that is consistently isolated between 7 and 36mT (Figure 13c). The results from this phase have the highest mean maximum angular deviation (MAD) values (Table 9) due to the small and oddly shaped nature of the samples that provide less consistent measurements between each spin in the magnetometer. Phase C flowstone also records a normal ChRM that is similar to that seen within phase B (Figure 13c), although with slightly steeper inclinations (Figure 13c, Stereo Plot).

The samples do not have strong secondary overprints as seen in many Plio-Pleistocene palaeo-cave deposits from the region (Dirks et al., 2010), which may indicate that they are younger or have a different sediment source and, thus, mineralogy holding the remanence. The coercivity of phase B and C flowstones is similar, and distinct from phase A flowstone, although all the demagnetisation spectra suggest the dominant mineral holding the remanence is ferrimagnetic (magnetite/maghaemite) as at many other CoH sites (Herries et al., 2006; Herries and Shaw, 2011; Herries et al., 2014).

Radiocarbon dating

Three weathered bone fragments of H. naledi were analysed via radiocarbon dating at Beta Analytic Inc. (Florida, USA). Analyses indicated that no collagen was present in any of the samples and that the bone appeared possibly cremated. This was investigated with a bone carbonate extraction technique. Tests did not support cremation and indicated that extensive secondary CaCO3 replacement had occurred, providing ages of 33.0 ± 0.2 ka and 35.50 ± 0.16 ka for two of the fragments. We interpret these ages to relate to late calcite precipitation in the bones that may reflect a wet period in the cave.

Discussion

The strategy in dating the fossils has been built on three components: (i) construct a detailed stratigraphic model for the cave sediments in the Dinaledi Chamber in which the position of the hominin-bearing deposits can be securely placed; (ii) date the sedimentary units that potentially bracket the hominin-bearing deposits; and (iii) date the H. naledi fossils directly. We will start this discussion by commenting on the reliability of the various dating techniques, and how they should be viewed relative to each other. We will then discuss the outcomes of each of the three strategic components, and their implications for the age of the H. naledi material. The broader implications of the age for the morphological evolution of hominins in southern Africa is discussed in detail in Berger et al., 2017, and will be briefly summarized at the end of this discussion.

Reliability of the age estimates

The dating techniques applied in this study do not all work in the same way, and hence the results must be viewed differently. U-series analysis on carbonates, 14C analysis of bone and palaeomagnetic analyses of flowstones (e.g., Herries and Shaw, 2011; Taylor and Bar-Yosef, 2014; Hellstrom and Pickering, 2015) are well established dating techniques requiring few, if any, à priori assumptions. In contrast, ESR and OSL results are strongly dependent on model assumptions for the environmental conditions that affected the locations from which the samples were taken.

U-Th results

Sample preparation and analytical procedures for U-Th disequilibrium dating are well established (see methodology section), and are likely to return highly reproducible (i.e., high precision) results. This is certainly the case here, where samples analysed in duplicate in independent laboratories (JCU and UoM) returned identical results within analytical uncertainties (Tables 1, 2 and 3). The only exception is that UoM was able to provide ages for older flowstones that date close to the detection limit for the technique, whereas JCU did not provide ages over 400 ka.

Although these results demonstrate high levels of precision, further evaluation of the geological meaning of the ages is required. In particular, the effects of possible post-depositional U uptake, which would result in apparent ages that are younger than the true age, can be assessed with textural analyses (e.g., Pickering et al., 2010), and the use of initial 234U/238U ratios (Tables 2 and 3; Kronfeld et al., 1994). Most of the analysed flowstones display similar initial 234U/238U ratios (1.8 to 2.4), with two notable exceptions in samples RS18 (243 ± 7 ka) and RS5 (290 ± 6 ka) that record 234U/238U ratios of 3 to 4. These are two of the oldest samples analysed, and both display evidence for recrystallization and secondary dissolution. Considering that the groundwater reservoir in the CoH has high (i.e., >7) initial 234U/238U ratios (Kronfeld et al., 1994) it is likely that the elevated 234U/238U ratios in samples RS5 and RS18 are due to U uptake during interaction with groundwater after flowstone deposition. In this case, these two age results should be viewed as minimum age estimates for the flowstones.

As with flowstone, analytical procedures for U-Th disequilibrium dating of teeth are well established (e.g., Grün et al., 2014). However, in this study there are significant differences in the U-Th disequilibrium ages of teeth reported by the two laboratories (Tables 4 and 5). This difference in measured ages is most likely due to the fact that the different laboratories dated different fragments of the teeth. The U-Th analyses show that the U distribution within the teeth, and especially within enamel, is highly variable, as reflected in the wide range of U-Th ages (Tables 4 and 5). Where a tooth displays consistent ages and initial 234U/238U ratios over a large domain, or where we have observed close coincidence in U-Th ages and initial 234U/238U ratios for dentine and adjacent enamel samples, we interpret the results to suggest that a U uptake event has been dated. Considering the variable distribution of U within the tooth samples, it is possible that the same tooth records more than one U uptake event in different domains within the tooth (most notably when comparing enamel vs dentine domains; Grün et al., 2014). Since Th is immobile, each U uptake event that affects the tooth will shift pre-existing U-Th systematics to portray a younger age (Grün et al., 2014). The variable U-Th disequilibrium ages are a clear indication that U uptake events took place, and provide a minimum age estimate for the true age of the teeth. Where apparent ages are consistent across much of the tooth (e.g., sample 1767) they may approach the true age of the U uptake events. The results presented in this study show that the hominin teeth are clearly older than 70 ka, as evidenced from the consistent results on the dentine of samples 1788 and 1810. An important result from this method is the older closed system age (ca. 200 ka) from enamel obtained for sample 1810B by GU-ANU (Table 5). This result indicates that there was an early phase of U uptake in the tooth that was later overprinted in the associated dentine. In this case, sample 1810 has a minimum age of around 200 ka, suggesting that the H. naledi fossils are older than 200 ka.

US-ESR and OSL results

ESR and OSL dating techniques are dosimetric dating techniques (Adamiec and Aitken, 1998; Murray and Wintle, 2000), and deliver results that are generally much more variable than U-series dating due to the relative lack of control of the conditions under which the samples accumulated radiation damage. In addition, analytical protocols between labs may vary significantly (e.g., SCU used an X-ray gun whilst CENIEH-GU used gamma-rays as their irradiation source), and final results are heavily dependent on a range of à priori model assumptions (such as water content, Rn loss or burial history through time). For OSL, similar à priori model assumptions must be made, and the interpretation of results is further hindered by the use of composite samples in which individual grains may have experienced different burial histories (Galbraith et al., 1999, 2005). Single grain analyses are possible (Duller, 2008), but far more labour intensive and, for the purpose of this study, were not required. Moreover, this is the first time that OSL has been applied to cave deposits in the CoH, and there is no comparative data available for this area. However, the results are consistent with the interpreted stratigraphy and other dating in the chamber, and highlight the potential for additional work.

To assure that all US-ESR results obtained by the different laboratories can be compared in an objective manner, we standardized the à priori model assumptions (Table 6), that is, the same analytical results for sediment chemistry, back ground radiation, water content, radon-loss and cosmogenic radiation, needed to calculate the environmental dose rate, were used by both laboratories. Therefore, any differences in age estimates relate to the measured equivalent dose (DE) and laboratory methodologies, and are not the result of model assumptions. Both laboratories also applied the same combinations of model parameters that would most likely result in either maximum or minimum age estimates. These are presented as two scenarios in which the determined age range will overlap with the true age of the fossils (Table 7).

When examining the US-ESR results for the teeth (Table 7), two trends are apparent: (i) The results for samples 1810 and 1788 from SCU and CENIEH-GU agree well within the listed uncertainties; and (ii) The calculated ages for sample 1767 are much younger than the other teeth. Regarding the second issue, samples 1767 and 1788 were collected from the top of sub-unit 3b within 1.3 m from one another, with the difference that sample 1767 lay directly on surface in the centre of the floor, whereas sample 1788 lay to the side under a cover of 2 cm of loose sediment (Figure 4). Given their position in the cave the teeth are expected to be of similar age. However, their ages as obtained by SCU vary by a factor of >2 (scenario 1: 104 ± 29 vs 247 ± 42 ka; scenario 2: 87 ± 22 ka vs 194 ± 34 ka; Table 7). The main difference between the two samples is that the internal dose rate of sample 1767 is ~20 times higher (Table 7), due to the high U concentration in the enamel (~2.5 ppm). Such high concentrations can lead to dose rate overestimations due to inappropriate alpha efficiency values (Duval et al., 2012). The high U values in sample 1767 are probably the result of its greater exposure to water, confirmed by its extremely weathered nature (Figure 6a). Given these factors, we do not trust the reliability of the age results for sample 1767 and have excluded this tooth from the final age estimates for the fossils.

The age estimates from the maximum and minimum age scenarios as calculated here are dependent on the amount of estimated Rn loss over time, that is, in assessing the best age estimate for the H. naledi fossils a major issue is whether 222Rn degassing was a process that operated continuously over the past 300 ka or not. 222Rn is a noble gas, radio-isotope that forms as part of the 238U decay chain, and its escape has a major effect on the total amount of gamma radiation generated by the sediments (e.g., Guérin et al., 2011), and consequently, the calculated US-ESR age (Table 7). The reason why 222Rn degassing occurs so readily probably relates to the crystallographic position occupied by U atoms. Uranium and Th are chiefly hosted in very thin Fe-Mn oxy-hydroxide coatings on grains within the sediments (Dirks et al., 2015; Makhubela et al., 2017), and given (alpha)-recoil in the 226Ra decay, escape of 222Rn (half-life 3.82 days) is likely. This process will have occurred throughout the history of the cave given that the formation of Fe-Mn oxy-hydroxides is an integral part of the chemical process that occurs within the unconsolidated cave sediments as a result of oxidation, auto-brecciation and weathering reactions (Dirks et al., 2015). It is, therefore, assumed that effective Rn degassing will have been an important process in the cave throughout the accumulation history of the Unit 3 sediments, although it seems unlikely that an extreme degassing environment similar to the 80% measured today was maintained during the entire history of burial. Therefore, we interpret the maximum US-ESR age estimates calculated for scenario 1 conditions to be the closest to the true age of the H. naledi fossils. If Rn degassing was somewhat less in the past, the older age bracket would move into the direction of 270 ka (i.e., the maximum age limit calculated under scenario 2 conditions).

The OSL results are more difficult to interpret than the US-ESR results, not only because we have to assume model parameters to estimate the environmental dose rate, but also because we have few constraints on the origin and provenance of the quartz grains that were sampled. OSL analyses were carried out for aliquots of ~30 grains and each analysis, therefore, is an average of the signals contained in the grains. There is significant within-sample scatter in measured total dose (De) values between different aliquots, meaning that age estimates are imprecise (uncertainties of 15–18%). Overdispersion in De ranges from 50–70%, which is much higher than would be expected for a well-bleached sample (Galbraith et al., 1999), and is a reflection of the cave environment from which the samples were taken (Duller, 2008). We interpret this to mean that the quartz grains in each aliquot consist of a mixture of grains with some derived from outside the cave (and carried into the cave over a period of time), and others derived from quartz veins and chert beds within the cave that have only been partly bleached or have never been bleached at surface at all. Add to this the natural signal variability that can occur due to crystallographic orientation and lattice defects (Olley et al., 2004; Galbraith et al., 1999, 2005) and a large overdispersion results. The Minimum Age Model (MAM) was chosen as the preferred statistical model to calculate age estimates for the sediments. This is a statistical averaging technique for aliquots that display a high degree of within-sample scatter (Olley et al., 2004; Galbraith et al., 2005), but still combines some grains that are well-bleached with others that are only partly bleached. Thus, the MAM age is likely to provide a maximum age estimate for the Unit 1 sediments, and must be viewed with caution. A more comprehensive sampling campaign will be required in future to fully establish the range of ages for Unit 1 across the chamber. Nevertheless, the preliminary results are consistent with the range of ages suggested for Unit 3 by ESR and U-Th analyses on capping flowstones (Figure 14).

An updated stratigraphy for the Dinaledi Chamber

The importance of a deep understanding of the stratigraphic position of the fossils and the geological processes that led to their deposition cannot be overstated considering the extremely complex nature of sedimentary cave fill in many cave systems (e.g., Wilkinson, 1985; Brain, 1993; Sasowsky, 1998; Stock et al., 2005; Stratford et al., 2014; Sutikna et al., 2016) involving repeated cycles of deposition, erosion and reworking, leading to complex and sometimes contradictory age results (e.g., Granger et al., 2015; Kramers and Dirks, 2017). This problem is well illustrated with the on-going debate on the age of Stw 573 (‘little foot’) in the nearby Sterkfontein Cave, where after 20 years of dating efforts no definitive age is yet established (see Partridge et al., 1999, 2003; Berger et al., 2002; Walker et al., 2006; Herries and Shaw, 2011; Pickering and Kramers, 2010; Granger et al., 2015; Kramers and Dirks, 2017). Another good example illustrating the difficulties of linking cave stratigraphy to a definitive age for the hominin fossils they contain is presented by the H. floresiensis remains in the Liang Bua cave, Indonesia (Morwood et al., 2004; Roberts et al., 2009; Sutikna et al., 2016).

The stratigraphy within the Dinaledi Chamber has been previously described by Dirks et al. (2015). The ages presented here help to resolve outstanding questions about the stratigraphy in the Dinaledi Chamber, and allow us to more closely define the distribution of correlative stratigraphic units (Figure 14), and thus constrain the age of the H. naledi fossils.

The oldest ages returned from the Dinaledi Chamber are from the baboon tooth that is embedded in sediment attributed to sub-unit 3a, followed by U-Th ages for Flowstone 1a, which directly covers erosional remnants of Unit 2 (Figure 14). Flowstone 1a consists of at least three generations of flowstone growth, named, from oldest to youngest, phase A, B and C (Figures 2b, 13a,b and 14). We dated phases B and C via U-Th, at 502 ka (RS23; Table 1) and 478 ka (RS22; Table 1) respectively, but the uncertainties are large because the ages are close to the upper dating limit of the U-Th technique. The oldest, phase A layer at the base of Flowstone 1a records reversed magnetic polarity indicating that it formed before 780 ka (Singer, 2014). The three age estimates are consistent with the stratigraphic position of the three phases in Flowstone 1a, and they indicate that the erosion remnant of Unit 2 encrusted by Flowstone 1a is also older than 780 ka. The fact that the erosion remnants of Flowstone 1a dip into the chamber suggests that at the time of formation of all three phases of Flowstone 1a, the debris cone of Unit 2 sediment was still in place; that is, erosion of Unit 2 sediment from below Flowstone 1a would have occurred sometime after 585 ka (i.e., the older age limit for phase C in Flowstone 1a) and possibly as late as 437 ka (i.e., the younger age limit of phase C in Flowstone 1a). Unit 2 contains rare fossils of macrofauna, including a long bone in the erosion remnant, which must be older than 780 ka as well. We interpret the floor sediments of sub-unit 3a that contain the baboon tooth (sample 1841) to represent, at last in part, the reworked remains of the debris cone that once existed below Flowstone 1a (Figure 8) as material was removed from the chamber via floor drains, thereby undercutting the debris cone, which responded by slowly slumping into the chamber – a process ongoing today. The baboon tooth could be part of the original, Unit 2 debris cone and, therefore, older than 780 ka, although the US-ESR age indicates that it could also be younger (with a mid point age of ~ 679 ka between a maximum age of 723 ± 181 ka and the minimum age of 635 ± 148 ka, with a possible age range of 487 ka to 904 ka). If the tooth is younger than 780 ka, it would suggest that it was derived from different sedimentary deposits not tested in this study, or that it may have entered the chamber separately during erosion of the Unit 2 debris cone, and its presence may reflect more direct entry points from surface into the chamber now sealed by flowstone. This possibility was tested with sample RS9, a flowstone sample filling a thin (<14 cm wide) fracture in the dolomite on the surface that occurs above the Dinaledi Chamber. This flowstone yielded equilibrium U-Th results meaning that it formed before ~ 600 ka (Table 1), which is consistent with the interpretation that the Dinaledi Chamber was closed to direct entry of coarser-grained sediment from the surface prior to the entry of H. naledi into the cave system and remained closed until the present (Dirks et al., 2016a).

Below Flowstone 1a are five other flowstones (Flowstones 1b-e and Flowstone Group 2; Figure 2b), which each cover erosional remnants of sediments that we originally grouped as Unit 2 (Dirks et al., 2015). The geochronology results presented here (Table 1) now permit a better evaluation of the flowstone stratigraphy in the chamber, and it is evident that Unit 2 represents a significantly older stratigraphic unit that is restricted to deposits directly below Flowstone 1a, but not to the sediment deposits below Flowstones 1b-e. Flowstone 1c returns an age of ~243 ka (Table 1), suggesting that the sediments below Flowstones 1b-e are significantly younger than Unit 2 sediments below Flowstone 1a (Figure 14). It was noted before that the sediments below Flowstones 1b-e are less indurated and less weathered than the sediments below Flowstone 1a, and that they contain H. naledi material (Dirks et al., 2015). Their distinct appearance and fossil content is now confirmed with the dating. Therefore, we reinterpret the H. naledi-bearing sediments below Flowstones 1b-e as part of Unit 3 (sub-unit 3b), which means that all H. naledi-bearing sediments in the chamber are now part of sub-unit 3b (Figure 8).

Cartoon illustrating the sedimentary history resulting in the deposition and redistribution of sediment of Units 2 and 3, and Flowstone Groups 1 to 3 in the Dinaledi Chamber.

Note that all hominin fossils are contained in sub-unit 3b, but that this sub-unit has been repeatedly reworked after its initial deposition. Fossil entry occurred during the initial stages of deposition of Unit 3 below the entry shaft and predated deposition of Flowstone 1c. H. naledi fossils may have continued to enter the Dinaledi Chamber as older parts of Unit 3 were eroded from below Flowstone 1c, and as remnants of all older units were reworked to be incorporated into Unit 3 sediments that accumulated along the floor of the Dinaledi Chamber.

https://doi.org/10.7554/eLife.24231.019

Apart from the poorly consolidated erosional remnants below Flowstones 1b-e, hominin-bearing Unit 3 sediments also cover most of the floor of the Dinaledi Chamber. The layer of sub-unit 3b sediment has been interpreted as a relatively thin sheet (~20 cm) of rubbly mud clast breccia material mixed with H. naledi fossils based on outcrops in the excavation pit and preliminary ground penetrating radar results (Naidoo, 2016; Figures 2 and 8). Age brackets for sub-unit 3b were obtained by dating underlying outcrops of sub-units 1a and 1b via OSL, and by dating overlying flowstone units. In this context sample OSL5 is the most relevant for obtaining a maximum age estimate for sub-unit 3b, because it was taken from an outcrop of Unit 1 that is overlain by Unit 3. Here, a maximum age limit of 414 ka (the upper error limit of OSL5) can be assigned to sub-unit 3b if the OSL ages are taken at face value. Note however, that the maximum age limits for sub-unit 1b as determined from samples OSL3 and OSL4 are significantly less at 272 ka and 278 ka (upper error limits), respectively (Table 8), which supports the interpretation that sub-unit 1b formed due to erosion and redeposition on top of sub-unit 1a. The minimum age limit of sub-unit 3b can be more confidently constrained as it is overlain by flowstones with age ranges between 97 ka and 24 ka (Table 1). More importantly, a hanging remnant of sub-unit 3b with hominin material is covered by Flowstone 1c with a lower age limit of 236 ka obtained from the core of a stalactite overlying the rim of the flowstone remnant. This age provides the best minimum age estimate for sub-unit 3b, and by extension a minimum age for the H. naledi fossils.

U-Th dating of an erosional remnant of Flowstone 1 that occurs directly above an outcrop of sub-unit 1b from which sample OSL4 was taken, and appears to cover it, provides an age of 290 ± 6 ka, suggesting that Unit 1 in this location must be older than 284 ka. The OSL results (using the MAM model), however, suggest that the Unit 1 sediments in this location must be younger than 278 ka (Table 8; using MAM age models). This apparent paradox may indicate that the OSL ages are unreliable, but could mean that sub-unit 1b was deposited in an inverse stratigraphic order in relation to the flowstone. This is supported by physical evidence in the chamber in which a gap between the flowstone drape and underlying sediment widens towards the back of the outcrop (Figure 2c), implying that sub-unit 1b was deposited below an erosional remnant of Flowstone 1, and is, therefore, younger than this flowstone. Recrystallization-dissolution textures, and anomalously high 234U/238U ratios (>3) suggest that the age reported for this flowstone sample (RS5) should be treated as a minimum age.

Although the age constraints for sub-units 1a and 1b are imprecise they do suggest that Unit 1 in this part of the chamber is younger than Unit 2, and that the red mud clasts forming Unit 2 sediment were derived from source material matching our description of sub-unit 1a, but positioned higher up in the cave. This source material was possibly part of sub-unit 1c, or it could represent part of an older and as yet undefined sub-unit of Unit 1. No age assessment for sub-unit 1c deposits were done, because accumulations are too small to be tested with OSL or too difficult to access.

The U-Th ages from flowstones and teeth place constraints on the changing physical environment experienced in the cave chamber over time. Flowstone deposition in the Dinaledi Chamber occurred during discrete periods including 24–32 ka, 50 ka, 88–105 ka, and during older events around 242 ka, 290 ka, between ~437 ka and 683 ka, and >780 ka. The flowstones are associated with relatively low initial 234U/238U ratios of 1.8–2.4 (Tables 2 and 3). Flowstones formed in different parts of the chamber as drip points shifted, but no clear pattern in age distribution is apparent (Figure 1b) other than that the flowstones deeper in the cave generally appear to be younger. The U-Th ages for the teeth also define a number of apparent U uptake events at around 43–48 ka, 70–75 ka, 80–90 ka, 100–120 ka and ~200 ka (Tables 4 and 5). The initial 234U/238U ratios associated with each of these events is similar and anomalously high (6.9–8.1).

The periods of time during which flowstones formed in the cave, by and large, do not overlap with the periods of time during which U-uptake appears to have occurred in the teeth, although both types of events were probably associated with wet periods in the chamber. The systematic difference in the initial 234U/238U ratios obtained from flowstones, as compared to teeth, indicates that an isotopically distinct water source led to U-uptake in the teeth, such as groundwater in the dolomitic aquifer of the Malmani Group with reported anomalously high initial 234U/238U ratios (e.g., Kronfeld et al., 1994). Working on the assumption that the high initial 234U/238U ratios are derived from the groundwater reservoir, the observed age groupings suggest that U uptake events in teeth represent (partial) inundation events of the Dinaledi Chamber, whilst the flowstone formation events reflect periods during which the groundwater table had dropped below floor level, but extensive drip still occurred within the Dinaledi Chamber caused by water derived from the surface with generally lower 234U excess. The age groupings also indicate that episodic wet periods in the Dinaledi Chamber alternated with periods during which no flowstone was deposited.

Age estimates for H. naledi and implications for hominin evolution

Figures 1b and 14 summarize the results of all dating methods applied to the Dinaledi Chamber during the course of this study. It is clear from these results that the H. naledi assemblage in Unit 3 is of mid- to late-Middle Pleistocene age. The best age estimates for the H. naledi fossils come from the averaged US-ESR ages for samples 1788 and 1810: 229 +60/–46 ka (maximum) and 179 +49/–40 ka (minimum) for sample 1788, and 276 +59/–77 ka (maximum) and 220 +50/–60 ka (minimum) for sample 1810, with an age range of 139 ka to 335 ka. The maximum age scenario provides an average age for both teeth of 253 +82/–70 ka, and the minimum age scenario provides an average age of 200 +70/–61 ka. Considering the observed Rn loss in the cave sediments, the maximum age estimate is considered to be closer to the true age.

The lower age limit of 139 ka must be disregarded and shifted to ~200 ka considering a U-Th minimum age estimate for parts of enamel on tooth sample 1810 (Table 5). This minimum age limit can be constrained further to 236 ka based on U-Th age estimates for Flowstone 1c (242.0 ± 5.0 ka; 242.9 ± 6.6 ka; Table 1), which directly covers fossil material of H. naledi, noting that these ages may represent minimum age estimates for the flowstone as a result of possible U uptake during a period of raised groundwater levels (Figure 14).

The maximum age limit of 335 ka for the H. naledi fossils relies on 80% Rn loss throughout the burial history of the fossils and is probably an over-estimate. A separate maximum age estimate for sub-unit 3b can be obtained from the baboon tooth (sample 1841) in sub-unit 3a sediments devoid of hominin fossils, underlying the partly articulated remains of H. naledi, with US-ESR age estimates varying from 635 ± 148 ka (minimum) to 723 ± 181 ka (maximum) with an age range of 487 ka to 904 ka and a mid-point age of 679 ka. The older age estimate is considered to be more likely (considering the measured Rn loss). These maximum age estimates are consistent with the direct age estimates for the H. naledi fossils, but do not further constrain the upper age limit (Figure 14).

A further maximum age estimate for the H. naledi fossils can be obtained from age estimates for sub-unit 1a using sample OSL5. This sample provides a maximum age limit for sub-unit 3b, of ~414 ka (Table 8; using MAM). Although OSL ages are poorly constrained, and do not provide very precise age limits, this estimate is broadly consistent with the estimated age for reworking of Unit 2 sediments from below Flowstone 1a (437–585 ka) and the US-ESR age estimates for the teeth.

Considering all age results presented here the most parsimonious age estimate for the H. naledi fossils is sometime between 236 ka and 335 ka. More work will be needed in future to constrain these ages further (Figure 14).

Until now, it has been generally assumed that morphologically primitive hominins like H. naledi (Berger et al., 2015) did not survive into the later parts of the Pleistocene in Africa. This general assumption has commonly guided the interpretation of fossil discoveries with poor geological or stratigraphic context, including initial estimates for the age of the H. naledi fossils (Thackeray, 2016; Dembo et al., 2016). The new age estimates for H. naledi show that an approximate age for the hominin fossil fragments cannot be simply deduced from their morphology (Thackeray, 2016; Dembo et al., 2016). Detailed geological investigations are critical before any attempt to ascribe an age to the fossils is made, and even then great care must be taken in interpreting results, which may not always be conclusive (e.g. see famous examples such as Sterkfontein or Liang Bua; Partridge et al., 2003; Wilkinson, 1985; Walker et al., 2006; Roberts et al., 2009; Pickering and Kramers, 2010; Granger et al. 2015; Sutikna et al., 2016; Kramers and Dirks, 2017).

It is generally assumed that all African fossil hominins producing Middle Stone Age archaeological industries in the past 300 ka were part of a single variable species of early H. sapiens or an immediate precursor (e.g., Mcbrearty and Brooks, 2000; Lahr and Foley, 2001; Stringer, 2002). The new ages now show that H. naledi existed at the same time as the first Middle Stone Age tools were produced in southern and eastern Africa, whilst skeletal evidence shows that H. naledi was probably capable of tool use (Berger et al., 2015; Hawks et al., 2017). This raises the possibility of H. naledi being responsible for some of the MSA traditions. The implications of the new ages for H. naledi are discussed in detail in Berger et al., 2017.

Material and methods

Flowstone samples for U-Th dating

A total of seventeen flowstone samples (RS1, RS5-6, RS8, RS10-11, and RS 13–23) from the Dinaledi Chamber were dated via U-Th geochronology, including one set of blind duplicates (RS1 and RS15; Table 1, Figures 1b and 3). In addition, one flowstone sample (RS9) was taken on the surface (WGS84 571240–7121866) from a shallow pit about 11 m SW of the projected surface position of the excavation pit in the Dinaledi Chamber (Figure 3d). For each sample a powder was prepared and then split, with one half being dated at JCU and the other half being dated at UoM; that is, for each sample both JCU and UoM dated the same material.

In the Dinaledi Chamber samples of Flowstone Groups 1, 2 and 3 were collected from a variety of stratigraphic positions (Figures 1b, 2 and 3). All the sampled flowstones formed as sheets, crusts, or drapes overlying older sediment units, with the exception of samples RS13 and RS18, which were taken from a small stalactite that formed along the lip of an erosional remnant of Flowstone 1c. Additionally, samples RS14, RS16 and RS17 were taken from a flowstone drape along a dolostone side-wall of the chamber. In all instances the flowstones have a free upper surface, that is, they are not overlain or covered by sediment, and all flowstones are interpreted to be younger than the sediment units they cover. The one exception to this rule could be RS5, which comes from a partly resorbed erosion remnant of Flowstone 1 that appears to overlie Unit 1, but is separated from the top surface of Unit 1 by a small opening that widens with depth (Figure 2c). This leaves the possibility that this flowstone is an erosional remnant, and that Unit 1 (sub-unit 1a) sediments built up below it after it had been deposited. The location of each sample within the Dinaledi Chamber is shown in Figure 1b, and outcrop and close-up photos of the sampled flowstones are shown in Figure 3.

RS1 and RS15 are blind duplicate samples taken from a hanging remnant of Flowstone Group 2 that occurs in a N-trending fracture, ~10 m N of the excavation pit and ~3 m N of a major outcrop of sub-unit 1a sediment from which sample OSL3 was collected. The flowstone overlies largely unconsolidated floor sediments of Unit 3, which in this locality have eroded from underneath the flowstone to leave a hanging remnant ~8 cm above the current floor level (Figure 3i). The flowstone consists of a 15–18 mm-thick layer of calcite overlying an irregular surface of mud clast breccia, locally incorporating and growing around large mud clasts that were lying on the palaeo-surface. The flowstone is grey-white in colour and preserves 3–6 mm scale laminations visible due to subtle colour variations. The flowstone is recrystallized with elongated, acicular crystals of calcite growing from the base to the top of the layer across all internal laminations. The upper surface of the flowstone has a rough, pitted appearance as a result of partial resorption or dissolution of calcite along the grain boundaries of the needle-like crystals. Samples RS1 and RS15 were taken from a 3 mm-thick zone, 3 mm above the basal contact of the flowstone layer (Figure 3i).

RS5 was sampled from a thin sheet of Flowstone Group 1 in a WNW-trending fracture, ~4 m W of the excavation pit (Figure 1b). The flowstone overlies orange sandy mudstone belonging to sub-unit 1b from which sample OSL4 was taken (Figure 3a), but appears to be separated from this unit by a narrow opening that widens to the back of the outcrop (Figure 2c). The flowstone consists of an 8–22 mm thick, cream white layer of carbonate with a sponge-like, porous, sugary texture that largely masks (due to recrystallization of the primary calcite) underlying mm-scale laminations. The flowstone layer appears to be partly dissolved along its stratigraphic top with the external surface of the layer truncating internal laminations. Sample RS5 was taken from a 5 mm-thick horizon, 3 mm below the top of the flowstone layer (Figure 3a).

RS6 was sampled from a thin sheet of Flowstone Group 2 in a WNW-trending fracture, ~6 m W of the entry zone (Figure 1b). The flowstone overlies erosion remnants of Unit 1 and Unit 3. At the sample site, sediments of Unit 3 have been partly eroded from underneath the flowstone leaving a hanging remnant, 5–10 cm above the current floor level (Figure 3b). The flowstone consists of an 8–12 mm thick crust overlying an irregular sediment surface, incorporating fine (<3 mm) mud clasts in the base of the layer. It is white-grey in colour and semi-transparent, with limited evidence of internal layering except for a slightly lighter coloured basal layer that is several mm thick. The entire layer is recrystallized with fine, radiating acicular crystals of calcite growing upward from the basal contact. The upper surface has a rough pitted appearance as a result of partial resorption/dissolution along grain boundaries of the acicular crystals. Sample RS6 was taken from a 3 mm-thick horizon at the bottom of the flowstone (Figure 3b).

RS8 was sampled from a thin sheet of Flowstone 2 on the floor of the entry zone below the stack of hanging remnants of Flowstone 1a-e. The flowstone overlies sediments of Unit 3 that are partly eroded from underneath the flowstone leaving a 5–10 cm gap between the flowstone sheet and the current floor (Figure 3c). The flowstone consists of a 5–22 mm thick layer overlying an irregular surface of mud clast breccia. The grey-white flowstone preserves 3–5 mm thick layering visible as subtle colour variations, despite partial recrystallization and replacement by elongated acicular crystals of calcite. The basal 10 mm is composed of a mesh of fine aragonite needles. Above this zone acicular calcite replaces the aragonite. The upper surface of the flowstone has a rough, pitted appearance as a result of partial resorption/dissolution along grain boundaries of the acicular crystals. Sample RS8 was taken from the bottom 3–5 mm of the flowstone layer (Figure 3c).

RS9 was sampled from a surface outcrop in a shallow mine pit that occurs about 11 m SW of the projected surface position of the excavation pit in the Dinaledi Chamber (Figure 3d). The sample site occurs along strike of the same fracture along which the Dinaledi Chamber was formed at depth, and it is therefore possible that this surface outcrop in the past could have linked to the cave system below. The flowstone consists of a 12–25 mm thick layer of carbonate overlying an irregular surface of consolidated mud clast breccia similar to sediments of Unit 2 in the Dinaledi Chamber. The grey-white flowstone preserves 1–5 mm scale laminations visible due to colour variations and the presence of several thin brown marker surfaces. The laminations are locally recrystallized and overgrown by radiating, elongated crystals of calcite growing from the base to the top of the flowstone layer. Additionally, fibrous aragonite needles are widely distributed in sheaf-like patterns. The upper surface of the flowstone has a rough, pitted appearance as a result of partial resorption/dissolution along the grain boundaries of the acicular crystals. Sample RS9 was taken from a 4 mm-thick white horizon, 2 mm above the basal contact of the flowstone layer (Figure 3d).

RS10 was sampled from a thin crust of Flowstone Group 2, about 2 m W of the excavation pit and 0.2 m W of the location where tooth sample 1810 was found (Figure 3e). The flowstone directly overlies mud clast breccia of Unit 3 and hominin bone fragments. It consists of a 4–8 mm-thick laminated flowstone crust overlying an irregular sediment surface and incorporates fine (<3 mm) mudstone clasts within its basal laminae. This flowstone is white to grey in colour and is finely laminated and partly recrystallized, with recrystallization visible as white, fine, radiating needles of aragonite growing upward from the basal contact, along an irregular alteration front into grey-white, laminated calcite near the top of the layer. RS10 was taken from the laminated bottom 3 mm of the flowstone layer (Figure 3e).

RS11 and RS21 represent two samples taken from the top and bottom, respectively, of the same flowstone unit developed along the floor below an active drip point, 1.5 m E of the excavation pit. This flowstone consists of a basal layer of grey flowstone interpreted as Flowstone Group 2 overlying Unit 3 sediments, covered by a white flowstone layer containing small stalagmites interpreted as Flowstone Group 3 (Figure 3f). The sample collected for dating consists of a 20–28 mm thick, finely laminated flowstone including the two distinct layers described above (Figure 3f). The basal layer (RS21; Figure 3f) is 3–12 mm thick, and consists of brown-grey calcite resting on Unit 3 sediment. This layer is strongly recrystallized with radial, acicular crystals of calcite growing upward from the lower contact, which locally appears to have replaced an earlier generation of acicular aragonite. These crystals overgrow mm-scale laminations defined by white to brown colour variations. RS21 was sampled from the basal-to-central segment of this layer. The basal layer is overlain by an 8–16 mm thick layer of finely laminated (sub-mm scale) white speleothem. The basal 2–3 mm of this layer is recrystallized with fine aragonite needles radiating out from the base. Above that the flowstone consists of fine lamellae defined by subtle grey to white colour variations. Each lamina is composed of botryoidal aggregates of acicular aragonite. RS11 was taken from the top 3 mm of this white flowstone (Figure 3f).

RS13 and RS18 are two samples taken from the same stalactite developed along the lip of an erosional remnant of Flowstone 1c near the entrance into the Dinaledi Chamber (Figure 1b). In this location, Flowstone 1c covers the erosional remains of a mud clast breccia containing a long bone consistent with the H. naledi assemblage (Figure 3g), and interpreted as Unit 3. The stalactite connects to part of the speleothem layers that cover the bone.

The stalactite preserves well-developed internal layering, with layers asymmetrically developed around a core, in which layers thicken towards the outward facing side of the stalactite. From core to rim the stalactite reaches a maximum thickness of 53 mm and includes three separate zones that can be distinguished based on internal texture, layering, and colour (Figure 3g). The innermost zone forms an 8 mm-thick, finely laminated (sub-mm scale) core centred on a small mud clast and is terminated by a thin brown, mud-rich rim. This core is surrounded by a ~23 mm-thick central zone that consists of more coarsely layered (3–10 mm-thick), cream to grey-white coloured calcite with layering preserved as subtle colour variations, which at its base shows replacement by radiating sheaves of aragonite needles. This zone is mantled by a ~22 mm-thick outer zone of white calcite preserving only remnants of internal layering. This outermost zone is characterized by extensive replacement of abundant, older aragonite needles by coarse-grained calcite, creating a patchy texture. The sample has been affected by recrystallization resulting in the formation of radiating acicular crystals of calcite that grow from the core outward. The white outer layer also shows evidence of further recrystallization, with the formation of coarse (2–4 mm), equant calcite grains, many with highly irregular grain boundaries that overgrow the acicular grains. The outer surface of the stalactite has a rough, pitted appearance as a result of partial resorption/dissolution along the surface with dissolution along the grain boundaries of the acicular crystals. RS18 was sampled from a 3 mm-thick horizon near the base of the central zone. RS13 was sampled from the outermost part of the outer zone (Figure 3g).

RS14 was sampled from an irregularly shaped, cascade-like crust of Flowstone Group 2, along the side-wall of the main floor drain, between the entry shaft and excavation pit (Figures 1b and 3h). The sample of flowstone crust consists of an 8–11 mm thick layer of cream coloured carbonate displaying mm-scale laminations and a sugary, recrystallized texture with numerous, fine pore spaces along laminar surfaces. Sample RS14 was taken from a 3 mm-thick zone encompassing several fine laminations, ~5 mm above the base of the flowstone layer (Figure 3h).

RS16 and RS17 are two separate samples from a cascade-like crust of Flowstone Group 2 that formed within the main floor drain between the entry shaft and excavation pit (Figure 1b). This flowstone developed on top of the dolomite back-wall of the drain (Figure 3h). The sample consists of a mostly cream coloured flowstone that is up to 73 mm thick, with a massive sugary, recrystallized texture, preserving mm-scale laminations visible due to subtle colour variations. Many of the equant calcite grains contain remnant aragonite needles, reflecting an earlier phase of aragonite growth. Laminations along the basal 3–4 mm of this flowstone are brown in colour, whereas the top 10–12 mm of this flowstone layer consists of what is possibly a separate, younger unit of laminated grey-brown carbonate with small pore spaces developed along some of the laminar surfaces. Sample RS16 was taken from a 3–4 mm-thick layer directly above the basal zone with brown laminations. Sample RS17 was taken from a 4 mm-thick zone at the top of the cream-coloured laminated flowstone, immediately below the darker coloured top unit (Figure 3h).

RS19 was taken from a wedge-shaped sample of Flowstone Group 2 that formed along the lip of a drip pool directly overlying Unit 3 sediments, 1.2 m S of the excavation pit (Figure 1b). The flowstone is cream-coloured and up to 30 mm thick, and overlies a flat sediment surface. It preserves complex internal layering and a variety of textures (Figure 3j). A basal 2–4 mm-thick layer characterised by fine calcite needles growing at right angles to layering is overlain by an irregular mass of darker cream coloured, unstructured calcite with a sugary texture and numerous fine voids. Towards its top this unstructured mass is interlayered with and covered by several 1–4 mm-thick lamellae characterised by fine calcite needles growing at right angles to layering similar to the basal layer, but containing pore spaces. These in turn are overlain by an 8 mm-thick zone of finely laminated flowstone with a fine-grained (<0.5 mm) sugary texture and abundant fine pore spaces. RS19 was taken from the basal flowstone layer with radiating calcite crystals (Figure 3j).

RS20 was sampled from a thin sheet of Flowstone Group 2 in a WNW-trending fracture, ~2 m W of the excavation pit (Figure 1b). The flowstone forms a cascade-like drape that directly overlies orange mudstone of sub-unit 1a from which sample OSL5 was taken (Figure 3k). RS20 occurs directly above sample RS10, which was taken at the foot of the cascade (Figure 1b). The sampled flowstone layer is irregular in shape as it covers sediments with topography. It consists of a finely laminated 15–22 mm thick crust overlying sub-unit 1a sediment and includes a ~6 mm thick, laminated basal unit of white flowstone that incorporates small (3–10 mm) mud clasts, overlain by more coarsely laminated (mm-scale) grey brown carbonate free of inclusions. The flowstone is internally locally recrystallized with acicular aragonite crystals growing within ~3 mm thick zones at right angles to layering. RS20 was sampled from the basal layer of the sample (Figure 3k).

RS22 and RS23 are two samples from an eroded rim of Flowstone 1a near the entry shaft into the Dinaledi Chamber (Figure 1b). This flowstone overlies erosional remnants of well-indurated mud clast breccia assigned to Unit 2 (Figure 3l), and mostly consists of coarsely recrystallized white carbonate. The flowstone sample from which RS22 and RS23 were taken occurs down dip from the palaeo-magnetic sample taken from Flowstone 1a as described below (Figures 2b and 13). The flowstone layer is ~25 mm thick and comprises a 6 mm thick, basal unit of grey to brown calcite that is recrystallized into fine (sub-mm scale), equigranular grains of calcite overgrowing an older acicular texture. The basal layer corresponds to phase B carbonate described for the palaeo-magnetic sample, and is overlain by a clean white calcite unit (i.e., phase C in the palaeo-magnetic sample) that is coarsely recrystallized with 2–4 mm equidimensional calcite grains overgrowing (and partly destroying) an older texture formed by acicular grains. Small voids occur in the interstitial spaces between the coarse calcite grains. RS23 was taken from the grey basal unit (i.e., phase B) of the flowstone layer and RS22 was sampled from the central part of the upper white recrystallized unit (i.e., phase C, Figures 3l and 13b). In this sample, flowstone belonging to the older phase A carbonate is no longer present, as this layer pinches out along dip between the point where the palaeomagnetic sample was taken and the point where the U-Pb sample was taken as can be seen in Figures 2b and 13.

Tooth samples for ESR dating

Three H. naledi teeth (samples 1810, 1767 and 1788) and one baboon tooth (sample 1841) were collected from Unit 3, in the Dinaledi Chamber (Figures 1b, 4, 6 and 7) for ESR dating and U-Th analysis. Sample 1767 (full catalogue number U.W.101–1767) is an extremely worn upper premolar crown (Figure 6a) obtained from approximately 1 m SW of the excavation pit (Figure 4), and occurred on surface surrounded by mud clast fragments of Unit 3. This tooth is deeply weathered, and preserved only a small rim of enamel on the buccal margin with a maximum height of 4.5 mm. Otherwise the crown is a concave dentine surface worn to the cervix, with bright white, highly bleached dentine. The tooth is brittle and appears strongly affected by water action. Sample 1788 (full catalogue number U.W.101–1788) is a lower right second molar (Figure 6b) obtained from approximately 2 m WSW of the excavation pit (Figure 4), embedded within loosely packed, mud clast breccia of Unit 3, ~ 2 cm below the ground surface level. This tooth is partly broken at the root, but has an otherwise well preserved crown with thick, light-grey enamel. The distal root of the tooth is present and complete, but the lingual root is broken off just below the cervix. The tooth is morphologically consistent as an antimere of U.W.101–284. The dentine is highly bleached and brittle and appears affected by water action. Sample 1810 (full catalogue number U.W.101–1810) is a lower left third premolar or possibly lower left fourth premolar (Figure 6c) obtained from the SE corner of the excavation pit (Figure 4), embedded within sediments of Unit 3, ~5 cm below the original ground surface level. This tooth is well-preserved with thick, light-blue-grey enamel, and shows little evidence of bleaching or weathering, with only a very slight polishing wear on the distal crest of the protoconid. The morphology of the crown is similar to other lower third premolars in the collection, however, it is slightly shorter than many of those. Sample 1841 (full catalogue number U.W.101–1841) is a well-preserved tooth crown, morphologically consistent with a lower left second molar of Papio sp. This is a complete enamel crown of an unerupted tooth with no wear facets or interproximal facets in evidence, and the roots had not formed (Figure 7). The specimen was recovered from a sediment sample taken at a depth of 55–60 cm below the original ground surface of the cave floor near the base of the sondage dug in the centre of the excavation pit (Figures 1b, 2d and 4). This tooth occurs in sub-unit 3a, ~40 cm below the stratigraphically lowest occurrence of partly articulated remains of H. naledi, and represents the only non-hominin macrofossil recovered from Unit 3.

Sediment samples for OSL dating

Three OSL samples (OSL3, OSL4 and OSL5) were collected in the Dinaledi Chamber from erosion remnants of sub-unit 1a, in which sandy, laminated mudstones are exposed (Figures 1b and 5). These sandy intercalations were targeted because they contain fine-grained quartz and feldspar grains that can be extracted for analysis. For each sample a 30 cm length of aluminium piping with a diameter of 5 cm was hammered into the sediments in a horizontal direction or parallel to sedimentary laminations visible within the units. A core sample within the pipe was extracted for OSL analyses together with a sediment sample from the same unit to determine background radiation from measured values of U, Th and K.

Sample OSL3 comes from an erosion remnant of sediments of sub-unit 1b collected near the intersection point of two fractures trending N and E respectively, ~6 m N of the excavation pit (Figure 1b). Samples OSL4 and OSL5 come from an erosion remnant of Unit 1 sediment along an ENE-trending fracture, ~3 m W of the excavation pit. Sample OSL4 is obtained from sub-unit 1b directly below a thin, partly resorbed flowstone sheet attributed to Flowstone Group 1 (Figure 3a). Sample OSL5 occurs as an erosional remnant of sub-unit 1a, 1 m E, and stratigraphically 10–20 cm below sample OSL4. The Unit 1 sediments in this location are partly covered by Unit 3 sediments and a cascade of Flowstone Group 2 (Figure 3k).

Flowstone sample for palaeomagnetic analysis

The speleothem sampled for palaeomagnetic analysis comes from Flowstone 1a near the entry zone into the Dinaledi Chamber (Figure 2b). The sample is layered and comprises three distinct phases (from base to top: A-C) separated by thin clastic horizons that mark disconformities (Figure 13a,b).

The lower phase (phase A) is interstratified with visible clastic laminations. The internal laminations are truncated along the lower surface of the sample indicating that phase A flowstone was partly dissolved during a phreatic event after the flowstone had been deposited. The middle phase (phase B) consists of intercalated flowstone speleothem and detrital sediment layers, with the detrital layering concentrated towards the downslope part of the sample. Detrital material is generally less than in phase A, indicating decreasing amounts of clastic contamination. Like phase A, the internal layering of phase B is truncated along the lower surface of the sample, indicating that the phreatic dissolution event occurred after deposition of phase B. There is no apparent truncation surface between phase A and B flowstone, indicating that phase B formed on top of phase A after a period of non-deposition during which detrital material accumulated on top of phase A. The upper surface of phase B truncates internal layering reflecting dissolution during a phreatic event. This was followed by a period of non-deposition of flowstone during which a thin layer of detrital clastic material accumulated, before deposition of the upper layer (phase C) of flowstone occurred. Phase C comprises younger, cleaner flowstone which displays extensive recrystallization along the base of the unit with the formation of elongated calcite crystals. This zone of recrystallization could potentially also indicate a younger infill of a cavity that had formed between phase B and C flowstone, and has been avoided during sampling. Phase C flowstone contains little to no detrital inclusions, and suggests that sediment influx into the chamber was not occurring during its deposition.

Phase B and phase C flowstone correlate with samples RS23 and RS22 respectively, that were collected for U-Th dating. The top of the sample was oriented in the cave to magnetic N (−18.2o degrees from true N at this location with a −62.9o inclination). The inclination was accounted for by marking the sample on a completely flat surface of the block.

Bone samples for radiocarbon dating

Three weathered bone fragments of H. naledi were collected for radiocarbon dating including: (i) a tibia shaft fragment, 53 mm in length (U.W. 101–567); (ii) a femur shaft fragment comprising the whole circumference of the shaft, 79 mm in length (U.W. 101–857), and; (iii) a metatarsal or metacarpal shaft with no articular morphology, 48 mm in length (U.W. 101–065). All samples were collected from the surface of Unit 3 as isolated fragments near the excavation pit.

Analytical and computational dating methods

U-Th dating

Background to U-Th dating

Cave carbonates are proven archives of sediment chronology and terrestrial climate variation (e.g., Pickering and Kramers, 2010; Pickering et al., 2010). Cave carbonates less than ~ 600 ka in age can be precisely dated using the U-Th disequilibrium dating method (e.g., Hellstrom and Pickering, 2015). The disequilibrium technique differs from other radiogenic techniques like U-Pb or Rb-Sr in which the daughter product is stable and accumulates indefinitely. In the 238U decay chain, 234U (half-life of 245.5 ka) decays to 230Th (half-life of 75.4 ka), which itself decays to 226Ra. This means that rather than accumulating indefinitely with time, the concentration of 230Th in a sample gradually moves to a point where the number of decays of 230Th atoms equals the number of 230Th atoms produced via the decay of 234U (‘secular equilibrium’). Because Th is nearly insoluble in surface waters, flowstone does not usually contain initial 230Th, in contrast to U, which is soluble in oxidizing waters and is incorporated into flowstone at low concentrations (generally <5 ppm; e.g., Pickering et al., 2010). In U-Th dating, the accumulation of 230Th towards secular equilibrium and the decay of its immediate parent (234U) yields the age. In calculating a U-Th age, the ratio of 234U to its parent 238U must also be determined, as this ratio is generally elevated above secular equilibrium in natural waters. The assumption that initial 230Th concentrations in flowstone are close to zero may be violated by varying amounts of ‘detrital matter’, carrying initial 230Th. However, many cave carbonates form with essentially no initial Th. Where corrections for initial Th are small, potential variability in the isotopic composition of this Th is generally incorporated in the age error. The U-Th dating technique has an upper age limit of ~600 ka, determined by the half-life of 230Th, and by the precision with which the various isotopes can be measured in the laboratory (Cheng et al., 2013).

After initial tests for U-Th disequilibrium dating at JCU proved successful, a suite of flowstone samples was collected from the Dinaledi Chamber and prepared as duplicate samples for double blind dating analyses at James Cook University (JCU) and at the University of Melbourne (UoM).

Methodology: James Cook University (JCU) 

Sample preparation For each sample a 100–200 mg flowstone fragment was removed with a hand-held Dremel tool. The purest flowstone layers were targeted for sampling, and dark layers containing detrital material were avoided. Samples were taken parallel to layering, typically across a 3 mm thick zone and any attached sediment or impurities were removed.

Prior to it being dissolved, each flowstone sample was cleaned. Samples were first loaded into centrifuge tubes filled with ethanol and agitated in an ultrasonic bath for 10 min. This procedure was performed twice for each sample, with clean ethanol for each bath. The centrifuge tubes containing the sampled fragments were then filled with ultrapure water (18.2 MΩ) and agitated in an ultrasonic bath for approximately 2 min. This procedure was performed three times for each sample, changing the ultrapure water each time, after which samples were dried under a fume hood.

Dating protocol Chemical procedures largely follow Horwitz et al. (1992) and (1993). Dried samples were transferred to Teflon containers and spiked with a mixed 229Th-233U-236U tracer prior to dissolution in 3M HNO3. Chemical separation of U from Th was performed using either a chromographic extraction method using Eichrom UTEVA resin (Horwitz et al., 1992, 1993) or Eichrom TRU resin (Lou et al., 1997). The UTEVA procedure produced higher U yields and better separation of U from Th, and has since been adopted as the standard procedure at JCU. Analytical blanks from both procedures were indistinguishable and low (<10 picograms U). Prior to analysis samples were treated with 32% H2O2 to destroy any particles of resin.

Uranium and Th isotope measurements were performed with a ThermoScientific Neptune MC-ICP-MS instrument at the Advanced Analytical Centre of JCU. The instrument is equipped with a single central secondary electron multiplier (SEM) and 9 Faraday detectors and amplifiers with 1011 Ω resistors. Measurements were performed using a Cetac Aridus combined with a 100 μl PFA nebulizer for sample introduction. An exponential mass fractionation law was used to correct isotopic ratios. For U isotopes we normalized ratios to a 235U/238U ratio of 137.794 (Goldmann et al., 2015). For Th isotopes, samples were bracketed with standard solutions of CRM-145 and corrected using the mass bias determined for the U standard. For isotopes measured on the SEM, we corrected for tails using the log mean of the relevant half masses. For isotopes measured on the Faradays detectors, the shape of the tail and tailing parameters were defined daily using a >25 V of a solution of U005A; with these parameters a correction for the family of U tails was made.

We represent age uncertainties that include propagated 2σ envelopes on isotope ratios and decay constants, as well as an error envelope on the assumed initial 230Th/232Th. The assumed value for initial 230Th/232Th is 0.83 ± 0.50 (2σ). These are the main sources of uncertainty for the age estimates, and we treat them as three sources of uncorrelated uncertainty. Uncertainty on measured isotope ratios reflects counting errors and variability within a mass spectrometric analysis. Decay constant uncertainty envelopes are after Cheng et al. (2013), and we propagate uncertainty on tracer (spike) isotope concentrations. Uncertainties are represented as symmetric in both the older and younger direction and are expressed in ka.

Methodology: The University of Melbourne (UoM)

Sample preparation Samples were prepared at JCU as described above, and sent to UoM for analysis.

Dating protocol Analyses at UoM were done by multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS), using the analytical methods of Hellstrom (2003). An assumed value for the initial 230Th/232Th activity ratio of 1.5 ± 1.5 (2σ) was used to calculate corrected ages in conjunction with the decay constants of Cheng et al. (2013). All ages are expressed in ka and corrected for initial 230Th using Equation 1 of Hellstrom (2006). 234U/238U activity ratios were determined after Hellstrom (2003) and Drysdale et al. (2012). All uncertainties are presented as 2σ.

ESR dating

Background to ESR dating

Electron spin resonance (ESR) dating in combination with U-series data offer a largely non-destructive approach for direct dating of human fossil remains (e.g., Grün, 1989, 1997, 2009; Joannes-Boyau et al., 2010; Joannes-Boyau and Grün, 2011; Joannes-Boyau, 2013). The basic principles of ESR dating can be found in Grün (1989), (1997), and are briefly summarized here with reference to hominin teeth.

When the highly crystalline material (hydroxyl-apatite) that forms tooth enamel is exposed to ionizing radiation, resulting from the radioactive decay of naturally occurring radiogenic isotopes (mainly U, Th and K) and cosmogenic rays, unpaired electrons in the crystal lattice can be moved from their normal valence band to a higher energy level or excitation state. Some of these excited electrons become trapped in charge deficit sites within the crystal structure to form paramagnetic centres that can be measured with ESR spectroscopy. The number of trapped electrons builds up over time as a function of the strength of the gamma ray intensity (or dose rate) in the surrounding environment. For teeth buried in cave sediment deep underground, radiation is mainly derived from radioisotopes contained in the surrounding sediments and the tooth itself. Thus, a tooth acts as a natural dosimeter in which the total accumulated dose and dose rate can provide an age estimate (Grün, 1989, 1997). The ESR signal contained within a tooth and the dose rate can be measured directly. However, the dose rate can vary over time as U can be highly mobile in wet cave environments (e.g., Grün, 2009), and can move in and out of teeth (Grün et al., 2008a). The environmental dose rate can be measured using in situ gamma ray spectrometry, or can be determined from measured values of natural isotopes (mainly U, Th and K) and calculations of the cosmic ray contributions following models. The internal dose rate (inside the tooth) can be determined by measuring the present day 230Th/234U-ratios from which an uptake history for the tooth can be modelled (as opposed to applying assumed uptake models).

Using the combined results of U-Th analyses and ESR measurements, more accurate age estimates can be obtained than would be possible with ESR dating alone. To overcome the problem of not accurately knowing the complex U uptake history of a tooth, the U-Th data is used to establish the relationship between the ESR equivalent dose and apparent U-Th age as defined by the equation:

(1) U(t)=Um(t/T)p+1

In which U(t) is the U concentration at t, Um is the measured U concentration, T is the age of the sample and p the uptake parameter linked to the uptake model determined from U-Th measurements in the tooth (closed system or early uptake: p= −1; linear uptake: p=0, late uptake: p>0 (Grün, 2009).

The methodologies used to obtain U uptake models and ESR dates are explained separately for each of the laboratories. For all reported ages, decay constants for 234U and 230Th are from Cheng et al. (2000).

Methodology for combined U-series and ESR dating: Southern Cross University (SCU)

Sample preparation Small fragments of enamel were removed from each of the four teeth with the help of a hand-held diamond saw following protocols in Grün et al. (2008b) and Joannes-Boyau, 2013. Any dentine attached to the enamel fragment was removed (1841 had no observable dentine), after which a layer of 100 μm was removed from the outer surface of each fragment with a rotary tool. For each tooth, the enamel fragments and a section of dentine directly underlying each enamel fragment were analysed for U and Th concentrations. U-series analyses were also performed on enamel and dentine from the remaining tooth in the immediate vicinity of the fragment to assess variations in U/Th isotopic ratios and calculate ESR ages.

Dating protocols: ESR dose evaluation ESR dating was performed at room temperature on a Freiberg MS5000 ESR X-band spectrometer at a 0.1mT modulation amplitude, 10 scans, 2 mW power, 100G sweep, and 100 KHz modulation frequency. At SCU, the samples were irradiated with X-rays in a Freiberg X-ray irradiation chamber, with a Varian VF50 X-ray gun at a voltage of 40KV and 0.5mA current, with dose rate calibrations depending on the output value of the X-ray gun. ESR intensities were extracted from T1-B2 peak-to-peak amplitudes of the ESR signal of enamel (Grün, 2000a).

Each enamel fragment was mounted into a para-film mould within a Teflon sample holder to record the angular dependency in the ESR response. Irradiation was performed by exposure to the X-ray gun with no shielding of the source. To estimate the equivalent dose (DE), each fragment was irradiated in steps with exponentially increasing irradiation times (for samples 1767, 1788 and 1810, these steps were: 90s, 380s, 1080s, 1800s, 3600s, 7200s, 14400s, 2,8800s and 7,9200s, and for sample 1841: 90s, 380s, 1080s, 1800s, 3690s, 7200s, 1,4400s, 2,8800s, 4,3200s and 9,9000s). During each irradiation step, the output of the X-ray gun was recorded to calculate the dose rate received by the sample (for samples 1767, 1788, 1810 and 1841 these values were 0.178Gy/s, 0.169Gy/s, 0.188Gy/s and 0.240Gy/s respectively. For each irradiation step the fragment was measured over 180o in x, y and z-configurations (Joannes-Boyau and Grün, 2011; Joannes-Boyau, 2013). Isotropic and baseline corrections were applied uniformly across the measured spectra. The amount of NOCOR’s in the natural signal was estimated using the protocol of Joannes-Boyau (2013). The ESR dose response curves were obtained by using mean ESR intensities and associated standard deviations from the repeated measurements.

Fitting procedures were carried out with MCDOSE 2.0 software using a Markov Chain Monte Carlo (MCMC) approach based on the Metropolis-Hastings algorithm. The program uses a Bayesian framework, where the solution is presented as a full probability distribution of the equivalent dose (Metropolis et al., 1953). DE values were obtained by fitting a Single Saturating Exponential (SSE) at the appropriate maximum irradiation dose (Dmax) following Duval and Grün (2016) (using 1767 Dmax = 1264 Gy, 1788 Dmax = 2465 Gy, 1810 Dmax = 2735 Gy and 1841 Dmax = 3526 Gy).

Dating protocols: U series analysis The U and Th concentrations in each of the enamel fragments and surrounding dentine were measured by laser ablation, using an ESI NW193 ArF Excimer laser coupled to a MC-ICPMS Neptune Plus at the UoW. Sections of enamel and dentine were mapped using small rasters to document compositional variability in the teeth and constrain diffusion processes (Figure 9a).

Photographs illustrating the sampling approaches taken by SCU-UoW and GU-ANU in obtaining the U-Th results presented in Tables 4 and 5.

(a) Comparison of sampling grids across the enamel-dentine boundary measured by SCU-UoW (red lines) vs. GU-ANU (blue circles). SCU-UoW (red lines) measured a series of parallel, shallow (<5 μm) pits along grid lines across the teeth and averaged U concentrations across each grid. GU-ANU (blue circles) measured the average composition of the tooth in single spots that were laser-bored along profiles across the teeth, and report results for each spot. (b, c) Locations of LA-ICP-MS spot analyses for teeth samples 1788 (b) and 1810 (c) conducted by GU-ANU. The detailed transects are shown in panels (d) to (h).

https://doi.org/10.7554/eLife.24231.020

A total of 86 separate U-series analytical runs were performed across the dentine and enamel surface for the three H. naledi teeth. Each individual run consists of an average value obtained across a raster or ablation track measuring 200 μm x 700 μm in size; that is, a succession of short measurements was taken along a raster and then averaged into one value. Measurements were performed at an ablation rate of 20 Hz and a translation speed of 50 μm/s.

The rasters were positioned in a series of transects following the growth axis of the dental tissue in locations immediately adjacent to the area from which the ESR fragment was taken, and on the ESR fragments themselves (Figure 9a). To evaluate the ESR internal dosimetry of each tooth, three zones were analysed: (i) one along the enamel growth axis; (ii) one perpendicular to the Dentine Enamel Junction (DEJ), and; (iii) one on the dentine (Figure 9a). Additional measurements were taken across each tooth in areas away from the ESR fragment to assess U variability and diffusion gradients. The U-series age estimates (Table 4) are based on the average U-series isotope values for each ablation run. No age calculations were done for areas of the tooth where the U concentrations were below 0.5 ppm or where the U/Th ratio was below 250 (marked in red in Table 4). Ages were calculated with Isoplot 3.75 (Ludwig, 2012), and uncertainties are reported as 2 σ.

Baseline and drift were corrected using analysis of the NIST 612 glass standard, while two coral standards (the MIS7 Faviid and MIS5 Porites corals from the Southern Cook Islands; Woodroffe et al., 1991) were used to correct 234U/238U and 230U/238U ratios and assess the accuracy of measurements. Each coral standard was analysed by solution MC-ICPMS at UoW and used for reference. To account for potential matrix effects, a bovid tooth fragment from South Africa with known isotope concentrations (U-series at equilibrium) was used to verify measurements. To account for tailing effects, measurements were carried out at half-masses of 229.5 and 230.5 for 230Th and 233.5 and 234.5 for 234U.

Methodologies for combined U-series and ESR dating: CENIEH, Griffith University and Australian National University

Sample preparation One enamel fragment was extracted from each of the two H. naledi teeth 1788 and 1810, and analyzed.

Dating protocols: ESR dose evaluation The two enamel fragments (samples 1788 and 1810) were measured by ESR following the analytical procedure developed by Grün et al. (2008b). Dose evaluations were carried out at the CENIEH using a sub-exponential dose step distribution (Grün and Rhodes, 1992) for the following gamma doses (6.705 Gy/min): 0, 13.4, 40.2, 93.9, 201.2, 415.7, 844.8, 1649, 3058, 5471, 8690, 12713, 17943, 25989, 34861 and 61412 Gy.

ESR measurements were performed at room temperature with a EMXmicro 6/1 Bruker ESR spectrometer coupled to a standard rectangular ER 4102 ST cavity, with the following acquisition parameters: 1–10 scans, 2 mW microwave power, 1024 points resolution, 15 mT sweep width, 100 kHz modulation frequency, 0.1 mT modulation amplitude, 20 ms conversion time and 5 ms time constant. To ensure reproducible measurements, each fragment was mounted in a para-film mould within a Teflon holder in a Z-configuration only (Grün et al., 2008b), which can be inserted into a Bruker ER 218PG1 programmable goniometer. Because the ESR signals in fragments show very strong angular dependences, the ESR spectra of each dose step were recorded every 10° over 360°. ESR intensities were extracted from T1-B2 peak-to-peak amplitudes of the ESR signal of enamel (after Grün, 2000a).

Fitting procedures were carried out with Microcal OriginPro 9.1. software using a Levenberg-Marquardt algorithm by chi-square minimisation. Data were weighted by the inverse of the squared ESR intensity (1/I2) (Grün and Brumby, 1994a). The dose response curves (DRC’s) were obtained by averaging the T1-B2 ESR intensities recorded for all the angles at a given irradiation dose. The final DE values were obtained by fitting a Single Saturating Exponential (SSE) through the ESR intensities and by selecting the appropriate maximum irradiation dose (Dmax) in order to avoid dose overestimation (Duval and Grün, 2016; Table 10).

Dating protocols: U series analysis Laser ablation U-series analyses were carried out at the Australian National University (ANU), using a custom-built laser sampling system interfaced between an ArF Excimer laser and a Finnigan Neptune MC-ICP-MS (Eggins et al., 2003, 2005), following principles and procedures described in Grün et al. (2014). To account for tailing of 238U into the ion counters for 234U and 230Th, measurements were carried out at half-masses of 229.5 and 230.5 for 230Th and 233.5 and 234.5 for 234U. The tailing corrections were 7 cts/V(238U) and 17 cts/V(238U) for 230Th and 234U, respectively.

U-series data were obtained from distinctive spot analyses on polished surfaces. Firstly, all spot locations were cleaned with the laser set to 263 μm for 10 s, followed by the analytical run with the laser set to 203 μm for 60 s. The rim from the cleaning run is clearly visible in Figure 9. The enamel of sample 1788 (Figure 9b) was analysed along two transects at an oblique angle to the surface to increase the number of analyses across the enamel layer. The dentine was analysed on a piece that separated just below the two enamel tracks. The results from the enamel spots in transect A for sample 1788 are biased towards the domain close to the dentine. It was further noted that the last two analyses contained some dentine material, and these analyses were, therefore, neglected (Figure 9d). Sample 1810 was analysed along two tracks perpendicular to the enamel surface (Figure 9c). For sample 1810, analyses of enamel spots only show higher U concentrations in transect B (Figure 9h) where the spots occur close to the dentine boundary, while in transect A (Figure 9g) all enamel spots have uniformly low U concentrations. The average enamel concentrations were derived from the averages of the two transects.

The analytical data of the enamel and dentine sections (Table 5) were combined to provide the data input for the ESR age calculations. Because the enamel layer analyzed by ESR was not cleaned on both sides, an average external alpha dose rate component of 8 ± 2 μGy a−1 was used based on the alpha attenuation values of Grün (1987).

Apparent U-Th ages were calculated with Isoplot 3.75 (Ludwig, 2012), and uncertainties are reported as 2σ. No age calculations were done for areas of the tooth where the U concentrations were below 0.5 ppm or where the U/Th ratio was below 250 (marked in red in Table 5). Ages were calculated assuming closed system behaviour (CS), and compared with age results assuming continuous diffusion models (after Sambridge et al., 2012).

Determining the environmental dose rate

Apart from radiation derived from U and Th contained within the dental tissue of the teeth, age calculations must take the environmental dose rate into account. The environmental dose rate mainly results from gamma and beta radiation derived from the immediate surroundings of the teeth with an additional component from cosmic radiation, which in a deep cave environment is usually very small. In calculating the ages we have used a cosmic dose rate of 15 ± 1 μGy a−1 for all samples assuming that the fossils were overlain by a 20 m thick roof of dolomite with a density of 2.80 ± 0.05 g/cm3 (Barbouti and Rastin, 1983).

Gamma and beta radiation from the immediate surroundings of the teeth comes from U, Th and K in the sediments in which the teeth are embedded, and is partly attenuated by the water content of the sediments. Thus, the U, Th, K and water content of the sediments needs to be measured (Table 6). The measured water content in sediment surrounding sample 1841 is 27.7%. This value is expected to vary over time, but not by much given that the Dinaledi Chamber occurs deep inside the cave, close to the water table, where sediments are expected to have always been close to water saturated. Therefore, in calculating the ages we have assumed the water content to be 25 ± 10%. Uranium, Th, K concentrations were measured by ICP-MS at SCU and at the UoW using both leaching (in a 1:3 mixture of nitric and hydrochloric acid) and total dissolution (in a 1:3 mixture of nitric and hydrochloric acid with additional HF using an Agilent 7700 solution and a Thermo Icap) methods. Leaching results gave lower U concentrations reflecting incomplete dissolution of all U-bearing phases. Only the total dissolution results (Table 6) have been used to calculate the environmental dose rate.

If the teeth were not fully covered by sediment up to a depth of about 30 cm (which is the average attenuation length of gamma-rays in material with a density of ~2.5 g/cm3) an estimate has to be made for the burial history of the teeth as well as the more general background radiation in the cave. The environmental dose rate in the Dinaledi Chamber was measured in situ with a portable gamma ray spectrometer on the surface of Unit 3, next to the places where samples 1767, 1788 and 1810 were collected. We measured dose rates for Th and K, that were equal to or somewhat higher than those derived from the chemical analysis of the sediments, which suggests that the background gamma radiation in the cave may be a little higher than in the sediments. However, the in situ gamma measurements varied considerably from one place to the next, whereas the measured concentrations of U, Th and K in sub-units 3a and 3b are consistent (Table 6). Samples 1767, 1788 and 1810 were collected from near surface where they may have resided for a long time, and, therefore, may have received between 25% and 50% of their gamma dose rate from the wider cave environment. However, the resulting gamma dose rates for this scenario are not significantly different from a situation in which the teeth are fully buried when considering the spectrometer readings. Given the uncertainties with the in situ gamma ray spectrometer measurements (see below), we are confident that the analytical data of the sediment provide more robust constraints for calculating the environmental dose rates. Therefore, the teeth have been modelled as if fully encased in sediment assuming infinite matrix dose rates for sediment and using the measured values of U, Th and K listed in Table 6.

Gamma dose rate reconstructions derived from analytical data of sediment samples collected around ESR samples 1767, 1788 and 1810 (closed circles and diamonds), combined with samples from a vertical profile in the excavation pit and sondage (open circles and diamonds).

The data show little variation in dose rate with depth (see text for explanation).

https://doi.org/10.7554/eLife.24231.021

The gamma dose rates calculated for sediment collected from the immediate vicinity of the sampled teeth (Figure 10) were compared with gamma dose rates calculated from U, Th and K concentrations for sediment samples collected at regular intervals along a 53 cm deep, vertical profile in the sondage at the center of the excavation pit (Figure 10). For this profile samples 1 to 4 were collected from a 13 cm thick layer of hominin-bearing sediment belonging to sub-unit 3b, and samples 5–8 were collected from underlying sediments belonging to sub-unit 3a, to a total depth of 53 cm. The variation in the gamma dose rate shows no clear trend with depth (Figure 10), and the samples along the vertical profile were used to obtain an average gamma dose rate. Sample 2 from the top 3 cm of Unit 3 was excluded because of anomalously high Th concentrations (this sample also contains many small bone fragments).

An additional problem in estimating the gamma radiation for the sediments may arise if 222Rn loss occurs as a result of degassing. This is of importance, because virtually all (98%) of the gamma radiation generated in the 238U decay chain is produced by 222Rn and its daughters (e.g., Guérin et al., 2011). If 222Rn loss is detected, then corrections have to be made. In situ gamma ray spectrometer measurements yielded K and Th values broadly in agreement with analysed concentrations, but did not detect U. Since U is determined via the (gamma) emission in the decay of 214Bi, which is a post-222Rn nuclide in the 238U decay chain, we conclude that the absence of this signal is due to 222Rn loss (Aitken, 1985). The 222Rn loss was confirmed by analyzing a sediment sample that was collected next to sample 1841, for which high resolution, Ge-gamma spectrometry showed ~80% Rn loss.

It is difficult to estimate whether Rn degassing occurred during the entire burial history of the teeth. Therefore, age calculations were performed for two different scenarios: (i) a situation where it is assumed that the present day situation of 80% Rn loss persisted during the entire burial history, and (ii) a situation in which no Rn loss occurred (Table 7). Assuming water content of 25 ± 10%, the average gamma dose rate for the sediments has been calculated at 724 ± 116 μGy.a−1 assuming no radon loss, and 534 ± 69 μGy.a−1 assuming 80% Rn loss (Figure 10).

Combined US-ESR age calculations

All age calculations are provided with 2σ uncertainties, and were carried out using the US-ESR program of Shao et al. (2014), which utilizes the dose rate conversion factors of Guérin et al. (2011). In doing the calculations, the input parameters and criteria listed in Table 6 were used, and age results are given in Table 7. In all calculations we have made the following assumptions: (i) post-230Th daughter elements are in equilibrium in dental tissues, which is the standard assumption in ESR dating; and (ii) complete (effective) burial of the samples occurred (i.e., infinite matrix assumption for the gamma dose rate measured in sediment).

Results have been calculated for the two scenarios (Table 7): (1) 80% Rn loss in the sediment; and (2) post-Rn equilibrium in dental tissue and sediment (i.e., no radon degassing). In both scenarios the water content has been taken as 25 ± 10%. Scenario 1 is based on measured, current-day values and probably provides a maximum age estimate, because it is unlikely that the high degree of Rn loss observed today would have occurred throughout the history of the cave. Scenario 2 will provide a minimum age estimate, because Rn loss has been observed. These two scenarios provide the most reasonable range for the age of the fossil teeth.

Additional modelling was carried out to assess the effects of early U uptake on the ESR age, in a closed system setting (CSUS-ESR, Grün, 2000b). This showed that the differences in US-ESR and CSUS-ESR model ages are less than 4%, thats is, which is well within the uncertainty ranges of the listed US-ESR ages (Table 7). Therefore, CSUS-ESR ages are not further considered.

ESR dose evaluation: inter-laboratory comparison

Each laboratory (SCU and CENIEH) independently measured the DE values following the methods outlined above. To ensure reliable DE values, the maximum irradiation dose (Dmax) was selected in accordance with the recommendations made by Duval and Grün (2016), in order to avoid DE overestimation (i.e., for DE values between 100–500 Gy, the Dmax/DE ratio has to be kept between 5–10; for De values between 1000–2000 Gy the Dmax/DE ratio has to be kept between 1–2; Table 10). Normalised dose response curves (DRC’s) are shown in Figure 11.

Table 10

ESR fitting results obtained by SCU and CENIEH-GU. Both laboratories employed a Single Saturating Exponential (SSE) fitting function. Dmax was selected in accordance with Duval and Grün (2016) to avoid DE overestimation. SCU results in brackets show DE values that were obtained by SCU using the CENIEH-GU procedure (see text for details).

https://doi.org/10.7554/eLife.24231.022
SCUCenieh-gu
SampleDE (Gy)Dmax (Gy)Dmax/DEDE (Gy)Dmax (Gy)Dmax/DE
1767194 ± 4 (193 ± 6)12647
1788232 ± 8 (232 ± 22)12045159 ± 11164910
1810296 ± 14 (281 ± 34)27359232 ± 2916497
18411676 ± 127 (1648 ± 500)35262

Samples 1767, 1788 and 1810 have DE values that vary within a narrow range between 200 and 300 Gy, while the DE value of sample 1841 is significantly higher (>1500 Gy). For the two samples that were measured by both laboratories, the SCU procedure systematically provides higher DE results. These differences partly result from different fitting procedures: when plotting the SCU experimental data points using the CENIEH-GU fitting procedure, the calculated DE values shift by < 2% for samples 1767, 1788 and 1841, and −6% for sample 1810 (Table 10). Both laboratories also used different irradiation sources (gamma-rays at CENIEH, and X-rays at SCU), which may have had some influence on results. A third factor that may have most fundamentally influenced the difference in measured DE values is the radiation sensitivity observed for each fragment (Figure 11); for sample 1810, the DRC’s from CENIEH and SCU are similar, but for sample 1788 they are different, indicating that the response of the two fragments from sample 1788 to the radiation source was distinctly different. Each laboratory had sampled its own fragment from different domains of the tooth, with different radical concentrations and crystallinity, and the U-concentrations in the fragment used by SCU were somewhat higher than those used by GU-CENIEH (Tables 4 and 5). However, in spite of these differences, the ages agree within error (Table 7).

ESR dose response curves (DRC’s) obtained for the samples 1767, 1788, 1810 and 1841.

To facilitate comparison, all DRC’s have been normalised to the intensity of the natural point (=1).

https://doi.org/10.7554/eLife.24231.023

The use of enamel fragments in measuring the dose allows us to differentiate between the relative contributions of non-oriented CO2- radicals (NOCOR’s) versus anisotropic radicals (AICOR’s) (e.g., Grün et al., 2008b). Joannes-Boyau and Grün (2011) recently showed that gamma irradiation in the laboratory may produce additional unstable NOCOR’s when compared to gamma irradiation in a natural environment, which could lead to an overestimation of the measured dose if this contribution is not removed. To evaluate this possible bias, we followed Method 3 described in Joannes-Boyau (2013) for the extraction of the NOCOR’s from the main radiation-induced ESR signal (Figure 12). When a fragment is rotated over 360°, the ESR intensity varies. The ratio of the maximum (Imax) and minimum (Imin) intensities (Imax/Imin) is used as a proxy to quantify the increased anisotropy potentially induced by either gamma or X-ray irradiations. The evolution of this ratio with the irradiation dose is shown in Figure 12. When comparing the results from the two laboratories it is clear that both obtain similar results. For measurements conducted at CENIEH the Imax/Imin ratios for samples 1788 and 1810 remain near-constant (between 1.22–1.24) as the gamma dose varies. For measurements conducted at SCU the Imax/Imin ratios remain near-constant as well (and vary within uncertainty, between 1.6–2.0 for samples 1767, 1788 and 1810, and remain around 1.34 for sample 1841; Figure 12) as the X-ray dose varies. The differences in the Imax/Imin ratios for each tooth calculated by the two laboratories results from the orientation chosen, the spatial variations of the ESR signal within the enamel layer, and the different crystal orientation and fragment position during ESR measurements. The fact that the results from both laboratories show constant ratios indicates that no additional NOCOR’s have been created by both gamma and X-ray irradiations. Consequently, no corrections had to be applied to the measured DE values.

Evolution of the Imax/Imin ratio vs the irradiation dose for the four tooth samples.

(see text for explanation).

https://doi.org/10.7554/eLife.24231.024

OSL dating

Background to OSL dating

Optically stimulated luminescence (OSL) dating is a widely used method for estimating the last time that sediments were exposed to sunlight within the past 300–500 ka (e.g., Aitken, 1985; Murray and Wintle, 2000). Sand-sized grains of quartz and K-feldspar (two commonly occurring minerals) are preferred for OSL dating. These grains may be measured collectively in a single composite sample (an aliquot), which provides an average signal, or as individual grains, which provides greater insights into the depositional history of the sediments.

OSL dating is a radiation dosimetric dating technique based on the time-dependent accumulation of radiation damage in minerals (Adamiec and Aitken, 1998; Murray and Wintle, 2000), as a result of exposure to low levels of ionising radiation in the environment. The intensity of radiation damage reflects the total amount of energy (the ‘equivalent dose’) absorbed from background radiation by the mineral over time. The radiation damage can be removed from the mineral by exposure to heat or light, which is accompanied by the release of a small amount of light or luminescence. OSL dating estimates the age when sediment was last exposed to light (‘bleached’) during erosion, transport and deposition of the mineral grains. Once sediments are buried and no longer exposed to sunlight, the luminescence signal can start to build up again (Duller, 2007).

The latent luminescence signal that has built up in a sediment sample can be released and recorded in the laboratory using light (the OSL technique). This luminescence signal is related to the environmental radiation dose the mineral has received since the last exposure to sunlight. If the environmental dose rate is determined together with the equivalent dose contained in the sample, it is possible to determine an age for the sediment, or rather a depositional age which measures the last time the sediment was exposed to sunlight or heat.

Methodology for OSL dating: University of the Witwatersrand (Wits)

Sample preparation For samples OSL3, 4 and 5, sediment was removed from the sample tubes under controlled, safe-light laboratory conditions. Material located within 2 cm of the ends of the tubes was removed to isolate any quartz grains potentially exposed to light during sampling. This material was used to measure water content, and to determine the dosimetry of the sample. The remaining sediment was treated with 33% hydrochloric acid and 20% hydrogen peroxide to remove carbonate and organic components. Quartz grains were isolated from denser minerals and feldspars by using solutions of sodium poly-tungstate with specific gravities of 2.70 g/cm3 and 2.62 g/cm3, respectively. After rinsing, drying and sieving, the fine sand (180–212 µm) fraction was etched for 40 min in 40% hydrofluoric acid to remove the outer layer (~10–15 µm-wide) affected by alpha radiation and any remaining feldspars. Subsequently, 33% hydrochloric acid was added to remove acid soluble fluorides. Each sample was dried and re-sieved in preparation for equivalent dose determination.

Determining the Equivalent Dose (De) OSL measurements were carried out on the 180–212 μm grain-size fraction. A monolayer of grains was prepared on steel discs in aliquot sizes of ~30 grains. Luminescence measurements were performed on an automated Risø TL/OSL -DA-20 reader. De values were obtained through calibrating the ‘natural’ optical signal acquired during burial, against ‘regenerated’ optical signals obtained by administering known amounts of laboratory dose. De estimates were obtained using the Single-Aliquot Regenerative-dose (SAR) protocol of Murray and Wintle (2000). An appropriate preheat temperature was determined using a ‘preheat-dose recovery test’. A test dose of 27 Gy was used to monitor sensitivity change. Up to five different regenerative doses were given to define the linear portion of the dose response from which De was determined. The OSL signals were stimulated at 125°C for 40 s with blue LED at 90% power and a final OSL measurement was used to clear out any signal that may be found in thermally unstable traps. The De was evaluated using an exponential and linear fit to a single regenerative dose point. Errors on De assume poisson statistics, with an additional 1% uncertainty added to each OSL measurement (Galbraith, 2002; Duller, 2007).

To obtain a luminescence age, a burial dose (Db) is calculated from the aliquot measurements, in which individual values for De are combined to obtain a single value for Db. Given the often complex distribution of De values, Db is calculated using complex statistical models including the central age model (CAM), and the minimum age model (MAM) (Galbraith et al., 2005).

Measured De values for quartz grains show a degree of variability that depends in part on the crystal lattice structure of the grains and their burial history (e.g., complete vs incomplete bleaching). For well-bleached quartz where aliquots have been heated prior to irradiation the statistical variability, expressed as the standard deviation, in measured De values will be less than 20% (Olley et al., 2004; Galbraith et al., 2005). This variability in the distribution is referred to as overdispersion (Galbraith et al., 1999). An overdispersion value of 20% is used to guide the use of appropriate statistical models to calculate a burial age: MAM is used to determine the burial age when overdispersion exceeds 20%; CAM is used when overdispersion is below 20%. However, this is only a rough guide and environmental conditions need to be considered in deciding the statistical model to be used. The CAM and MAM ages were calculated with software provided by Geoff Duller (University of Aberystwyth, UK).

The Central Age Model (CAM) computes an age value much like a weighted average, but it assumes a natural distribution of De values rather than a single value from which to calculate the age. A CAM is used when it is assumed that samples experienced homogenous bleaching. The Minimum Age Model (MAM) is used if incomplete bleaching is expected to be the reason for an observed skewed dose distribution, or if (as in this case) the sample contains mineral grains that have never been at surface (Galbraith et al., 1999). The MAM uses a truncated normal distribution and fits it to the individual De data points to determine the proportion of grains that were fully bleached before they were deposited (Galbraith and Laslett, 1993).

Environmental dose rate determinations The concentrations of U, Th and K in the sediment samples of Unit 1 (sub-units 1a and 1b) were determined at the University of Johannesburg by isotope dilution on aqua regia leaching techniques. A mixed 236U-229Th spike (allowing measurement of (U, Th) disequilibrium) was added before leaching. U and Th were separated from major elements using ion exchange columns with Dowex 1 × 8 anion exchange resin; samples were loaded with 2 ml of 80% ethanol + 20% 5M HNO3, washed with 3 ml of the same solution and eluted with 0.5N HCl. Uranium and Th were analysed together on a Nu Instruments Plasma II multi collector ICP mass spectrometer, using an APEX-Q desolvating nebulizer. Strong excesses of 234U and 230Th (234U/238U activity ratios of 2.2–4.5, 230Th/238U activity ratios of 3.1–4.1) necessitated significant upward corrections to the dose rate for U, yielding age-dependent ‘effective U concentrations’ to be used for the dose rate calculations.

Dose rate calculations (after Aitken, 1985) incorporated beta-attenuation factors (Mejdahl, 1979), dose rate conversion factors (Adamiec and Aitken, 1998) and an absorption coefficient using the present water content (Zimmerman, 1971) with a 5% relative uncertainty to reflect potential temporal variations in past moisture content. The water content may affect the validity of the ages as it is possible that a different, possibly wetter, climate regime may have prevailed. This is suggested by the disequilibrium in the U-series measurements. The cosmic dose rate was determined as a function of altitude, latitude, longitude and depth, according to Prescott and Hutton (1994) equations, plus the soft component from Madsen et al. (2005).

Luminescence age determinations The luminescence age was obtained by dividing the palaeo-dose with the total dose rate. The error on the luminescence age estimates represents the combined systematic and experimental error associated with both the De and dose rate values. There is no datum for luminescence dates, therefore the age reported is taken from date of sampling (i.e., AD 2015).

Palaeomagnetic dating

Methodology for palaeomagnetic dating: La Trobe University (LTU)

The procedures for palaeomagnetic analysis of the speleothem sample from Rising Star Cave follow those outlined in Herries and Shaw (2011) and a comprehensive review of speleothem magnetism can be found in Lascu and Feinberg (2011).

Sample preparation The sample was drilled vertically, across the layering, using a non-magnetic rock drill to produce three 2.5 cm by ~5–6 cm cores from the upper, purer part of the flowstone. Care was taken to remove recent contamination. The surface of the flowstone has a calcified covering of fine clastic dust that is likely to be much younger. Therefore, the upper ends of the cores were removed to make sure that only primary flowstone was measured. The cores were then cut in half at their midpoint where more recent contamination has seemingly occurred within the sample (at the interface between different growth phases; Figure 13). This was done using an ASC Scientific non-magnetic saw with bronze saw blades to produce a total of six 2.5 by 2.5 cm subsample cores from the upper part of the flowstone; 3 from the uppermost 2.5 cm (phase C flowstone) and 3 from the lower 2.5 cm (phase B flowstone). Thinner samples could not be produced as the samples were weak. Only a small part of the lowest, clastic rich layer (phase A flowstone) was preserved on the base of the block sample (Figure 13a) and this layer was cut into two 2 × 2 cm cubes for analysis.

Samples and results of palaeomagnetic analyses forFlowstone 1a.

(a) Outcrop photo of hanging erosion remnant of Flowstone 1a from which the palaeomagnetic sample was taken. The three flowstone phases separated by detrital horizons are clearly visible, and their magnetic polarity has been marked (N = normal; R = reverse). The stratigraphic top is towards the top of the photo; (b) close-up of a hand sample taken for palaeomagnetic analysis from Flowstone 1a in the Dinaledi Chamber. The sample is layered and comprises three distinct phases (from base to top: A-C marked in yellow) separated by thin clastic horizons that mark disconformities indicated with red dashed lines. The larger-scale extent of the three phases can be seen in (a); (c) intensity spectra, Zijderveld plots, and stereo plots for samples from phases A to C taken from (b). Phases B and C show normal polarity and phase A shows reversed and intermediate polarity directions.

https://doi.org/10.7554/eLife.24231.025

Palaeomagnetic field determinations Because the samples all consist of flowstone speleothem, alternating field (AF) demagnetisation was the sole method of magnetic cleaning that was used on the samples. AF has been shown to be effective for recovering the primary palaeomagnetic signal formed within South African speleothems for both detrital inclusions deposited during phases of flooding or within the water forming the speleothem itself (detrital remanent magnetisation; DRM), and for chemical precipitation (Chemical Remanent Magnetisation; CRM) of iron phases within dripwater (Herries and Shaw, 2011; Pickering et al., 2013). Samples were demagnetised using an AGICO LDA5 AF demagnetiser and measured using an AGICO JR6 spinner magnetometer on the high speed setting. Samples were analysed using the program Plotcore to establish the primary remanence direction using principle component analysis of Zijderveld plots. Multiple samples were taken from each layer within the flowstone speleothem and analysed using Fisher statistics and the Program FISH2 to establish the Palaeolatitude (Plat.) for each layer. This was then used to assign the polarity of each layer, with Plat. Values > + 60o/−60o are considered to represent normal or reversed polarity.

Radiocarbon dating

Methodology for radiocarbon dating

Radiocarbon dating is a commonly used method for dating materials that contain carbon, by using the decay of the radioactive carbon isotope 14C with a half-life of ~5730 years. Because of the relatively short half-life of 14C, this technique generally only returns reliable results for ages less than 50 ka, and it is widely used in Archaeological applications (e.g., Taylor and Bar-Yosef, 2014).

Sample preparation Two bone fragments collected along the floor of the Dinaledi Chamber near the top of sub-unit 3b were sent to Beta Analytic Inc. in Miami, Florida. Here, the outer surfaces of the bone fragments were acid etched with 10% HCl (at room temperature) after which samples were rinsed to a neutral pH and dried. Samples were then ground to a powder and pre-treated with 1N acetic acid for 24 hr, rinsed, dried and weighed.

The pre-treated bone powder was acidified in 85% phosphoric acid at 70°C in a closed chemistry line that had been purged of any CO2 (to <10−15 atoms). CO2 produced from the sample was introduced into a reaction vessel containing an aliquot of cobalt metal catalyst. Hydrogen was introduced and the cocktail heated to 500°C, to crack CO2 and form carbon (graphite). The graphite was pressed into a pellet for analysis.

Analyses and data processing Analyses for radiocarbon dating were performed using accelerator mass spectrometry (AMS). Analyses were calibrated with graphite produced from the NIST-4990C modern reference standard. Reported δ13C was measured relative to the PDB-1 on the sample itself. Total fractionation using the AMS δ13C correction was done to derive at a ‘conventional radiocarbon age:’ Ages are calculated using BetaCal 3.17 provided by Beta Analytic following procedures outlined in Bronk Ramsey (2009) and using the SHCAL13 database (Hogg et al., 2013). Dates are reported as radiocarbon years before present (‘BP’ with ‘present’ taken as AD 1950).

Chronostratigraphic summary of radio-isotopic dating results, and interpretation of the depositional ranges of stratigraphic units, flowstones and H.

naledi fossils in the Dinaledi Chamber. Following the preferred US-ESR maximum age model and associated uncertainties for ESR samples 1788 and 1810, a maximum depositional age of 335 Ma was determined, while the minimum depositional age of 236 ka was constrained by Flowstone 1c (sample RS18), which covers H. naledi material in the entry zone.

https://doi.org/10.7554/eLife.24231.026

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Decision letter

  1. George H Perry
    Reviewing Editor; Pennsylvania State University, United States

In the interests of transparency, eLife includes the editorial decision letter and accompanying author responses. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.

Thank you for submitting your article "The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa" for consideration by eLife. Your article has been reviewed by five peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Ian Baldwin as the Senior Editor. One of the five reviewers, Chris Stringer, has agreed to share his name. The other reviewers remain anonymous.

The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you prepare a revised submission.

This paper provides the first dating results for the recently discovered and described Homo naledi taxon. As such, the potential importance of the results for our understanding of hominin evolution is very high. The reviewers were in agreement that the paper’s base is strong, with separate, generally consistent results obtained by the two excellent labs. There were, however, a large number of comments raised (on which the reviewers were not in disagreement) that need to be addressed before the manuscript can be considered for acceptance by eLife. These concerns are considered substantial but addressable. Please note that given the number of issues that need to be addressed and the technical nature of the paper, we will ask reviewers to evaluate the revised manuscript (as quickly as possible) prior to considering it for acceptance.

As the Reviewing Editor, I am choosing to take the unusual step (for eLife) of providing the full reviews as part of the decision letters for the co-submitted papers for two reasons. First is the interconnectedness among the multiple papers, which is reflected in the reviews (as some reviewers participated in the review of multiple papers). Seeing the more direct reader reactions to each paper in the context of others should be helpful (and should be taken into account) as you consider the larger revision process for the entire group of papers. Second, included within the reviews are many detailed comments that are too numerous to repeat as part of the decision letters, but that also should be addressed. Note that one reviewer provided their specific comments in an attached document.

An overview summary of the most critical issues that must be fully addressed (as above, this is only a small list of critical issues raised by reviewers) prior to further consideration:

1) Critical points concerning the relationships among the various stratigraphic units were raised by Reviewer 4 (in particular, see major comments 1 and 3 from that review) that must be addressed thoroughly in any revision. During the consultation process, other reviewers highlighted the importance of these points given the interdependence of most of the age/depositional models on those interpretations.

2) The overall synthesis/analysis of the various dating results is too limited at present, and choices on what results are highlighted at various points in the manuscript seem arbitrary at times. A more concerted and comprehensive effort to assimilate the different datasets in an evenly considered, summary results section (with a synthesis view agreed to by both dating labs) would help to address this concern. This issue also filters up to the abstract.

3) The manuscript currently reads as if various sections were composed by different authors with insufficient consistency in style and level of detail. Likewise, the tables need to be reworked with more care for consistency and interpretability.

4) The reviewers also felt that the discussion should also be expanded, and can be even without overtly duplicating the broader synthesis provided in the other papers.

5) Similarly detailed treatment for reporting the radiocarbon methods and results, as the other dating methods, should be provided.

6) The reviewers also had suggestions for the order of presentation that may help the reader more readily interpret the results.

Reviewer #1:

I will state up front that the dating methods used in this paper are not within my field of expertise. I was asked to review this paper as one component of the entire suite of submitted papers. Thus, I will leave the methodological critiques to those more qualified than me and comment more on the implications of the dates. The authors suggest that deposition of the hominin material was over a time period of about 100k between 200-300 ka. It does seem like the resolution and precision of the dates are not great and makes it difficult to properly interpret the context of the hominins. When the duration of deposition is considered, it then seems unusual that there would be so few hominins in the cave system, particularly if it is being used as a burial site (even if only for special individuals). Given the complexity of cave systems and their formation, I don't know that the authors have convincingly demonstrated that the chamber was completely inaccessible during the times of hominin deposition (especially with the wide range of dates and low resolution). That said, I sympathize with the inherent difficulties of dating fossils from cave systems and appreciate that the authors used multiple methods to try to pin down the dates and that this may be the best that can be done at this point.

Reviewer #2:

Although I have reservations about the way radiocarbon dating was attempted, as explained further below, and there is a need for more caution in some areas, the paper should be suitable for publication after revisions. I have marked up a text copy of the manuscript, which I attach, and summarise some of the points below.

The references for all four papers need work for consistency of formatting, journal abbreviations, accents etc.

"The results for RS18 (~242 ka) may provide a/provide a potential minimum age for the H. naledi fossils in this part of the cave." Insert some caution because some other age estimates are still younger than this figure.

"Dates acquired via U-Th and ESR techniques were obtained using a double blind approach for each technique to ensure robust, reproducible results, with each laboratory using their own analytical and computational approach. Methodologies and approaches taken by each laboratory that has contributed to this paper are described in detail in the methodology section." Why wasn't radiocarbon dating pursued in the same manner, using established research labs rather than a commercial lab? Why no details of the procedures: e.g., was ultrafiltration attempted?

"Some of the ESR ages (Tables 4, 5) independently suggest that some of the fossils around the excavation pit may be younger than 237 ka, but confirm a probable age of >200 ka for the fossils." Well a few of the ESR ages don’t confirm an age of 200 ka+ so this needs rewording.

Reviewer #2 Minor Comments:

Other suggested edits are added in an attached text version of the paper.

Reviewer #3:

This manuscript, "The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa" presents five different dating techniques applied to both the fossils and cave deposits found preserved in the Dinaledi Chamber of the Rising Star Cave and combines these methods to propose a depositional age for the Homo naledi fossils of between 200 and 300 ka. New stratigraphic data on the three sedimentary units and three flowstone units is provided, as well as details on the locations and descriptions of the dating samples. The geochronological data is provided in detail with a brief discussion on the depositional age (and inferred age) of the hominin fossils.

Overall this paper presents a large new geochronological data set for an exciting site home to a unique and huge collection of hominin fossils. Knowing the age of these fossils is critical in their interpretation and there has been much speculation as to their age. The authors certainly have thrown everything at dating the fossils and deposits, which given the nature of the fossil find is to be expected. However, there are many issues, the three major ones being:

1) there is no synthesis or analysis of the various geochronological data sets;

2) there is no discussion of how the new ages fit into the regional and global picture in terms of cave formation;

3) Exactly how the age of the fossils has been determined is not abundantly clear: this is certainly the most important message of the paper and needs to be clearly and carefully explained. The existing discussion on pages 20 and 21 is confusing and no clear story emerges.

The authors presume a huge prior knowledge of the region, caves and fossils, as well as the background and methods of the various dating techniques; I am not unfamiliar with the sites in this region and these dating techniques but struggled to follow a clear story with the manuscript. The confusing order of the sections, the disjointed writing styles from sections clearly contributed by separate co-authors, the lack of synthesis of the various dating techniques, the short and undeveloped discussion and the rather vague final age assignation all need serious work.

The Homo floresiensis (Hobbit) fossils found preserved in the limestone cave site of Liang Bua on the island of Flores in Indonesia are an example of how complex dating this type of site (fossils in a limestone/dolomite cave) and how long it takes to get good, robust data (see Morwood et al, 2004; Roberts et al., 2009 and Sutikna et al., 2016). There is scope for some comparison between this site and its multistranded chronology and the work presented here. Another example of using multiple strands of evidence to date cave deposits is the Marean et al (various years) work done at Pinnacle Points in South Africa. This is the kind of synthesis this paper is lacking.

So, as it stands this paper reads as a technical report of the different dating techniques, the type of document circulated between member of a large project to share information. Much work is needed to get this manuscript up to a standard ready for publication.

In detail:

1) There is no clear narrative. The paper reads like a technical report of the site, samples and results that would be circulated between co-authors – the data from the various methods is presented, often in excruciating detail (ESR) but there is no actual synthesis of the various data sets into a cohesive narrative.

2) The order of the paper is confusing and does not help in building a clear story – having the very detailed results section before the methods section does not make sense and makes reading the paper from beginning to end not easy. Some kind of discussion about what the different techniques used are all actually dating, which components of the cave system vs the fossils themselves etc would make a good introduction for the paper and segue into the more detailed methods section. Major rearrangement of the paper is needed, with a short clear methods section, then results.

3) Overall there are very few references to the literature – there is very little introduction to the Cradle and sites beyond repeated references to Dirks et al., 2015. The concept of the deposition of sediments in hominin caves being cyclic, with periods of erosion is by no means new and reference (and credit) needs to be given to Brain (1958, 1993, 1995) and Wilkinson (1983, 1985).

4) In the description of Unit 3, angular to sub-angular grains are classified as being reworked – on what basis? Such high angularity does not support reworking. Some micromorphology of these sediments (resin impregnated blocks then cut to make thin sections) would be very useful. How are the orange mudstones of Unit 1 and 3 differentiated from each other? It is also a little confusing and not entirely convincing to argue that Unit 2 is probably older than Unit 1 and was sourced from sediments that look like Unit 1 – there is very little actual evidence to back up this claim. A stratigraphic column summary diagram, plotted against age, would be useful.

5) The results section is very long and very detailed, all of the sections but especially the ESR/U-Th. The palaeomag results are the best presented and should be used as a model to redo the other sections. These different sections were clearly written by different people, as the long list of co-authors suggests, and need to be better synthesized together to produce a well-written document that flows well and is easier to read.

6) There is no discussion on the reproducibility of the various techniques – the authors are at pains to explain how the U-Th and ESR/U-Th analyses were both undertaken by two separate laboratories to produce blind duplications of the data, and yet there is no synthesis discussing this. Why was no blind duplicate done with the OSL samples?

7) There is no proper discussion. I realize there is a Berger et al submission alongside this manuscript which deals with the implications of the age proposed here, but there is still scope for a discussion of both the quality of the age data and what it all means in terms of the formation, development and filling of the Dinaledi Chamber, and of course the deposition and reworking of the hominin fossils. Given the long and illustrious list of co-authors this is surprising – among these people are world leaders in cave formation, dating and climate comparisons – suggesting that there has been little actual input from these authors in the discussion as it stands.

8) The big U-Th flowstone data set opens up the possibility for interesting comparisons with both local sites with U-Th dated flowstones (Gladysvale, Sterkfontein, Plovers Lake, Swartkrans); episodes of flowstone formation are strongly linked to climatic parameters (increased rainfall being the major one) and are expressed as similar aged flowstone deposits preserved in different caves. This comparison needs to be made here and would help build an argument as the when the deposition of the fossils took place.

9) There are also regional and more global records of known climate variability to which the data presented here can be compared, not just the U-Th flowstone data, but the OSL sediments data too. Seeing how the ages of flowstone and sediment deposition in the Dinaledi Chamber compare to other records is not only interesting but opens up the possibility to argue for glacial/interglacial deposition of the fossils and a more thorough picture of the changing landscapes outside the cave.

10) Following on from all these points about the lack of synthesis and discussion, as it stands the abstract is weak and once the paper is revised will need to be re-written into something more punchy. If some of the ages (OSL) are quoted directly in the abstract, then they all need to be. The abstract can also be a sentence of two longer and say something about the significance of these data – the reproducibility, the dating of difference aspects of the cave deposits and how these all fit together to produce a final age for the fossils.

Technique specific comments:

1) OSLa) The OSL section is weak. I understand a program was used to calculate the ages from the measured data but there is no discussion of these data relative to the literature as to which set of ages are more likely. OSL of cave sites is not easy, sites like Pinnacle Point in South Africa require significant method development, lead by Zenobia Jacobs, in order to date the sediments. It was certainly not as simple as crunching a single set of measurements through a program (written by someone else?). Some more detail as to why the Minimum Age model is most appropriate is needed.

b) Where does the maximum age for Unit 3 of ~400 ka come from? Is this a kind of midpoint age from the scatter (300-660 ka) of CAM ages? What evidence is there to suggest that this is the best approach?

c) To the best of my knowledge, this is the first use of OSL on Cradle cave sediments – this alone is worthy of a mention, as well as a caution that much work is still needed to thoroughly understand the OSL signal preserved in these grains.

d) Why was no blind test done for the OSL? Especially as these ages are heavily used to assign final ages to fossils.

e) Why do aliquots and not single grains? Especially in this complex cave setting where there has been much reworking.

f) Why not date the feldspar as well?

g) There is a very big difference between the two sets of ages calculated with no real discussion as to why this is.

2) U-Tha) Why were no thin sections made? For samples as important as these, every precaution to make sure the U-series system has not been disturbed should be taken. RS8 looks recrystalised?

b) Following on from this, some kind of pre-screening, laser ablation trace element profiles ideally, would have been very useful for imaging the location and concentration of U and Th.

c) There is no actual comparison between blind tests – why are JCU errors so much smaller?

d) Why are U ratios 234/238 and 230/232 ratios from JCU only reported in Table 1 as explained in caption – actual ratios are not shown in table. These data must be available from UoM and are available in Table 3. So what does this mean?

e) Methods and introduction section is very light, while Hellstrom and Pickering (2015) is a recent paper, this is a review paper and there needs some reference to original papers.

f) It is more accurate to say (page 17, line 533) that the later stage of flowstone formation was dated to 478,000 +107,000/-41,000 ka than give the full range of the error. That is not actually what the errors mean.

g) Why are the U-Th ages given as kyr before 1950 AD? They are not C-14 ages. This is not conventional with U-Th.

3) ESR/U-Tha) This section is heavy and hard going, even for a specialist reader. It needs to be shorter, clearer and have a better introduction – even just clearly explaining what ESR is measuring and what the advantage is to combining ESR with U-series.

b) The final ages are presented rather confusingly – again there needs to be some final synthesis: how old does the ESR suggest the fossils are?

Reviewer #3 Minor Comments:

1) The University of Melbourne is abbreviated (by itself) to UoM, not Melbourne University (MU).

2) A summary table of all the ages (not age data) will help pull everything together and allow for a comparison both between the blind duplicates of the same methods and between the different methods.

3) The text on a number of the figures (1, 3 and 10) is very small in places and will be tiny in the final typeset paper.

4) Figure 1 has the words 'Relative height (m), cave floor' twice.

5) It is useful to see all the field photos of the U-Th flowstone samples but these all need proper scale bars. So does panel C of Figure 3 and all of Figure 4.

6) Figure 8's caption is rather confusing, a little bit more introduction.

7) There appears to be some confusion over the caption for Figure 9: a total of three captions are given, two different ones for Figure 9 and the caption from Figure 10 as well.

Reviewer #4:

This paper may be the definition of "throwing the kitchen sink" at something. I appreciate the exhaustive analyses of all techniques at their disposal, although I do have a few concerns regarding their interpretations. I'm glad there are finally some dates out for the chamber now so that speculation is no longer needed. I don't have any major issues with the general ages proposed, but I'm also not an ESR expert, which ultimately is what the H. naledi ages are drawn from. The results seem reasonable, although I do have some questions/issues regarding the interpretations. Descriptive components are done rather well and I appreciate the very detailed materials and methods section (even if it is obvious that each section has a different "voice" to it). My more detailed commentary is noted below, but I do believe there are some more major issues that need to be addressed, even if most have to do with dates not associated with the hominin-bearing Unit 3.

1) They need to provide more sufficient evidence for the "time-transgressive" nature of Unit 1. All Unit 1 ages are younger than Unit 2. Proposing that Unit 2 (and 3) is composed of reworked Unit 1 is a sedimentological hypothesis (not a geochronological result) that needs to be tested.

I think they also need to be more clear on the reworking of Unit 1 forming Units 2 and 3 and reworking of Unit 2 forming Unit 3. Is this supposed to be happening within the Dinaledi Chamber? Outside of the chamber then being transported in via the debris cone?

2) In the original Dirks et al. (2015) paper, they note that their flowstone samples were unsuitable for dating, yet now they have all sorts of dates on the flowstones. What changed?

3) The reassignment of material from under Flowstones 1c-e from Unit 2 to Unit 3 is one of the most important components of this paper. Without it, the majority of their age/depositional models fall apart. This needs to be addressed much more thoroughly, perhaps with additional sedimentological analyses. Simply that it is less indurated is not sufficiently convincing.

Also need some sort of explanation as why the description of the fossil from Flowstone 1A (Unit 2) went from hominin (Dirks et al., 2015), to not. It seems like interpretations are being changed to fit the dates as opposed to being based on the primary evidence/material (sedimentology, fossils) themselves.

4) Several critical errors in table 1 (or the text) need to be fixed (see details below). The most important one is that sample RS18 is said to overly Unit 3 (hominin-bearing) in the text, but Unit 2 in the Table. This is a key date they use for anchoring the hominin fossils. Wondering if the change wasn't made in the table because they altered their unit assignments only after the dates were produced.

5) Tables 27 need substantial revisions. I know the work was done in different labs, but that doesn't mean the tables should be completely different. They need to be totally reformatted to match each other so that comparisons can be made between the two labs. As is, they have different fields, different units, etc.

6) The final age determination of the hominin fossils of 200-300 ka is not sufficiently explained. If based on ESR dates, then they need to more fully explain/justify why settled on 200-300 ka specifically as opposed to the ESR range of ~150-425 Ma? This appears to favor results of UW1810 and results from SCU/UOW (vs. GU/ANU). This seems rather arbitrary when in fact it is something that could be either modeled or calculated statistically. If it is just based of the younger age peak of 1767 (~200ka) and the older peaks of 1788 and 1810 (~275ka) in Figure 9, they should specifically state (and reference Figure 9).

Also, the yellow box in Figure 13 is not 200-300 ka, but more like 200-340 ka. Need to be consistent between text and figures. This is one of their main conclusions, yet not specifically supported.

Reviewer #4 Minor Comments:

- Line 88: Other papers format as refer to U.W. 101, not UW101. Change for consistency.

- Line 90: Lesedi Chamber papers says "some of which (facies and stratigraphic units) correlate to facies in the Dinaledi Chamber". Does not imply "sedimentologically distinct" as stated here.

- Lines 83 and 92: COH or CoH. Pick one.

- Line 167+: What specifically is used to correlate/group these discontinuous flowstone units across the chamber. You mention appearance is included (line 153), but no appearance is described. It seems that Group 2 is really just a group because it is not Group 1 or 3.

- Line 194: Should be noted that in Dirks et al. (2015) Figure 3 the fossil below Flowstone 1a is attributed to hominin. What changed the identification?

- Line 200: How can Unit 2 sediments be derived both from local erosion/reworking of Unit 1 and as a debris cone below a vertical fracture system? They can't be both autochtonous and allochthnous in relation to the chamber. I believe this needs to be clarified. Are the Unit 1 clasts derived from Unit 1 equivalents outside the chamber?

- Line 213/218. This also goes for Unit 3. Is the Unit 3 material derived from reworked Unit 1 and 2 material outside the chamber, and brought in via the debris fracture/debris cone? Please clarify.

- Line 202: Why is there no mention of the baboon tooth in Unit 2 here?

- Lines 203-260: This description doesn't seem to jive with what is depicted in Figure 7. The top cartoon should be more of a debris cone without a thick and even deposit running along the floor of the cave. Only AFTER the debris cone collapsed/eroded would Unit 2 material have spread/deposited along (evenly?) across the floor of the cavern. As currently depicted, if the debris cone in the top cartoon eroded, then the thickness of Unit 2 should be much, much thicker (not thinner) or you have to explain where all that collapse/eroded material went in the cavern (down the drains?).

- Line 211: It would be helpful to rephrase this sentence a bit to note how Unit 3 is differentiated from Unit 2. As is, they sound the exact same except for lithified (Unit 2) vs unlithified (Unit 3). Is that the only difference? Is that sufficient to re-assign the material below FS1c from Unit 2 to 3?

- Line 218: Along with Figure 7, is the interpretation then that the hominin remains were brought in along with the sediments from outside the chamber and deposited as part of the debris cone? Please clarify.

- Line 246: With other macro-fossils now identified in Unit 2, what are the implications for chamber accessibility in the past? (Especially as there is little Unit 2 exposed, but it has fossils.)

- Line 260-263. Need to provide some supporting evidence that Unit 1 was deposited during/after Unit 2 through modern times. Similarly, need to provide evidence that Unit 2 sediments are older than most of the Unit 1 deposits presently observed (no dating results presented at this point). What precludes it from being older? The only evidence provided (reworked into Unit 2) is the only concrete evidence provide for the sequence of the two units (and indicates older).

- Line 294: Should include or refer to a Figure 2 photo(?) showing FS2 directly overlying U3 and hominin fossils.

- Line 297: "fossils entered" suggests they walked in along with the deposition as opposed to being deposited/reworked along with Unit 3. Perhaps better to say they were deposited or transported.

- Line 317: Dirks et al. (2015) noted that flowstone samples included a detrital component derived from associated muds in all tested pilot samples which confounded U-Pb dating because of the high and isotopically variable background of common Pb it carries. But now they are apparently all suitable? Need an explanation as to why they were undatable in the last publication, but are now magically all datable.

- Line 332: Text says RS5 sample is from FS1, Table 1 says FS2. Which is it?

- Line 337+: Text uses Units, Table 1 uses Facies and they are not comparable! JCU/RS18 overlies Unit 3 (text) or Facies 2b (table)? This perhaps the most critical date as they argue it as the minimum for the fossils, but there is an error either in the text or the table.

- Line 368: Should state what the teeth are (e.g., upper premolar of H. naledi) either here or where each sample is discussed shortly later. Not just refer to figures that don't contain the information either (e.g., Figures 5, 8). Shouldn't have to wait until materials section at the end to get some basic information.

- Line 375: Why are Tables 6 & 7 presented before Tables 4 & 5 (line 444)? Need to reorder.

- Line 379: Needs a brief explanation/justification as to why U-Th ages should be regarded as minimum.

- Line 426: There is no data on Sample 1841 in Table 7.

- Lines 427-435. Why are Sample 1767 and 1810 (and the age of Naledi in relation to it) being discussed under Sample 1841? This should have a different header.

- Line 493: Should provide radial plots for the samples for evaluation/visualization of the data.

- Lines 507-511: Even if one agrees with the time-transgressive argument of Unit 1 (and that's a big if), these are the ages you have at the moment. Similarly, they still need to be reconciled with the flowstone ages that cover them, which is brushed aside here.

- Line 572/573: This totally ignores the results of RS23 from the BASE of FS1a which has a date of 683-449 Ka and is not compatible with the pmag of older than 780ka. The authors focus on the top sample RS22 as it fits their pmag, but seem to selectively ignore the data that doesn't fit. This was not discussed in the paleomag section and it is totally omitted here. If RS23 is not from the base, or is from higher up and in the Normal section of FS1a, then that needs to be properly documented here. In Figure 13 they state RS23 as "mid", but in Table 1 it is "base" and in the description of the sample (Line 912) and Figure 2l it is at the base.

- Lines 568-595: It seems like the determination to reallocate the sediments associated to Flowstones 1c-e from Unit 2 to Unit 2 was based more on the geochronology results than sedimentological analysis. Different levels of induration could be the result of other processes besides being different depositional units. It seems like they are changing their interpretation post-hoc to fit their new ages rather than based on the actual sedimentology.

- Lines 604-607: Their argument for Unit 1 to be time-transgressive is not very convincing. All 3 of their samples from 2 different parts of the cave say Unit 1 is younger than Unit 2. It doesn't match their interpretation of Unit 2 being reworked material Unit 1 so they propose that it is time-transgressive, yet they provide no data to support this. Seems that this hypothesis could be tested by additional sampling to find pieces of reworked Unit 1 in Unit 2 (or 3) that are suitable for OSL analysis. If dramatically older, then I'd believe their conclusion. If not, then they need to seriously re-evaluate their current ages of either Unit 1 or Unit 2.

- Line 640/641: Again, Table 1 says RS18 overlies Facies 2b (=Unit2?), not Unit 3. Perhaps it was Unit 2 until they decided to change it Unit 3 because of the age (i.e., changing based on age, not sedimentology).

- Lines 644-647: This is confusing sediment age with depositional age. Reworking sediment doesn't change the age of the sediment, it simply reflects a different period of deposition. It would be more appropriate to say that Unit 3 is a reworked unit and that different deposits of it in the chamber may have been deposited at different times. However, it is also worth noting that although H. naledi may have been deposited over an extended period of time, they also may not have. There is not sufficient evidence presented to say one way or the other.

- Line 657: This is cherry picking the U-Th tooth data as it is only 1 (the oldest) of 14 results. Should just stick to the ESR data.

- Line 719: Why 200-300 ka? If based on ESR dates, then need to explain/justify why settled on 200-300 ka specifically as opposed to the ESR range of ~150-425 Ma? This appears to favor results of UW1810 and results from SCU/UOW (vs. GU/ANU). This seems rather arbitrary when in fact it is something that could be either modeled or calculated statistically. If it is just based off the younger age peak of 1767 (~200ka) and the older peaks of 1788 and 1810 (~275ka) in Figure 9. Then should specifically state (and reference figure 9).

Also, the yellow box in figure 13 is not 200-300 ka, but more like 200-340 ka. Need to be consistent between text and figures. This is one of their main conclusions, yet not specifically supported.

- Lines 729+: Appreciate the detailed materials and methods.

- Figure 1. Why not use the update surface map from the Elliot et al. submission that also includes the location of domal stromatolites, chert markers and mylonite markers? Should at least use consistent maps between papers.

- Figure 12B: I'm assuming that this wasn't actually analyzed as Phase A and B are only a cm thick yet samples were 2-2.5cm cores.

- Table 1: It would be helpful to sort the table by flowstone group (or possible age), not HW sample number to compare proposed clusters of flowstone ages easier. Blind duplicates of the same sample or base/top of the same flow shouldn't be rows apart. Also, text only refers to Units, table refers to Facies, and they are not comparable! Why are RS10 and RS5 listed if there is not data?

Should delete (similar to no HW to pair with RS1).

Text says RS5 sample is from FS1, Table 1 says FS2. Which is it?

Text says RS18 overlies Unit 3, Table says RS18 overlies Facies 2b (=Unit2?). Which is it?

- Tables 2 & 3: Need to be formatted exactly the same (same fields, units, etc.) for a proper comparison.

Data for RS1 is missing from Table 3. As it is a blind duplicate it needs to be included so the blind comparison can be compared.

Sorry, but the different formatting of Figures 27 is sloppy.

- Tables 4 & 5. Again, why are these tables formatted differently and with different information.

Also, why are they presented before Tables 5 & 6, but discussed/referenced after them in the text?

- Tables 6 & 7. Again, why are these tables formatted differently and with different information?

- Table 6 is 4 tables, not 1. What do * represent? Needs to be explained.

- Table 7: Missing data for Sample 1841.

Reviewer #5:

At first reading, this manuscript raises more questions than answers. H. naledi unquestionably has primitive characteristics and originally was expected to date to at least 1 Ma. Dating that places these specimens at 200-300 ka suggests several scenarios.

1) The dating is correct. H. naledi originated at some unknown time, perhaps 1-3 Ma, and survived until the Middle Pleistocene, in a similar fashion to the proposed survival of H. floriensis. Note that H. floriensis was isolated from other species; H. naledi would have co-existed with possibly several other species of hominins. In itself, that is plausible; we are learning that the existence of a single hominin species is quite recent. However, this hypothesis conflicts with the evolutionary assumption that more primitive species cannot compete with more advanced, and thus to be convincing it would need to be bolstered by some evidence of an advantage that compensated for primitive features or an analysis that these features were irrelevant.

2) The dating is correct but the fossils are reworked from some other deposit. This hypothesis has been rejected on the grounds that there is no known entrance into the cave other than the one found by this group. It is further challenged by the sheer number of finds; survival of so many pieces is more plausible over 300 ka than 1 Ma.

3) The dating has been done with great precision and care, but there is a factor of which the analysts were unaware, or perhaps that could not be measured.

Reviewing a 96-page manuscript means that the reviewer must concentrate on a portion of it. Of the various dating methods used, only the combined ESR-U series method deals specifically with the fossil ages. It seems reasonable therefore to focus on the details of this method in commenting on the manuscript.

Let us consider the scenarios in reverse order. By definition, something that cannot be measured cannot play a role in calculations. Of the known factors, the only possible problem with the dating lies in the evaluation of the external dose rate. The cave has experienced significant transformations over time. The external dose rate is as much as 80-90% of the total dose rate for the hominin teeth. The text notes that sediment radioisotope contents are in Table 8; that table lists sediments from Unit 1 for OSL, not Unit 3. A reference is made to 'average' sediment values; it would be of interest to say how many samples were used. Also, the values for Unit 2 are very similar to those for Unit 3, reinforcing the suggestion (p. 8, line 213) that Unit 3 reflects reworking of Unit 2. On the whole, there seems little leeway for significant changes in external dose rate.

What about reworking? To say that 'there is no evidence that the present entrance has significantly changed' is not the same as saying that there is evidence it could not possible have changed, the latter being an unreasonable standard, of course. Internal reworking – where the fossils were originally deposited in a thicker Unit 2 and eroded onto a deflational surface in what is now Unit 3 – would not be likely to change the age, at least not from 200 ka to 1 Ma, since as noted in the preceding paragraph the enclosing sediment remains essentially the same.

That leaves the first scenario, which is one that is not dealt with in this manuscript. It will be interesting to see what sorts of interpretation are made along that line.

Therefore this manuscript needs only minor revision. The authors should explain more fully the number and locations of sediment samples, preferably adding yet one more table instead of referring to Table 8 (p. 38, line 1203).

Reviewer #5 Minor Comments:

Page 15, line 447: 'did' should be 'was'. Page 41, line 1296: 'enable one to differentiate'.

As noted in the review, the authors have not submitted sediment data for ESR dating that indicates how many sediment samples were used for each sample and where they came from.

[Further revisions were requested before acceptance.]

Thank you for resubmitting your work entitled "The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa" for further consideration at eLife. Your revised article has been evaluated by a Reviewing Editor and five reviewers.

The reviewers were pleased with the improvements made to the manuscript, but several major remaining concerns were still noted. Many of the major concerns that need to be addressed are technical in nature, so they are provided in full detail below as provided by the reviewers in their comments, rather than summarized.

In addition, there was discussion among the reviewers during the consultation process concerning the last line of the Abstract and the penultimate paragraph of the Discussion (that begins on line 1009), which were viewed as unnecessarily critical of prior authors' work and of the challenges in accurately dating hominin fossils. In addition, at the end of the Abstract, it may be better to simply state that "These dating results indicate a much younger age for the H. naledi fossils than have previously been hypothesized based on their morphology."

Technical Points:

1) Lines 175-178: The addition is appreciated, but a sentence at least on how the material "accumulated inside fractures and along ledges" needs to be added. I would also drop the last sentence in this paragraph and move it to the discussion of Unit 1 (out of place here).

2) As a result of the revised units and stratigraphy (esp. "facies 1c" and "informal upper and lower members of Unit 3), the authors have now introduced inappropriate and inconsistent terminology. This is not just an issue of semantics.

Lines 217-229: The introduction of facies 1c is problematic, not as a subunit in general, but as a subfacies in particular. The confusion and misuse of facies happens often and here is a chance to correct it. Quoting Maill (facies guru), in sedimentology, "lithofacies are defined on the basis of its distinctive lithologic features, including composition, grain size, bedding characteristics, and sedimentary structures. Each lithofacies represents an individual depositional event. Lithofacies may be grouped into lithofacies associations or assemblages, which are characteristic of particular depositional environments". Thus, the basis of different subfacies here based on "relative topographic position in the cave" (i.e., facies 1c) is not valid criteria. Specifically, facies 1a is fine (non-lithified, horizontally laminated, orange mud). Facies 1b is fine (laminated mud with fine sand and rodent remains) and distinct from 1a. Facies 1c is "similar in appearance and composition to the laminated, muddy sediments of facies 1a, but they occur "in different places". This is not a properly differentiated as a separate facies. Facies 1a in a different location in the cave topography is still facies 1a unless it can be differentiated appropriately. There are many examples in sed/strat where the same/similar facies are repeated multiple/different times in a succession. This is again an issue at the end of the paragraph where the facies differ in "relative age and position within the cave chamber", which is not a characteristic of facies. Facies 1c needs to be differentiated from 1a on the basis of composition, grain size, bedding, or sedimentary structures to be valid.

Lines 270-276: Unit 1 is divided (incorrectly) into 3 subfacies. Unit 3 is divided into 2 informal members. This inconsistency is confusing and unnecessary. Also, members are formal lithostratigraphic units of formations. It is OK to provisionally have informal members, but this is almost always in the context of a sequence where there are other formal members (as part of a formation), which this sequence does not have, nor is it part of a defined formation. For example, you could have formal Members A, B, C, D and then informal members E and F, but randomly throwing in informal members into this context is exceptionally odd. Ironically, the authors could subdivide Unit 3 into facies 3a and 3b as the presence/absence of fossils is a characteristic that can be used to differentiate facies. Also, what happens if they do ultimately find H. naledi fossils in the "lower member"? Something that would easily fix all of this is if they just used informal sub-units for all (e.g., 1a, 1b, 1c, 2, 3a, 3b), that way they can be consistent and define them as they wish as units have no formal definition while facies and member do. The fact that all of the sedimentary material in the cave appears to multiple phases of reworking the same material over and over suggests everything is genetically related and easily dealt with as a series of related units.

Lines 304-315 (and elsewhere): Again, until other ages are generated for facies 1c subfacies or its stratigraphic relationship/contacts with other units can be observed/demonstrated, the time-transgressive explanation for Unit 1, and the relationship between Units 1 and 2 are just a hypothesis. Similarly, their assertion that facies 1c (as opposed to 1a or 1b) must have been the unit that provided the source material to Unit 2 (now 3?) is not confirmed by evidence and, again, is just a hypothesis. The authors are very definitive about their interpretation: "it is clear that older laminated orange mud deposits ascribed to facies 1c in Unit 1 occurred above Unit 2 and must have provided the source material now found as much clasts within Unit 2". As there are no dates for facies 1c, and as facies 1c is lithologically the same as 1a, this is a hypothesis, not an unquestionable fact. I have no problem if this is presented as a hypothesis: it might even be likely, but it is not definitive and I think the authors need to back away from such a claim. The authors note the challenges of OSL dating these deposits, yet rely almost exclusively on the OSL ages for a "young" facies 1a/b argument. An alternative explanation is that Unit 1a/b is older than Unit 2 and the OSL dates are incorrect (aliquots as opposed to single grain). Or perhaps the 1a looking material was brought into the chamber from elsewhere where similar depositional environments also produced laminated orange mud. This all needs to be demonstrated or proposed as a hypothesis (which can be tested by more/future dating even if far down the line).

3) Somewhere, the authors should to be more specific of the possible age of H. naledi from this chamber, versus the best fit age of H. naledi specimens dated here. For example, flowstone group 1c does provide a minimum age for the specimen that is stuck underneath it, and the ESR ages do provide a maximum age for the 2 teeth. The authors suggest that the fossils entered the cave over a period of time and may have continued during the deposition of upper Unit 3 (lines 299-303). As such, I have no problem with the authors saying those 3 particular fossils have a best fit of 236-335 ka, but does anything preclude the other hominid specimens from being associated with older or younger parts of upper unit 3 with the potential to span approximately 90ka (min of above RS1/15 above U3) to 414 ka (max of OSL5)? At minimum, a red dashed vertical line should be added to Figure 14 at ~414 ka for the oldest possible age to match the minimum line at ~100 ka.

4) Line 465: This sentence is confusing as presently constructed. It seems to report that something is both younger than unit 1 and older than unit 1. It would be better to write "younger than ages derived from facies 1a, but slightly older than ages derived from facies 1b in this location."

5) The U-Th ages must be quoted as just ka, using kyr BP is a radiocarbon convention and does not apply to U-Th - there is no industrial carbon adjustment to U-Th ages, so to quote them as kyr BP is misleading and incorrect.

6) In Table 4, "Dose" should be "De" to prevent confusion with subsequent discussion of artificial doses given to samples. Thicknesses are μm, not mm and according to the table, 100 μm was removed from the dentine and the sediment, not enamel and dentine, due to misplaced headers. The removal from dentine was not mentioned in the methods section.

7) There was no dentine on the baboon tooth (line 618) but would a modern analogue suggest that there should have been dentine on at least the inside? It probably doesn't matter since the dentine survival time would be a relatively small portion of the entire burial time, but the authors might comment on this.

8) Figure 8: With the addition of another unit, it is very challenging to differentiate the little sliver of Unit 2 (below Flowstone 1a) and Unit 3 upper because of the similarity in color, especially in the upper panel. It would be helpful to address this. Also, given the revisions, what now is the explanation/model for the deposition of Unit 2? Virtually all of Unit 2 is now assigned to lower Unit 3. In the previous submission, Unit 2 was under the flowstone and underneath the hominid fossils on the cave floor. Now it is stuck up under the uppermost flowstone and nowhere modeled to be anywhere on the cave floor, just completely washed away(?). While the authors do touch upon this in the text, they should consider adding back in a revised panel to explain Unit 2 a bit better.

[Further revisions were requested before acceptance.]

We appreciate that you have been extremely responsive to the various reviews, including your recent detailed comments. However, the reviewers collectively do not feel that the manuscript can be published without revisions that fully address the remaining outstanding concerns on the sedimentology. We also want to clarify that while many of the most detailed comments on these topics in previous rounds of review were from one reviewer who has consistently provided their expertise and extensive time to help improve the paper (Reviewer 4 from the original round of review), all of the reviewers have expressed agreement and consensus on these points during consultation sessions.

Perhaps one of the major continuing complications and challenges in these revisions is the effort to maintain consistency with the earlier descriptions in the Dirks et al. 2015 paper. Simply stated, the reviewers feel strongly that the use of facies as units in Dirks et al. 2015 was incorrect; updated stratigraphy needs to be used in the present paper alongside a simple, clear statement of change from the original interpretations. Editorially, we agree that the present paper should standalone and use the most up-to-date, appropriate descriptions and approach. Doing otherwise is introducing complication and would be perpetuating confusion.

https://doi.org/10.7554/eLife.24231.027

Author response

In revising the original manuscript we have made some major changes and have re-written sections, mostly following the recommendations made by the reviewers. We also made some significant changes that were not mentioned by the reviewers, but that needed to be done with respect the ESR data.

For ESR we have now standardized the modelling input parameters for the ESR models. Originally the results provided by the two labs varied significantly, largely because each lab had made different à priori model assumptions (as a result of this being a double blind experiment), which would have been hard to spot by any non-specialist. To allow for more objective comparisons of the two different data sets, we have now based all ESR modelling on mutually agreed to in-put parameters for the environmental dose rates (presented in Table 4), and we have introduced two modelling scenarios; one resulting in maximum age estimates; the other in minimum age estimates with the true age somewhere in between.

We have explained this approach in detail in the revised manuscript. These changes also go a long way in addressing some of the concerns raised by the reviewers regarding consistent bracketing of age ranges for the fossils.

In response to the main editorial issues:

1) Critical points concerning the relationships among the various stratigraphic units were raised by Reviewer 4 (in particular, see major comments 1 and 3 from that review) that must be addressed thoroughly in any revision. During the consultation process, other reviewers highlighted the importance of these points given the interdependence of most of the age/depositional models on those interpretations.

We believe that this has now been addressed; see our detailed comments in response to reviewers 3 and 4 in particular. In brief:

A) We have introduced an extra facies (facies 1c) with Unit 1, to explain that components of Unit 1 occur in different topographic positions within the cave, and that some could have contributed to the sediment provenance of Unit 2.

B) We have removed Unit 2 as underlying Unit 3 from the floor sediments of the Dinaledi Chamber, and restricted Unit 2 outcrops to occur below flowstone remnants near the entrance (as originally defined by Dirks et al., 2015). Instead we have subdivided Unit 3 into a hominin-bearing upper Unit 3 member and a hominin-free lower Unit 3 member, with the upper and lower members occurring along the floor of the chamber and the upper member also occurring below flowstone remnants at the entrance into the chamber. The reason for changing this back to Dirks et al. (2015) is that all floor sediments are probably significantly younger than the Debris cone and are probably better grouped with Unit 3 than with Unit 2. Unit 2 near the entrance is >780 ka old (from paleomag), and started eroding after formation of Flowstone 1a came to an end, which could be as late as 437 ka (the lower age limit of Flowstone 1a). It is this erosional process of the debris cone, probably driven by sediment moving down the drains, which causes the material to spread out along the floor.

C) To illustrate these relationships more clearly we have added an extra figure (Figure 2), which shows cross sections through the cave. We have also completely redrawn Figure 14 to more clearly reflect these relative timing relationships as well.

D) We have expanded our discussion around how the ages help re-define the stratigraphic units.

2) The overall synthesis/analysis of the various dating results is too limited at present, and choices on what results are highlighted at various points in the manuscript seem arbitrary at times. A more concerted and comprehensive effort to assimilate the different datasets in a evenly considered, summary results section (with a synthesis view agreed to by both dating labs) would help to address this concern. This issue also filters up to the abstract.

This has been addressed in several ways:

A) We have extensively rewritten the discussion section, expanded it and introduced a section that looks specifically at the quality of results obtained by the different methods and how these results should be compared

B) We have introduced a new Figure 14 that more clearly summarizes how the age results should be interpreted and how they constrain the age of various geological units in the cave chamber

C) Part of the problem with the age results was that the ESR results from the two labs, which are central to the age estimates for the fossils, had not been standardized; i.e. the two labs were using different model assumptions in calculating their environmental dose rates, and in consequence, their ages. We have now standardized the modelling approach for ESR with fixed model parameters that have been varied between two scenarios resulting in minimum and maximum age estimates. As a result the paper is easier to read, and ages are now better and more consistently constrained.

D) We have defined the age constraints in a clear and objective manner (using the listed uncertainties), and we have applied these age estimates in a consistent manner throughout the paper.

3) The manuscript currently reads as if various sections were composed by different authors with insufficient consistency in style and level of detail. Likewise, the tables need to be reworked with more care for consistency and interpretability.

The core of the entire paper was written by one person (PD), with input and edits from experts for various sections. For the methodology sections we have had to rely extensively on input from participating labs, so some style differences in this part are inevitable, but even here we have tried to homogenise the ‘tone’, and we included introduction sections written by the same person (PD). Please note that this paper discusses 6 different dating techniques, provides detailed sedimentology of complex stratigraphy, talks about paleoanthropological and archaeological constraints and even includes some anatomy. All these fields have their own vocabulary and ways of describing things (e.g., provenance in sedimentology is referred to as provenience in archaeology; should we refer to the baboon tooth as baboon or cf. Papio etc.).

For a long, complex, multi-disciplinary paper like this, I am afraid that some style differences will be inevitable, however, like I said, we have tried to homogenize the style as best as possible.

4) The reviewers also felt that the discussion should also be expanded, and can be even without overtly duplicating the broader synthesis provided in the other papers.

This has now been done as explained under point (Aitken, 1985) above.

5) Similarly detailed treatment for reporting the radiocarbon methods and results, as the other dating methods, should be provided.

We have now treated the radiocarbon dating in the same way as the other techniques; but we have not explained things to the same amount of detail, because we only did some preliminary testing with 14C, and then decided not to pursue things further. Although this was already explained in the paper, we have now expanded the dating strategy section to make this more explicit.

6) The reviewers also had suggestions for the order of presentation that may help the reader more readily interpret the results.

The reviewers asked for a methodology section up front. In our original submission we followed the format suggested by eLife; i.e., results are presented before the methodologies. After consultation with the journal editors we have now included a general section entitled “Dating the H. naledi fossils”, which explains the dating strategies and approaches taken, and acts as an easy to read introduction of methodologies. This section has now been placed directly before the results.

Responses to the reviewers’ comments follow:

Reviewer #1:

I will state up front that the dating methods used in this paper are not within my field of expertise. I was asked to review this paper as one component of the entire suite of submitted papers. Thus, I will leave the methodological critiques to those more qualified than me and comment more on the implications of the dates. The authors suggest that deposition of the hominin material was over a time period of about 100k between 200-300 ka. It does seem like the resolution and precision of the dates are not great and makes it difficult to properly interpret the context of the hominins. When the duration of deposition is considered, it then seems unusual that there would be so few hominins in the cave system, particularly if it is being used as a burial site (even if only for special individuals).

Point taken, but the dating techniques have their limitations. We have now clearly explained what the age range is for the fossils, and for the sediment unit that contains the fossils. This still allows for almost 100ka of time, which we cannot constrain much further, even though we have given indications of our preferred interpretation.

This paper is about geochronology. I think we have presented the data in an objective, detailed and transparent manner. How the age constraints should be interpreted with respect the time period over which H. naledi entered the cave, or its behavioural patterns is largely speculation and has been dealt with elsewhere (e.g., accompanying Berger et al., co-submission).

Given the complexity of cave systems and their formation, I don't know that the authors have convincingly demonstrated that the chamber was completely inaccessible during the times of hominin deposition (especially with the wide range of dates and low resolution). That said, I sympathize with the inherent difficulties of dating fossils from cave systems and appreciate that the authors used multiple methods to try to pin down the dates and that this may be the best that can be done at this point.

First, in terms of inaccessibility, we have performed surface geophysics, laser scanning of the chamber, and extensive caving surveys, all of which have yielded zero evidence for alternative entry routes into the Dinaledi Chamber. Additionally, we have shown that major sedimentological differences exist between the Dinaledi Chamber and other chambers in the cave system. Geochemical analysis shows a distinct difference between sediment of the Dragons Back Chamber and the Dinaledi Chamber. We appreciate that this is difficult to accept, but we can find no evidence to refute this claim.

Second, because we are dealing with an active sedimentary system, obtaining ages for material that is participating in the active processes of continuous reworking is exceedingly hard.

Reviewer #2:

Although I have reservations about the way radiocarbon dating was attempted, as explained further below, and there is a need for more caution in some areas, the paper should be suitable for publication after revisions. I have marked up a text copy of the manuscript, which I attach, and summarise some of the points below. The references for all four papers need work for consistency of formatting, journal abbreviations, accents etc.

Done, but only up to a point. Regarding references, the eLife website says:

"Please note, authors do not need to spend time formatting their references and can submit manuscripts formatted in a variety of reference styles, including Harvard, Vancouver, and Chicago. Wherever possible, please do not truncate the number of authors in the references list, but please do provide a DOI if possible." We have made sure that each reference has all of its information.

"The results for RS18 (~242 ka) may provide a potential minimum age for the H. naledi fossils in this part of the cave." Insert some caution because some other age estimates are still younger than this figure.

This is a valuable comment and issues are now discussed extensively in the discussion section.

"Dates acquired via U-Th and ESR techniques were obtained using a double blind approach for each technique to ensure robust, reproducible results, with each laboratory using their own analytical and computational approach. Methodologies and approaches taken by each laboratory that has contributed to this paper are described in detail in the methodology section." Why wasn't radiocarbon dating pursued in the same manner, using established research labs rather than a commercial lab? Why no details of the procedures: e.g., was ultrafiltration attempted?

As explained in the text carbon dating was done “as due diligence to obtain an indication if carbon dating should be further pursued”. This was most easily done by sending samples to a commercial lab to see if it works. Given these initial results and the destructive nature of the technique, carbon dating was not further pursued. We have clearly explained this in the text (and have now expanded on this explanation in the new version).

The initial results from the commercial lab indicated that carbon dating was not going to work. Subsequent U-Th and ESR work made it clear that carbon dating should not be further pursued, and attempting blind dates at research labs would be pointless as far as the purpose of this study is concerned, and we did not want to unnecessarily impose on people’s time and expenses. We are only reporting the carbon dates here for completeness sake, and the fact that it corroborates flowstone formation around 30ka.

However, we have added a more detailed methods section on 14C dating, and we have brought the description of the samples and technique in line with the other methods.

"Some of the ESR ages (Tables 4, 5) independently suggest that some of the fossils around the excavation pit may be younger than 237 ka, but confirm a probable age of >200 ka for the fossils." Well a few of the ESR ages don’t confirm an age of 200 ka+ so this needs rewording.

Part of the problem with some of the dating results was that the ESR results from the two labs, which are central to the age estimates for the fossils, had not been standardized because of the double blind strategy employed; i.e. the two labs were using different model assumptions in calculating their ESR ages (i.e. their environmental dose rates). We have now identified the best input parameters and standardized the modelling approach for ESR with fixed model parameters that have been varied between two scenarios resulting in minimum and maximum age estimates. As a result the paper is easier to read, ages are now better and more consistently constrained, and it has been easier to explain how the age results place constraints on the ages of the sediments and fossils.

Reviewer #2 Minor Comments:

Other suggested edits are added in an attached text version of the paper.

Done.

Reviewer #3:

[…] However, there are many issues, the three major ones being:

1) there is no synthesis or analysis of the various geochronological data sets;

Although we did have quite an extensive analysis of the new stratigraphy in the cave and what the ages meant for the age of the fossils, we agree that more work was required to improve clarity and readability.

We have now expanded the discussion section significantly and have included an entire section on the quality of the age data and how the various age estimates should be understood and compared, which should go a long way in addressing this issue.

2) there is no discussion of how the new ages fit into the regional and global picture in terms of cave formation;

Although true, this is well outside the scope of this particular paper, and it would be inappropriate to discuss this here without more work. Indeed, we have two PhD students (both coauthors on this paper) who are conducting significant additional analyses and specifically focusing on the “global picture” of cave formation in the Rising Star Cave. We (they) have much work still to do before this comes into focus. Rather, this paper is about dating the H. naledi fossils. All methods have been designed with that aim in mind.

3) Exactly how the age of the fossils has been determined is not abundantly clear: this is certainly the most important message of the paper and needs to be clearly and carefully explained. The existing discussion on pages 20 and 21 is confusing and no clear story emerges.

This is a good point. We have now extensively rewritten the discussion section, and have included a more standardized approach to generating the ESR results. See further comments on this issue in our various responses below.

The authors presume a huge prior knowledge of the region, caves and fossils, as well as the background and methods of the various dating techniques;

Extensive background has been provided for each of the dating techniques, much more than is usual in dating papers of this kind. This has been done to make the techniques more accessible for a wider audience. To provide more, would transform the paper into a review paper, which is not the intent here.

However, we have included some more info on the regional geology as requested.

I am not unfamiliar with the sites in this region and these dating techniques but struggled to follow a clear story with the manuscript. The confusing order of the sections…

The sections follow the prescribed format of the journal in which results are presented before methods. We have tried to overcome some of this problem by including an abbreviated discussion of methods up front.

…the disjointed writing styles from sections clearly contributed by separate co-authors, the lack of synthesis of the various dating techniques, the short and undeveloped discussion and the rather vague final age assignation all need serious work.

We have expanded this and clarified the discussion as requested, however, we have also intentionally left out discussions related to paleoclimate and cave formation, which form the subject matter of two ongoing PhD student projects.

Nevertheless, the comment about a lack of synthesis is true, and we have completely rewritten the discussion section and expanded it with a section comparing the various techniques. We have also more clearly defined the age brackets, and standardized the ESR approach, and included a new summary figure and extra sections, all of which should make it much more explicit why certain age brackets were chosen.

The Homo floresiensis (Hobbit) fossils found preserved in the limestone cave site of Liang Bua on the island of Flores in Indonesia are an example of how complex dating this type of site (fossils in a limestone/dolomite cave) and how long it takes to get good, robust data (see Morwood et al, 2004; Roberts et al., 2009 and Sutikna et al., 2016). There is scope for some comparison between this site and its multistranded chronology and the work presented here. Another example of using multiple strands of evidence to date cave deposits is the Marean et al (various years) work done at Pinnacle Points in South Africa. This is the kind of synthesis this paper is lacking.

This is a valid point and we have included some new references and discussion with respect to Liang Bua and the difficulty of obtaining good results. We have also applied similar strategies to those used by Marean et al. and others for Pinnacle Points to summarise our various results (e.g., see Figure 14). However, we also wish to highlight that the caves mentioned by the reviewer are mature excavation sites with extensive excavation histories and multiple dating and stratigraphic studies. To date, only a single excavation pit is available for comparison in the Dinaledi Chamber and this paper presents the first attempt at dating this complex cave system. Simply put, we have no previous results or data to compare this to, but we do not doubt that this study will provide the framework for future work as more of the chamber is excavated and more focused studies are developed.

So, as it stands this paper reads as a technical report of the different dating techniques, the type of document circulated between member of a large project to share information. Much work is needed to get this manuscript up to a standard ready for publication.

In detail: 1) There is no clear narrative. The paper reads like a technical report of the site, samples and results that would be circulated between co-authors – the data from the various methods is presented, often in excruciating detail (ESR) but there is no actual synthesis of the various data sets into a cohesive narrative.

Here we have to cordially disagree, although we have certainly made efforts to make this clearer. Specifically, to address this concern, we have added a new, highly detailed figure (Figure 2), which we hope better explains the relationships between the geology in the cave and the dates presented here and we have modified Figure 14 to help synthesise the various results. We have expanded the discussion. We wish that there was a simple, narrative to tell, however the results are not all entirely straightforward and we have intentionally tried not to interpret the data.

2) The order of the paper is confusing and does not help in building a clear story – having the very detailed results section before the methods section does not make sense and makes reading the paper from beginning to end not easy.

This is the prescribed format of the paper, but we have now addressed this to some degree with permission from the editors.

Some kind of discussion about what the different techniques used are all actually dating, which components of the cave system vs the fossils themselves etc would make a good introduction for the paper and segue into the more detailed methods section. Major rearrangement of the paper is needed, with a short clear methods section, then results.

With agreement from the editors we have now done this. Immediately before the results section we have included a section entitled “Dating the H. naledi fossils’. In this section we provide a general background to the problems with dating fossils in the cradle, with sideways references to other fossil sites in caves as well (esp. the H. floresiensis site) as suggested by this reviewer. We have further extended this section, with a more detailed explanation of how the dating strategy was designed, why certain techniques (U-Th, ESR and palaeomagnetics) were pursued, whilst other techniques (14C and OSL) were not continued beyond preliminary studies.

3) Overall there are very few references to the literature – there is very little introduction to the Cradle and sites beyond repeated references to Dirks et al., 2015. The concept of the deposition of sediments in hominin caves being cyclic, with periods of erosion is by no means new and reference (and credit) needs to be given to Brain (1958, 1993, 1995) and Wilkinson (1983, 1985).

No disrespect was intended. Given that the original submission was already over 90 pages long, we did omit much of the background literature. We have now included and expanded introduction to the caves and fossil deposits in the Cradle with additional references as suggested by this reviewer.

4) In the description of Unit 3, angular to sub-angular grains are classified as being reworked – on what basis?

Please note that for the most part, we interpret the reworking to result from gravitational driven collapse and slumping processes in the cave due to wetting and drying cycles. This is distinct from reworking processes in alluvial settings that involve considerable transport in fluids that would indeed cause considerably greater textural maturity as the reviewer implies. This is a well-supported phenomenon in Karst sedimentology. As explained in the text, material rolls in from fractures and collapses from below flowstones 1b-e; material occurs as loosely packed clumps of clay, in places on top of flowstone 2 remnants. In addition we have described flowstone 2 skirtings along the side wall with the floor-level of Unit 3 dropping below that, we have described drains, cross-cutting Mn-oxide tide marks on bone, etc. This is now clearly and repeatedly described in the text and is what forms the basis for our interpretation of repeated reworking.

Such high angularity does not support reworking.

Again, this is a concept that is quite true in alluvial settings, but cannot be applied equally to karst systems. The fact that grains are angular does not mean they are not reworked, it means that transportation routes have been short and there has not been much physical abrasive activity during the transportation process, nor has there been significant involvement of water transport. The primary agent of reworking and sediment movement is mass-wasting (gravitational forces).

Some micromorphology of these sediments (resin impregnated blocks then cut to make thin sections) would be very useful. How are the orange mudstones of Unit 1 and 3 differentiated from each other?

This was all presented in Dirks et al. (2015), and this work is clearly cited throughout.

It is also a little confusing and not entirely convincing to argue that Unit 2 is probably older than Unit 1 and was sourced from sediments that look like Unit 1 – there is very little actual evidence to back up this claim.

Not at all; the sediments of Unit 1 are near-identical in appearance and geochemistry to sediment blocks of Unit 1 inside Unit 2 (as presented in Dirks et al. (2015)), with the one big difference that Unit 2 and Unit 3 sediments have been oxidized and affected by Fe-Mn oxy-hydroxide infiltration. Again, all of this is well cited in Dirks et al. (2015); hence, we have not repeated this here.

A stratigraphic column summary diagram, plotted against age, would be useful.

This is an extremely helpful comment and we have added three new cross-sections to better illustrate the stratigraphic relationships of the units and dates presented. We have also updated our summary diagram (Figure 14) to make the various relationships clearer. We have also discussed these complex relationships in greater detail in the text and figure captions.

Based on this comment, we have also decided to introduce a further facies in Unit 1 (i.e. facies 1c) which is similar in appearance (laminated mudstone) to facies 1a (from Dirks et al., 2015), but which forms on ledges and in cracks away from the cave floor. In contrast facies 1a forms on the cave floor. All this has now been better (we hope) explained in the text.

5) The results section is very long and very detailed, all of the sections but especially the ESR/U-Th. The palaeomag results are the best presented and should be used as a model to redo the other sections. These different sections were clearly written by different people, as the long list of co-authors suggests, and need to be better synthesized together to produce a well-written document that flows well and is easier to read.

We have worked hard to make these sections more readable. However, the results sections were all written by the same person (PD) with input from individual contributors. All contributors also edited and approved the written sections. I disagree that there is much of a difference in writing style across the results sections; we are dealing with a range of very different techniques that require a different approach when being explained. Most of the results section is simply a summary of the tabulated results highlighting the main points.

Where differences do occur is in the methodology section, because these are based on the lab and methodology descriptions provided by each of the individual labs. The technical details are lab specific and therefore not easily ‘homoginized’. To overcome some of this issue and make the principles of the dating techniques more accessible to a general reader, we added a general description of each technique at the start of each methodology dating section, These were all written by the same person (PD) and edited and approved by the individual labs.

6) There is no discussion on the reproducibility of the various techniques – the authors are at pains to explain how the U-Th and ESR/U-Th analyses were both undertaken by two separate laboratories to produce blind duplications of the data, and yet there is no synthesis discussing this. Why was no blind duplicate done with the OSL samples?

This is a valid and useful point. A detailed synthesis of this has now been included in the discussion section under the heading “Reliability of the age estimates”.

7) There is no proper discussion. I realize there is a Berger et al submission alongside this manuscript which deals with the implications of the age proposed here, but there is still scope for a discussion of both the quality of the age data and what it all means in terms of the formation, development and filling of the Dinaledi Chamber, and of course the deposition and reworking of the hominin fossils.

Some of this was actually discussed at length (we included an entire section on discussing the revised stratigraphy based on the new ages including the deposition and reworking of the fossils). Nevertheless, we have expanded the discussion, especially by focusing more on the quality of the data presented as recommended by the reviewer, and we have added a summary of what the ages mean for hominin evolution.

Given the long and illustrious list of co-authors this is surprising – among these people are world leaders in cave formation, dating and climate comparisons – suggesting that there has been little actual input from these authors in the discussion as it stands.

Indeed we have been very lucky to have the help of many World-class collaborators on this project. However, the suggestion that there has been little actual input from these authors is certainly not true. Some have contributed more than others, however the main point that the reviewer makes about dating and climate comparisons is well and truly outside of the focus of this paper. Climate and cave formation studies will come, however the focus of the manuscript is solely intended to be around the age for H. naledi.

8) The big U-Th flowstone data set opens up the possibility for interesting comparisons with both local sites with U-Th dated flowstones (Gladysvale, Sterkfontein, Plovers Lake, Swartkrans); episodes of flowstone formation are strongly linked to climatic parameters (increased rainfall being the major one) and are expressed as similar aged flowstone deposits preserved in different caves. This comparison needs to be made here and would help build an argument as the when the deposition of the fossils took place.

This is indeed very interesting, but again it is very much outside the scope of this paper. As one reviewer points out, we effectively throw the kitchen sink at dating the fossils and this is the sole focus of the study. Comparisons of flowstone formations with other caves are the focus of a number of ongoing student and coauthor projects. We hope that the reviewers and editors will understand that these results will follow in time, but that they require a great deal of additional work still.

9) There are also regional and more global records of known climate variability to which the data presented here can be compared, not just the U-Th flowstone data, but the OSL sediments data too. Seeing how the ages of flowstone and sediment deposition in the Dinaledi Chamber compare to other records is not only interesting but opens up the possibility to argue for glacial/interglacial deposition of the fossils and a more thorough picture of the changing landscapes outside the cave.

We know and agree, but this is well outside the scope of this paper as indicated above. In particular the OSL results are exciting, but they necessarily are going to require a great deal of focused work in the cave to fully understand and interpret.

10) Following on from all these points about the lack of synthesis and discussion, as it stands the abstract is weak and once the paper is revised will need to be re-written into something more punchy. If some of the ages (OSL) are quoted directly in the abstract, then they all need to be. The abstract can also be a sentence of two longer and say something about the significance of these data - the reproducibility, the dating of difference aspects of the cave deposits and how these all fit together to produce a final age for the fossils.

Thank you. We agree that the abstract would benefit from a bit more punch. The abstract has now been changed to reflect some of this. However, the paper simply contains too much information, and we are not able to provide all of it in the abstract. So we have tried to keep the core message in the abstract simple, especially because many of the readers of this paper will not be experts.

Technique specific comments:

1) OSL a) The OSL section is weak. I understand a program was used to calculate the ages from the measured data but there is no discussion of these data relative to the literature as to which set of ages are more likely. OSL of cave sites is not easy, sites like Pinnacle Point in South Africa require significant method development, lead by Zenobia Jacobs, in order to date the sediments. It was certainly not as simple as crunching a single set of measurements through a program (written by someone else?). Some more detail as to why the Minimum Age model is most appropriate is needed.

We have expanded the explanations in this regard, both in the data section and in the discussion section. A full OSL study of the cave system is being planned.

b) Where does the maximum age for Unit 3 of ~400 ka come from? Is this a kind of midpoint age from the scatter (300-660 ka) of CAM ages? What evidence is there to suggest that this is the best approach?

We have expanded the explanations in this regard, both in the data section and in the discussion section.

c) To the best of my knowledge, this is the first use of OSL on Cradle cave sediments – this alone is worthy of a mention, as well as a caution that much work is still needed to thoroughly understand the OSL signal preserved in these grains.

Good points; we have expanded discussion on the OSL somewhat to reflect the preliminary nature of the work, and the challenges with obtaining good dates by OSL. Note however, that the OSL dates are of modest value here to defining the age of H. naledi because the absolute relationship between Unit 1 and 3 is not yet clear, which is why an in depth study was not pursued beyond the initial work (this has now been explained in the new methodology section preceding presentation of the results). We have shown that the technique holds promise, but future work will require single grain analysis and analyses of feldspars and this will require considerable work in future.

Note also that we did do trials of single grain analyses and feldspar analyses with U. Wollongong (Zenobia Jacobs and Bert Roberts), but due to the complexity of the system and the fact that the initial results did not contribute significantly towards gaining a deeper understanding of the age of the fossils, we have limited our data presentation to reporting the initial results from Wits, following the advice of Jacobs and Roberts.

d) Why was no blind test done for the OSL? Especially as these ages are heavily used to assign final ages to fossils.

See above; note that these ages are not ‘heavily used’ to assign ages to the fossils; only ESR and U- Th are significant in that regard. However, the OSL ages do provide insight in the age of Unit 1; confirm the general stratigraphic models proposed; and are consistent with the general age range during which the deposits, including the fossils, accumulated. For those reasons we thought it appropriate to include the results, with ample caution.

Because the OSL ages are not vital in determining the age of the fossils, there was no need to do a double blind test. Note that few studies on fossils in the CoH report double blind dates. Double blinds are time consuming, hard to organise and difficult to coordinate. Most labs are very busy and it would not be correct to unnecessarily impose on people’s time and resources to conduct the work unless absolutely necessary.

e) Why do aliquots and not single grains? Especially in this complex cave setting where there has been much reworking.

See above. Because we made use of the University of the Witwatersrand lab, which only has the ability to date aliquots. Given that this project is coordinated through Wits, it was important to use that lab. Also, preliminary single grain analyses were undertaken at the University of Wollongong as discussed above, but this work will require a fully focused (and funded) project in future.

f) Why not date the feldspar as well?

As above.

g) There is a very big difference between the two sets of ages calculated with no real discussion as to why this is.

This has been corrected; a mix up with sample numbers occurred in the lab, leading to a wrong (much younger) age being reported for OSL 5 in the original manuscript. This has been corrected and more discussion has been added. This was a simple, but confounding mistake that has happily been resolved.

2) U-Th a) Why were no thin sections made? For samples as important as these, every precaution to make sure the U-series system has not been disturbed should be taken. RS8 looks recrystalised?

All the detailed descriptions of the U-Th samples in the paper are based on thin-section work and extensively discuss recrystallization textures, sample by sample. The reviewer may have missed this section?

b) Following on from this, some kind of pre-screening, laser ablation trace element profiles ideally, would have been very useful for imaging the location and concentration of U and Th.

This is not as critical for U-Th as it would have been for U-Pb (the reviewer appears to have U-Pb in mind in making this comment.). As explained, we did do preliminary test work to determine whether to apply U-Pb vs. U-Th dating. In the end it was clear that U-Th was the best option and we obtained excellent results, reproducible by two independent labs.

c) There is no actual comparison between blind tests – why are JCU errors so much smaller?

The JCU ages are not that much smaller; rather, they are very similar and for a number of flowstones they are bigger (see table 1 for the direct comparison). Note that we have re-edited the tables so that they all appear in a similar format, which makes comparison easier.

d) Why are U ratios 234/238 and 230/232 ratios from JCU only reported in Table 1 as explained in caption – actual ratios are not shown in table. These data must be available from UoM and are available in Table 3. So what does this mean?

Table 1 is a summary table that compares results from JCU and UM. Table 2 presents the actual data from JCU (including the ratios the reviewer refers to) Table 3 presents the actual data from UM. Note that we have re-edited the tables so that they all appear in a similar format, which makes comparison easier.

e) Methods and introduction section is very light, while Hellstrom and Pickering (2015) is a recent paper, this is a review paper and there needs some reference to original papers.

See our explanation under (5), why we have chosen for a relatively light introduction to the methods section. Note that our descriptions of methods are significantly longer than in any paper that deals with dating fossils in the CoH, which is not specifically focused on method development. We made choices as to how long and how detailed we should make the descriptions. Some more literature references have been added.

f) It is more accurate to say (page 17, line 533) that the later stage of flowstone formation was dated to 478,000 +107,000/-41,000 ka than give the full range of the error. That is not actually what the errors mean.

Okay.

g) Why are the U-Th ages given as kyr before 1950 AD? They are not C-14 ages. This is not conventional with U-Th.

In Archaeology it is not uncommon to quote both U-Th and C ages in kyr before 1950 AD to facilitate easy comparison. We have chosen to follow this approach given that both techniques were used in this paper, and some of the dated flowstones are less than 10 kyr old. In addition, this approach was chosen because younger sediments also exist in other parts of the cave system, which we are dating by 14C. This will facilitate comparisons in future studies too.

3) ESR/U-Th a) This section is heavy and hard going, even for a specialist reader. It needs to be shorter, clearer and have a better introduction – even just clearly explaining what ESR is measuring and what the advantage is to combining ESR with U-series.

We have rewritten this section to better explain how the ages have been obtained, and also to explain how common model parameters for the environmental dose rate were established.

b) The final ages are presented rather confusingly – again there needs to be some final synthesis: how old does the ESR suggest the fossils are?

This has been rewritten and made much more explicit.

Reviewer #3 Minor Comments:

1) The University of Melbourne is abbreviated (by itself) to UoM, not Melbourne University (MU).

Corrected.

2) A summary table of all the ages (not age data) will help pull everything together and allow for a comparison both between the blind duplicates of the same methods and between the different methods.

Such a table was included as Figure 14.

3) The text on a number of the figures (1, 3 and 10) is very small in places and will be tiny in the final typeset paper.

All figures have been checked and corrected to make sure font sizes are of sufficient size.

4) Figure 1 has the words 'Relative height (m), cave floor' twice.

Corrected.

5) It is useful to see all the field photos of the U-Th flowstone samples but these all need proper scale bars. So does panel C of Figure 3 and all of Figure 4.

Corrected.

6) Figure 8's caption is rather confusing, a little bit more introduction.

Corrected; more explanation has been added to the text.

7) There appears to be some confusion over the caption for Figure 9: a total of three captions are given, two different ones for Figure 9 and the caption from Figure 10 as well.

Corrected.

Reviewer #4:

[…] My more detailed commentary is noted below, but I do believe there are some more major issues that need to be addressed, even if most have to do with dates not associated with the hominin-bearing Unit 3.

1) They need to provide more sufficient evidence for the "time-transgressive" nature of Unit 1. All Unit 1 ages are younger than Unit 2. Proposing that Unit 2 (and 3) is composed of reworked Unit 1 is a sedimentological hypothesis (not a geochronological result) that needs to be tested.

I think they also need to be more clear on the reworking of Unit 1 forming Units 2 and 3 and reworking of Unit 2 forming Unit 3. Is this supposed to be happening within the Dinaledi Chamber? Outside of the chamber then being transported in via the debris cone?

These are very valid concerns and we have tried to address this as follows:

A) We realise that the time-transgressive nature of Unit 1 can be somewhat confusing, more so because it includes different facies and erosional remnants that have been preserved at different topographic levels in the cave. To make things simpler to understand we have subdivided unit 1 into three facies:

- facies 1a & facies 1b which is the laminated orange mudstone found as erosional remnants along the cave floor; this unit was deposited as the combined result of mud settling in stagnant water (facies 1a) and the occasional influx of coarser material due to water flow and water pooring in from above (facies 1b), presumably during flood events (as described in Dirks et al., 2015, 2016).

- facies 1c, which is a new facies that we have introduced to explain why some Unit 1 sediments are probably older than Unit 2. Facies 1c also consists of orange laminated mudstone, similar to facies 1a, with the one important distinction that this unit accumulates on ledges and in cracks higher up in the cave and that it has been interpreted to result from mud carried in through cracks and fractures by water that slowly seeps along cave walls.

In the paper we have treated the three facies as if they are all part of the same stratigraphic unit (they have the same composition and share a high content of characteristic, orange cave mud; Dirks et al., 2015). However, this clearly causes confusion with the reviewers who question how Unit 1 sediments that appear to be younger than Unit 2 (and physically lower down in the cave stratigraphy) can possibly be incorporated in Unit 2. By defining facies 1c, we can make it explicit that this component of Unit 1 occurs as erosional remnants in fractures and on ledges throughout the cave including physical positions above Unit 2 at the entry into the Dinaledi chamber; they can therefore contribute to unit 2.

B) Note that the explanation would have probably been easier to read if the oldest unit was called Unit 1, the second oldest Unit 2 etc. However, to prevent inconsistency, we follow the Unit numbering/descriptions of Dirks et al. (2015), which were based on lithostratigraphic arguments and were done before any geochronological constraints were available.

C) The text and figures been reworked to reflect the above changes

D) Extra sections have been added as Figure 2, to further illustrate some of the complex stratigraphic relationships that exist in the cave.

2) In the original Dirks et al. (2015) paper, they note that their flowstone samples were unsuitable for dating, yet now they have all sorts of dates on the flowstones. What changed?

At the time of submission of the Dirks et al. (2015) paper, it was assumed (based on the descriptions of the fossils) that the deposit was older then the limit of c. 500 ka for U/Th disequilibrium dating. Therefore, preliminary work was carried out to assess the possibility of U-Pb dating, which allows dating of much older flowstone material. This did not look hopeful because of the presence of detrital material (and therefore abundant common Pb, which interferes with the signal) in most flowstones, as mentioned in Dirks et al. (2015). However, subsequent preliminary U/Th disequilibrium dating, which is much less critically affected by detrital material than U-Pb dating (because use is made of U and Th ratios and not Pb directly) revealed a much younger age range than originally anticipated, mostly well within the range of U/Th disequilibrium dating. Since this method is both more robust and more precise in the >500 ka range than U-Pb dating, no further U-Pb dating efforts were made.

We have now expanded the section in which we explain our dating approach and this has been made clear.

This reassignment of Unit 2 sediments to Unit 3 is not simply based on induration as is now more clearly stated in the text and discussed at length in the discussion under the heading “An updated stratigraphy for the Dinaledi Chamber”. We open the discussion by stating: “The ages presented here help to resolve outstanding questions about the stratigraphy in the Dinaledi Chamber, and allow us to define more closely the distribution of correlative stratigraphic units (Figure 13).” In other words, the reassignment of lithological units to their appropriate chronostratigraphic position was firstly based on the new age results.

It is normal practice in stratigraphy to re-define units based on chronostratigraphic constraints once these constraints have been obtained. We have obtained new ages that have allowed us to refine the lithostratigraphy presented in Dirks et al (2015) into a more precise subdivision of Units 2 and 3 as presented here.

3) The reassignment of material from under Flowstones 1c-e from Unit 2 to Unit 3 is one of the most important components of this paper. Without it, the majority of their age/depositional models fall apart. This needs to be addressed much more thoroughly, perhaps with additional sedimentological analyses. Simply that it is less indurated is not sufficiently convincing.

We also clearly state in the discussion section that: “However, the geochronology results now permit a better evaluation of the stratigraphy in the chamber, and it is evident that Unit 2 represents a significantly older stratigraphic unit that is restricted to deposits directly below Flowstone 1a, but not to those below Flowstones 1b-e. Flowstone 1c returns an age of ~242 ka (Table 1), indicating that the Unit 3 sediments below Flowstones 1b-e are probably significantly younger than sediments below Flowstones 1a (Figure 14). In addition, these sediments are less indurated and less weathered than the sediments below Flowstone 1a, and they contain H. naledi material (Dirks et al., 2015).”

In other words, unit 2 is not simply redefined on the basis of induration, but more importantly on the basis of new chronology and the observed absence of hominin bone material. We appreciate this comment and have explained all of this in greater detail, because it is of great importance to the paper.

Also need some sort of explanation as why the description of the fossil from Flowstone 1A (Unit 2) went from hominin (Dirks et al., 2015), to not. It seems like interpretations are being changed to fit the dates as opposed to being based on the primary evidence/material (sedimentology, fossils) themselves.

Nowhere in the text of Dirks et al (2015) was it stated that the fossil material below flowstone 1a was hominin even though Figure 3 in Dirks et al. (2015) has caused confusion because it shows a bone with the caption assigning all bones to Hominin, including a bone drawn under flowstone 1a. The assignment of the bone as hominin in this cartoon figure was unintentional (a mistake), and we are grateful to the reviewer to point this out to us. However, the relevant text on the matter from Dirks et al., 2015, does not make any claims that the bones below 1a are hominin, but instead they:

- differentiate between the deposits below 1a and those below 1b-e and indicate that bones weather out from the non-indurated parts of unit 2 below flowstones 1b-e

- never state that hominin bones occur in the consolidated Unit 2 sediments below Flowstone 1a. In all honesty, caves are really difficult to work in, and we admit that we did not get everything right the first time and did make several mistakes. We recognize that this caused some confusion by originally assigning all facies 2 sediments below Flowstones 1a-e to the same stratigraphic unit (Unit 2), and by making the mistake in Figure 3 in Dirks et al (2015). However, we are now trying to clear this up by more accurately differentiating between the indurated sediments below the older flowstone 1a (Unit 2) and the less indurated hominin- bearing sediments below the younger flowstones (Unit 3).

4) Several critical errors in table 1 (or the text) need to be fixed (see details below). The most important one is that sample RS18 is said to overly Unit 3 (hominin-bearing) in the text, but Unit 2 in the Table. This is a key date they use for anchoring the hominin fossils. Wondering if the change wasn't made in the table because they altered their unit assignments only after the dates were produced.

The reviewer is correct in assuming that we altered the unit assignment after the dates came in as is usual in the stratigraphic allocations of sediments to units when chronostratigraphic constraints are acquired (as explained above). The real reason for the mix-up, however, is that an older version of the table was sent in by accident. The table has now been corrected and the text and figures are mutually consistent.

5) Tables 27 need substantial revisions. I know the work was done in different labs, but that doesn't mean the tables should be completely different. They need to be totally reformatted to match each other so that comparisons can be made between the two labs. As is, they have different fields, different units, etc.

This has now been done.

6) The final age determination of the hominin fossils of 200-300 ka is not sufficiently explained. If based on ESR dates, then they need to more fully explain/justify why settled on 200-300 ka specifically as opposed to the ESR range of ~150-425 Ma? This appears to favor results of UW1810 and results from SCU/UOW (vs. GU/ANU). This seems rather arbitrary when in fact it is something that could be either modeled or calculated statistically. If it is just based off the younger age peak of 1767 (~200ka) and the older peaks of 1788 and 1810 (~275ka) in Figure 9, they should specifically state (and reference Figure 9).

Good points, part of the problem with the paper was that the ESR results from the two labs, which are central to the age estimates for the fossils, had not been standardized; i.e. the two labs were using different model assumptions in calculating their ESR ages (i.e. their environmental dose rates). We have now standardized the modelling approach for ESR with fixed model parameters that have been varied these parameters between two scenarios to derive minimum and maximum age estimates. As a result the ESR results have been presented more clearly, ages and age ranges have now been better and more consistently constrained, and objective and transparent criteria (based on reported age ranges) have been applied consistently throughout the text and figures. We believe that has addressed the problems raised by the reviewer.

Also, the yellow box in figure 14 is not 200-300 ka, but more like 200-340 ka. Need to be consistent between text and figures. This is one of their main conclusions, yet not specifically supported.

This has been done and this figure has been completely redrawn.

Reviewer #4 Minor Comments:

- Line 88: Other papers format as refer to U.W. 101, not UW101. Change for consistency.

Done.

- Line 90: Lesedi Chamber papers says "some of which (facies and stratigraphic units) correlate to facies in the Dinaledi Chamber". Does not imply "sedimentologically distinct" as stated here.

The fact that facies and units may correlate or look the same does not mean that the Dinaledi Chamber cannot be sedimentaologically distinct. For instance, certain types of rock, such as the orange mudstone will form in standing water in isolated pools within a cave chamber. Each pool may form very similar looking deposits, because the muds are largely derived from the insoluble product of dolomite dissolution during cave formation. So the units look similar and may even have formed at the same time. However, the cave chamber in which they formed may have been completely isolated. In this case isolation refers to the fact that the component of externally derived sediment contributing to the total sediment load is relatively small.

- Lines 83 and 92: COH or CoH. Pick one.

Done.

- Line 167+: What specifically is used to correlate/group these discontinuous flowstone units across the chamber. You mention appearance is included (line 153), but no appearance is described. It seems that Group 2 is really just a group because it is not Group 1 or 3.

We have tried to explain this a bit better; but in the end you are right, FG2 is everything that is not 1 or 3.

- Line 194: Should be noted that in Dirks et al. (2015) Figure 3 the fossil below Flowstone 1a is attributed to hominin. What changed the identification?

Accepted, a mistake was made in the figure in Dirks et al. (2015), but not in the text; see explanation above.

- Line 200: How can Unit 2 sediments be derived both from local erosion/reworking of Unit 1 and as a debris cone below a vertical fracture system? They can't be both autochtonous and allochthnous in relation to the chamber. I believe this needs to be clarified. Are the Unit 1 clasts derived from Unit 1 equivalents outside the chamber?

Valid concern and we have addressed this; see our detailed explanation above. We have changed the text to address this important issue by introducing facies 1c in Unit 1.

- Line 213/218. This also goes for Unit 3. Is the Unit 3 material derived from reworked Unit 1 and 2 material outside the chamber, and brought in via the debris fracture/debris cone? Please clarify.

As before, this has now been addressed.

- Line 202: Why is there no mention of the baboon tooth in Unit 2 here?

This has now been included.

- Lines 203-260: This description doesn't seem to jive with what is depicted in Figure 7. The top cartoon should be more of a debris cone without a thick and even deposit running along the floor of the cave. Only AFTER the debris cone collapsed/eroded would Unit 2 material have spread/deposited along (evenly?) across the floor of the cavern. As currently depicted, if the debris cone in the top cartoon eroded, then the thickness of Unit 2 should be much, much thicker (not thinner) or you have to explain where all that collapse/eroded material went in the cavern (down the drains?).

We have explained in the text in several places that the debris cone is eroded from below as material is moved down the drains; as this material is removed from below, the debris cone slumps inwards. We have further addressed this issue, which is a totally valid criticism, by referring to all the floor sediments as Unit 3 (as was originally done in Dirks et al., 2015), and by dividing Unit 3 into a lower (hominin free) and upper (hominin-bearing) member. The reason for changing this back to Dirks et al. (2015) is that all floor sediments are probably significantly younger than the Debris cone and are probably better grouped with Unit 3 than with Unit 2.

Unit 2 near the entrance is >780 ka old (from paleomag), and started eroding after formation of Flowstone 1a came to an end, which could be as late as 437 ka 9the lower age limit of Flowstone 1a). It is this erosional process of the debris cone, probably driven by sediment moving down the drain that causes the material to spread out along the floor.

We have updated the text and figures to reflect this better.

- Line 211: It would be helpful to rephrase this sentence a bit to note how Unit 3 is differentiated from Unit 2. As is, they sound the exact same except for lithified (Unit 2) vs unlithified (Unit 3). Is that the only difference? Is that sufficient to re-assign the material below FS1c from Unit 2 to 3?

As explained above. We come back to this issue extensively within the discussion section, but we have now clarified the issue up front as well by adding to the definition of Unit 2 as follows:

“however, the revised definition of Unit 2 accounts for the much more indurated nature and distinctively darker colour associated with deposits under Flowstone 1a, as well as the absence of hominin fossils, and the new geochronological constraints presented below”.

- Line 218: Along with Figure 7, is the interpretation then that the hominin remains were brought in along with the sediments from outside the chamber and deposited as part of the debris cone? Please clarify.

This issue has been discussed (and clarified) at length in Dirks et al. (2015), and a reference to this should suffice, as it is immaterial to the core aims of this paper. However, we do explain that fossils came in through the same entry route as the sediments that contributed to the debris cone as shown in Figure 8.

- Line 246: With other macro-fossils now identified in Unit 2, what are the implications for chamber accessibility in the past? (Especially as there is little Unit 2 exposed, but it has fossils.)

No difference to earlier interpretations; see Dirks et al., 2016 for a more extensive discussion of this. Again, this is an interesting issue, but not the subject of this paper.

- Line 260-263. Need to provide some supporting evidence that Unit 1 was deposited during/after Unit 2 through modern times. Similarly, need to provide evidence that Unit 2 sediments are older than most of the Unit 1 deposits presently observed (no dating results presented at this point). What precludes it from being older? The only evidence provided (reworked into Unit 2) is the only concrete evidence provide for the sequence of the two units (and indicates older).

Hopefully we have explained things more clearly by introducing facies 1c with an extended explanation of the stratigraphy in the chamber, and our sampling strategy. Of course, the data presented as part of this study will provide the age constraints that the reviewer is asking for here.

- Line 294: Should include or refer to a Figure 2 photo(?) showing FS2 directly overlying U3 and hominin fossils.

Okay.

- Line 297: "fossils entered" suggests they walked in along with the deposition as opposed to being deposited/reworked along with Unit 3. Perhaps better to say they were deposited or transported.

We disagree with this. “Entered” is an interpretation neutral term and can mean many different things. We intended it to be that way because Dirks et al., 2015 suggest that the fossils may have been carried in, dumped in or even walked in. Dirks et al., 2015 excluded the possibility that the fossils were transported in based on good sedimentological evidence, and nothing we have seen since has given us any reason to believe differently.

- Line 317: Dirks et al. (2015) noted that flowstone samples included a detrital component derived from associated muds in all tested pilot samples which confounded U-Pb dating because of the high and isotopically variable background of common Pb it carries. But now they are apparently all suitable? Need an explanation as to why they were undatable in the last publication, but are now magically all datable.

See our explanation under point 2 above. We have also expanded the text to make this more clear.

- Line 332: Text says RS5 sample is from FS1, Table 1 says FS2. Which is it?

It is FS1; this has now been updated.

- Line 337+: Text uses Units, Table 1 uses Facies and they are not comparable! JCU/RS18 overlies Unit 3 (text) or Facies 2b (table)? This perhaps the most critical date as they argue it as the minimum for the fossils, but there is an error either in the text or the table.

This has been corrected.

- Line 368: Should state what the teeth are (e.g., upper premolar of H. naledi) either here or where each sample is discussed shortly later. Not just refer to figures that don't contain the information either (e.g., Figures 5, 8). Shouldn't have to wait until materials section at the end to get some basic information.

This has been corrected.

- Line 375: Why are Tables 6 & 7 presented before Tables 4 & 5 (line 444)? Need to reorder.

This has been corrected.

- Line 379: Needs a brief explanation/justification as to why U-Th ages should be regarded as minimum.

Explanations have been included, and a much longer section on how to evaluate the different dating techniques has been added to the discussion.

- Line 426: There is no data on Sample 1841 in Table 7.

This has been corrected.

- Lines 427-435. Why are Sample 1767 and 1810 (and the age of Naledi in relation to it) being discussed under Sample 1841? This should have a different header.

This has been corrected.

- Line 493: Should provide radial plots for the samples for evaluation/visualization of the data.

We don’t have these data.

- Lines 507-511: Even if one agrees with the time-transgressive argument of Unit 1 (and that's a big if), these are the ages you have at the moment. Similarly, they still need to be reconciled with the flowstone ages that cover them, which is brushed aside here.

Valid point, we have rewritten the text to address this in more detail.

- Line 572/573: This totally ignores the results of RS23 from the BASE of FS1a which has a date of 683-449 Ka and is not compatible with the pmag of older than 780ka. The authors focus on the top sample RS22 as it fits their pmag, but seem to selectively ignore the data that doesn't fit. This was not discussed in the paleomag section and it is totally omitted here.

No, this is a misunderstanding, we actually did say that the dating sample corresponds to the mid-point (i.e. Phase B) in the Paleomag sample (the various layers in the flowstone taper out laterally). In the description of the palaeomagnetic sample we say towards the end of the description: “Phase B and Phase C flowstone correlate with samples RS22 and RS23 that were collected for U-Th dating.” We have rewritten the text and figures to make this clearer and say this earlier. We have also added a new Figure 2 to show these relationships more clearly.

If RS23 is not from the base, or is from higher up and in the Normal section of FS1a, then that needs to be properly documented here. In Figure 13 they state RS23 as "mid", but in Table 1 it is "base" and in the description of the sample (Line 912) and Figure 2l it is at the base.

It was not intended to be confusing, but I can see it is. The paleomag sample was taken at a different spot from the U-Th sample and further back (i.e. closer to drip point source – see our new Figure 2a) along flowstone 1a. The lower unit A measured in the paleomag analysis tapers out along the dip direction of the flowstone (as can be seen in Fig. 13), whilst units B and C continue. Thus, the base of flowstone 1a where the sample for U-Th dating was taken corresponds to the mid-section of flowstone 1a in the place where the paleomag sample was taken. We have now changed the text to better explain this.

- Lines 568-595: It seems like the determination to reallocate the sediments associated to Flowstones 1c-e from Unit 2 to Unit 2 was based more on the geochronology results than sedimentological analysis. Different levels of induration could be the result of other processes besides being different depositional units. It seems like they are changing their interpretation post-hoc to fit their new ages rather than based on the actual sedimentology.

As explained above.

- Lines 604-607: Their argument for Unit 1 to be time-transgressive is not very convincing. All 3 of their samples from 2 different parts of the cave say Unit 1 is younger than Unit 2. It doesn't match their interpretation of Unit 2 being reworked material Unit 1 so they propose that it is time-transgressive, yet they provide no data to support this. Seems that this hypothesis could be tested by additional sampling to find pieces of reworked Unit 1 in Unit 2 (or 3) that are suitable for OSL analysis. If dramatically older, then I'd believe their conclusion. If not, then they need to seriously re-evaluate their current ages of either Unit 1 or Unit 2.

No, we clearly state that the fragments of Unit 1-like mudstone were derived from an earlier deposit of laminated orange mudstone that was similar in composition to the Unit 1 sediments; i.e. we acknowledge that earlier deposits of Unit 1 like material must have been present in the cave, and have contributed to the accumulation of Unit 2. In other words we know that the ages for Unit 1 as currently preserved in the cave are younger that the ages of Unit 2, and we also know that there are other deposits of unit-1 like material higher in the cave that may be the source for the fragments in Unit 2, and that we have not been able to test in this study (please note that the fractures in which these sediments occur are extremely hard to access). We have now made this more explicit in the text and we have added facies 1c to specifically reflect these remanants of Unit 1 higher in the cave. The new Figure 2a, hopefully also helps in explaining this better.

Regarding the hypothesis testing, we have established that Unit 2 is older than 780 ka. It would be impossible to sample Unit 1-like fragments that are incorporated in Unit 2 for OSL analysis; these fragments are much too small for that.

- Line 640/641: Again, Table 1 says RS18 overlies Facies 2b (=Unit2?), not Unit 3. Perhaps it was Unit 2 until they decided to change it Unit 3 because of the age (i.e., changing based on age, not sedimentology).

Corrected. Also, getting an age to establish stratigraphy is a normal process in stratigraphy.

- Lines 644-647: This is confusing sediment age with depositional age. Reworking sediment doesn't change the age of the sediment, it simply reflects a different period of deposition. It would be more appropriate to say that Unit 3 is a reworked unit and that different deposits of it in the chamber may have been deposited at different times. However, it is also worth noting that although H. naledi may have been deposited over an extended period of time, they also may not have. There is not sufficient evidence presented to say one way or the other.

We have presented the arguments why we think H. naledi may have been deposited over a period of time, but we have not expressed an absolute view on this and I think we are very careful in our wording regarding this; I think this is clear in the text where we state: “Staining patterns on bone fragments, skeletal element representation, and the fact that bones can be seen to weather out from erosional remnants of Unit 3, indicate that part of the fossil assemblage has been reworked. The presence of well-articulated remains in the excavation pit, away from the chamber entrance, indicates that some of the remains entered the cave intact. The mixed taphonomic signature suggests that fossils entered the cave over a period of time, which is minimally assumed to be during deposition of Unit 3, and before deposition of Flowstone 1c. Fossil entry may have continued as sediment accumulations of Unit 3 near the entry shaft were reworked and redistributed along the cave floor (Figure 7).”

- Line 657: This is cherry picking the U-Th tooth data as it is only 1 (the oldest) of 14 results. Should just stick to the ESR data.

No this is not cherry-picking, but is a function of how the combined U-Th-ESR technique operates. Note that the U-Th ages in the teeth reflect U-uptake events (which are an integral part that dictates the models applied for the ESR dating); they do not reflect a true age for the teeth, but provide an estimate for the minimum age.

Various uptake events can, and are likely to overprint each other, so therefore we look for the oldest uptake event we can find in the teeth, which in this case is the 200 ka event. It just so happens that we have found one spot in the teeth that records this old age reflecting early U-uptake; this age will, therefore, set a likely minimum age for the fossils (compare this to detrital zircon ages where the youngest zircon age will be closest to the actual depositional age of the sediment even if older grains are far more numerous!).

- Line 719: Why 200-300 ka? If based on ESR dates, then need to explain/justify why settled on 200- 300 ka specifically as opposed to the ESR range of ~150-425 Ma? This appears to favor results of UW1810 and results from SCU/UOW (vs. GU/ANU). This seems rather arbitrary when in fact it is something that could be either modeled or calculated statistically. If it is just based of the younger age peak of 1767 (~200ka) and the older peaks of 1788 and 1810 (~275ka) in Figure 9. Then should specifically state (and reference Figure 9).

See our explanations for this above. This has been extensively reworded.

Also, the yellow box in Figure 13 is not 200-300 ka, but more like 200-340 ka. Need to be consistent between text and figures. This is one of their main conclusions, yet not specifically supported.

This has been rewritten and corrected.

- Lines 729+: Appreciate the detailed materials and methods.

- Figure 1. Why not use the update surface map from the Elliot et al. submission that also includes the location of domal stromatolites, chert markers and mylonite markers? Should at least use consistent maps between papers.

Done.

- Figure 12B: I'm assuming that this wasn't actually analyzed as Phase A and B are only a cm thick yet samples were 2-2.5cm cores.

You can see from 12A that there is sufficient material for analysis. 12B is an off-cut for the close-up photo.

- Table 1: It would be helpful to sort the table by flowstone group (or possible age), not HW sample number to compare proposed clusters of flowstone ages easier. Blind duplicates of the same sample or base/top of the same flow shouldn't be rows apart. Also, text only refers to Units, table refers to Facies, and they are not comparable! Why are RS10 and RS5 listed if there is not data? Should delete (similar to no HW to pair with RS1).

Table has been cleaned up.

Text says RS5 sample is from FS1, Table 1 says FS2. Which is it?

Corrected.

Text says RS18 overlies Unit 3, Table says RS18 overlies Facies 2b (=Unit2?). Which is it?

Corrected.

- Tables 2 & 3: Need to be formatted exactly the same (same fields, units, etc.) for a proper comparison.

Corrected.

Data for RS1 is missing from Table 3. As it is a blind duplicate it needs to be included so the blind comparison can be compared.

The blind duplicate was only done in the lab external to JCU (so that we could check the results from that lab). Because this is a double blind, the results from the external lab at UoM serve as a check on the JCU results.

Sorry, but the different formatting of Figures 27 is sloppy.

Corrected.

- Tables 4 & 5. Again, why are these tables formatted differently and with different information.

Corrected.

Also, why are they presented before Tables 5 & 6, but discussed/referenced after them in the text?

As explained above.

- Tables 6 & 7. Again, why are these tables formatted differently and with different information?

As explained above.

- Table 6 is 4 tables, not 1. What do * represent? Needs to be explained.

Corrected.

- Table 7: Missing data for Sample 1841.

Corrected.

Reviewer #5:

[…] Dating that places these specimens at 200-300 ka suggests several scenarios.

1) The dating is correct. H. naledi originated at some unknown time, perhaps 1-3 Ma, and survived until the Middle Pleistocene, in a similar fashion to the proposed survival of H. floriensis. Note that H. floriensis was isolated from other species; H. naledi would have co-existed with possibly several other species of hominins. In itself, that is plausible; we are learning that the existence of a single hominin species is quite recent. However, this hypothesis conflicts with the evolutionary assumption that more primitive species cannot compete with more advanced, and thus to be convincing it would need to be bolstered by some evidence of an advantage that compensated for primitive features or an analysis that these features were irrelevant.

Interesting, but this comment is better referred to the Berger et al paper.

2) The dating is correct but the fossils are reworked from some other deposit. This hypothesis has been rejected on the grounds that there is no known entrance into the cave other than the one found by this group. It is further challenged by the sheer number of finds; survival of so many pieces is more plausible over 300 ka than 1 Ma.

Note that this argument has been principally rejected based on sedimentological grounds; there is no evidence of (a large amount of) coarse-grained material being transported into the chamber from outside! This is made clear in the text.

3) The dating has been done with great precision and care, but there is a factor of which the analysts were unaware, or perhaps that could not be measured.

Reviewing a 96-page manuscript means that the reviewer must concentrate on a portion of it. Of the various dating methods used, only the combined ESR-U series method deals specifically with the fossil ages. It seems reasonable therefore to focus on the details of this method in commenting on the manuscript.

Let us consider the scenarios in reverse order. By definition, something that cannot be measured cannot play a role in calculations. Of the known factors, the only possible problem with the dating lies in the evaluation of the external dose rate. The cave has experienced significant transformations over time. The external dose rate is as much as 80-90% of the total dose rate for the hominin teeth. The text notes that sediment radioisotope contents are in Table 8; that table lists sediments from Unit 1 for OSL, not Unit 3.

OSL was done on different sediments (Unit 1) compared to the sediments in which the teeth were embedded (Unit 3); this is clearly explained in the text. The average U, Th, K values of Unit 3 are listed in Table 4.

A reference is made to 'average' sediment values; it would be of interest to say how many samples were used.

This is explained in the methodology section and shown in Figure 10.

Also, the values for Unit 2 are very similar to those for Unit 3, reinforcing the suggestion (p. 8, line 213) that Unit 3 reflects reworking of Unit 2. On the whole, there seems little leeway for significant changes in external dose rate.

The reviewer is correct that there is little leeway. However we have significantly expanded on this section and have done additional modelling to make sure we fully understand the issues associated with the external dose rates (see the detailed updates in this regard in the results and methodology sections, and the introduction of maximum and minimum age scenarios).

What about reworking? To say that 'there is no evidence that the present entrance has significantly changed' is not the same as saying that there is evidence it could not possible have changed, the latter being an unreasonable standard, of course. Internal reworking – where the fossils were originally deposited in a thicker Unit 2 and eroded onto a deflational surface in what is now Unit 3 – would not be likely to change the age, at least not from 200 ka to 1 Ma, since as noted in the preceding paragraph the enclosing sediment remains essentially the same.

Exactly.

That leaves the first scenario, which is one that is not dealt with in this manuscript. It will be interesting to see what sorts of interpretation are made along that line.

This however has been dealt with in the accompanying Berger et al paper. We have now included some of the main conclusions from that paper in this paper as well in response to some of the other review comments.

Therefore this manuscript needs only minor revision. The authors should explain more fully the number and locations of sediment samples, preferably adding yet one more table instead of referring to Table 8 (p. 38, line 1203).

With the rewrite of the ESR section this has been done.

Reviewer #5 Minor Comments:

Page 15, line 447: 'did' should be 'was'. Page 41, line 1296: 'enable one to differentiate'.

As noted in the review, the authors have not submitted sediment data for ESR dating that indicates how many sediment samples were used for each sample and where they came from.

Corrected; this has been made clearer.

[Further revisions were requested before acceptance.]

In making further revisions to the manuscript we have reverted back to a more detailed description of Facies and Units that allows us to better address the concerns raised by the reviewers. Initially we had tried to keep things relatively simple by omitting detail on facies and Unit descriptions, but that results in over-simplification as correctly pointed out by the reviewers. We have explained our corrections in more detail below.

In addition, there was discussion among the reviewers during the consultation process concerning the last line of the Abstract and the penultimate paragraph of the Discussion (that begins on line 1009), which were viewed as unnecessarily critical of prior authors' work and of the challenges in accurately dating hominin fossils.

We have changed the wording to appear less critical.

In addition, at the end of the Abstract, it may be better to simply state that "These dating results indicate a much younger age for the H. naledi fossils than have previously been hypothesized based on their morphology."

This has been done.

Technical Points:

1) Lines 175-178: The addition is appreciated, but a sentence at least on how the material "accumulated inside fractures and along ledges" needs to be added. I would also drop the last sentence in this paragraph and move it to the discussion of Unit 1 (out of place here).

We have followed both recommendations; this has now been done.

2) As a result of the revised units and stratigraphy (esp. "facies 1c" and "informal upper and lower members of Unit 3), the authors have now introduced inappropriate and inconsistent terminology. This is not just an issue of semantics.

Lines 217-229: The introduction of facies 1c is problematic, not as a subunit in general, but as a subfacies in particular. The confusion and misuse of facies happens often and here is a chance to correct it. Quoting Maill (facies guru), in sedimentology, "lithofacies are defined on the basis of its distinctive lithologic features, including composition, grain size, bedding characteristics, and sedimentary structures. Each lithofacies represents an individual depositional event. Lithofacies may be grouped into lithofacies associations or assemblages, which are characteristic of particular depositional environments". Thus, the basis of different subfacies here based on "relative topographic position in the cave" (i.e., facies 1c) is not valid criteria. Specifically, facies 1a is fine (non-lithified, horizontally laminated, orange mud). Facies 1b is fine (laminated mud with fine sand and rodent remains) and distinct from 1a. Facies 1c is "similar in appearance and composition to the laminated, muddy sediments of facies 1a, but they occur "in different places". This is not a properly differentiated as a separate facies. Facies 1a in a different location in the cave topography is still facies 1a unless it can be differentiated appropriately. There are many examples in sed/strat where the same/similar facies are repeated multiple/different times in a succession. This is again an issue at the end of the paragraph where the facies differ in "relative age and position within the cave chamber", which is not a characteristic of facies. Facies 1c needs to be differentiated from 1a on the basis of composition, grain size, bedding, or sedimentary structures to be valid.

We have retained Facies 3c, but we have expanded the descriptions of the different facies and we have included bed-form characteristics that clearly differentiate Facies 1c from Facies 1a and 1b. We now state: “Deposits of Facies 1c are similar in composition to the laminated, muddy sediments of Facies 1a, but they are distinguished from Facies 1a by having non-horizontal (including subvertical) laminations with limited lateral continuity and curved surfaces. Sediment of Facies 1c is consistently observed along chert ledges, and in solution pockets and fractures in the Dinaledi Chamber, and are interpreted to have originated as localised accumulations of muddy material that entered the chamber through thin (mm-scale) fracture networks. The mud is mostly the product of the cave formation process, representing the insoluble residue left over when cavities develop via dissolution in dolomite (Dirks et al., 2015).”

Lines 270-276: Unit 1 is divided (incorrectly) into 3 subfacies. Unit 3 is divided into 2 informal members. This inconsistency is confusing and unnecessary. Also, members are formal lithostratigraphic units of formations. It is OK to provisionally have informal members, but this is almost always in the context of a sequence where there are other formal members (as part of a formation), which this sequence does not have, nor is it part of a defined formation. For example, you could have formal Members A, B, C, D and then informal members E and F, but randomly throwing in informal members into this context is exceptionally odd. Ironically, the authors could subdivide Unit 3 into facies 3a and 3b as the presence/absence of fossils is a characteristic that can be used to differentiate facies. Also, what happens if they do ultimately find H. naledi fossils in the "lower member"? Something that would easily fix all of this is if they just used informal sub-units for all (e.g., 1a, 1b, 1c, 2, 3a, 3b), that way they can be consistent and define them as they wish as units have no formal definition while facies and member do. The fact that all of the sedimentary material in the cave appears to multiple phases of reworking the same material over and over suggests everything is genetically related and easily dealt with as a series of related units.

We think it is better not to introduce Facies 3A and 3B for the reasons mentioned by the reviewer: there is a possibility in future that naledi material could be discovered in the Unit 3 sediment, which now appear devoid of fossils. We have now done the following:

  • As explained above we have retained Facies 1A, 1B and 1C,

  • We have removed all reference to members, and instead have called the upper and lower part of Unit 3, sub-unit 3a and sub-unit 3b as suggested by the reviewers.

  • Likewise, we have introduced two sub-units to describe Unit 1 sediments along the cave floor.

  • We have made it clear that Facies 1c sediment, which accumulates along ledges and in cavities along the cave walls and along the entry zone, could have been part of a further sub-unit of Unit 1, which we hypothesize, may have existed in the cave.

  • We have changed the text and figures throughout to be consistent with these new subdivisions.

  • We have been very careful in our wording not to be too definitive about the provenance of Facies 1c material that may have ended up in Unit 2.

Lines 304-315 (and elsewhere): Again, until other ages are generated for facies 1c subfacies or its stratigraphic relationship/contacts with other units can be observed/demonstrated, the time-transgressive explanation for Unit 1, and the relationship between Units 1 and 2 are just a hypothesis. Similarly, their assertion that facies 1c (as opposed to 1a or 1b) must have been the unit that provided the source material to Unit 2 (now 3?) is not confirmed by evidence and, again, is just a hypothesis. The authors are very definitive about their interpretation: "it is clear that older laminated orange mud deposits ascribed to facies 1c in Unit 1 occurred above Unit 2 and must have provided the source material now found as much clasts within Unit 2". As there are no dates for facies 1c, and as facies 1c is lithologically the same as 1a, this is a hypothesis, not an unquestionable fact. I have no problem if this is presented as a hypothesis: it might even be likely, but it is not definitive and I think the authors need to back away from such a claim.

This wording has been changed to reflect that this is an interpretation and not definite.

The authors note the challenges of OSL dating these deposits, yet rely almost exclusively on the OSL ages for a "young" facies 1a/b argument. An alternative explanation is that Unit 1a/b is older than Unit 2 and the OSL dates are incorrect (aliquots as opposed to single grain). Or perhaps the 1a looking material was brought into the chamber from elsewhere where similar depositional environments also produced laminated orange mud. This all needs to be demonstrated or proposed as a hypothesis (which can be tested by more/future dating even if far down the line).

Point taken and the wording has been changed as explained above.

3) Somewhere, the authors should to be more specific of the possible age of H. naledi from this chamber, versus the best fit age of H. naledi specimens dated here. For example, flowstone group 1c does provide a minimum age for the specimen that is stuck underneath it, and the ESR ages do provide a maximum age for the 2 teeth. The authors suggest that the fossils entered the cave over a period of time and may have continued during the deposition of upper Unit 3 (lines 299-303). As such, I have no problem with the authors saying those 3 particular fossils have a best fit of 236-335 ka, but does anything preclude the other hominid specimens from being associated with older or younger parts of upper unit 3 with the potential to span approximately 90ka (min of above RS1/15 above U3) to 414 ka (max of OSL5)? At minimum, a red dashed vertical line should be added to Figure 14 at ~414 ka for the oldest possible age to match the minimum line at ~100 ka.

In the abstract and in various parts of the text we explain that we have ages that constrain the fossil-bearing unit (sub-unit 3b in our new terminology), that we have ages for 3 fossil teeth themselves, which provide a tighter age constraint and that within our preferred age range for the fossils we think that the maximum age model is most likely considering the high degree of Rn loss in the sediments. In other words, we are quite specific on how we think the results should be interpreted, and in doing so we closely followed recommendations made by the reviewers during the earlier review round. To address the above comment we have adjusted the text, and we have added further detail to Figure 14, following the recommendation made.

4) Line 465: This sentence is confusing as presently constructed. It seems to report that something is both younger than unit 1 and older than unit 1. It would be better to write "younger than ages derived from facies 1a, but slightly older than ages derived from facies 1b in this location."

Corrected.

5) The U-Th ages must be quoted as just ka, using kyr BP is a radiocarbon convention and does not apply to U-Th - there is no industrial carbon adjustment to U-Th ages, so to quote them as kyr BP is misleading and incorrect.

Reference to kyr BP has been removed from the text.

6) In Table 4, "Dose" should be "De" to prevent confusion with subsequent discussion of artificial doses given to samples. Thicknesses are μm, not mm and according to the table, 100 μm was removed from the dentine and the sediment, not enamel and dentine, due to misplaced headers. The removal from dentine was not mentioned in the methods section.

Mistakes in this table have been corrected. No material was removed from sediment; this line was mistakenly duplicated in the table.

7) There was no dentine on the baboon tooth (line 618) but would a modern analogue suggest that there should have been dentine on at least the inside? It probably doesn't matter since the dentine survival time would be a relatively small portion of the entire burial time, but the authors might comment on this.

We don’t know; there is no visible evidence for dentine, and any statement on this would be a guess that cannot be easily tested. Also a small amount of dentine if it had existed would make little difference regarding the result. We prefer not to speculate here.

8) Figure 8: With the addition of another unit, it is very challenging to differentiate the little sliver of Unit 2 (below Flowstone 1a) and Unit 3 upper because of the similarity in color, especially in the upper panel. It would be helpful to address this. Also, given the revisions, what now is the explanation/model for the deposition of Unit 2? Virtually all of Unit 2 is now assigned to lower Unit 3. In the previous submission, Unit 2 was under the flowstone and underneath the hominid fossils on the cave floor. Now it is stuck up under the uppermost flowstone and nowhere modeled to be anywhere on the cave floor, just completely washed away(?). While the authors do touch upon this in the text, they should consider adding back in a revised panel to explain Unit 2 a bit better.

We have revised Figure 8 to reflect this. The issue of reworking is explained in quite a bit of detail in the text as well.

[Further revisions were requested before acceptance.]

[…] Perhaps one of the major continuing complications and challenges in these revisions is the effort to maintain consistency with the earlier descriptions in the Dirks et al. 2015 paper. Simply stated, the reviewers feel strongly that the use of facies as units in Dirks et al. 2015 was incorrect; updated stratigraphy needs to be used in the present paper alongside a simple, clear statement of change from the original interpretations. Editorially, we agree that the present paper should standalone and use the most up-to-date, appropriate descriptions and approach. Doing otherwise is introducing complication and would be perpetuating confusion.

In making further changes to the manuscript we have referred directly to the detailed recommendations made by reviewer 4 in review round two. This means that we have now exactly followed the reviewer suggestions to abandon the use of facies and refer to all the stratigraphic entities as informal units and subunits. We have only retained mention of facies where we make direct reference to Dirks et al., 2015, and such references have been made explicit. Otherwise we have used Units 1, 2 3 and sub-units 1a, 1b, 1c and 3a, 3b throughout, as recommended. The distribution of these sub-units is illustrated in Figure 2. These changes mainly affect the section on ‘lithologic and stratigraphic context for dating’, which has been updated. The changes will make it much easier for people to read and understand.

As a point of correction, Dirks et al (2015) do not use facies as units. However, in response to reviewer 4, all of the previous concerns raised with respect the use of facies, units and sub-units have now been addressed.

https://doi.org/10.7554/eLife.24231.028

Article and author information

Author details

  1. Paul HGM Dirks

    1. Department of Geoscience, James Cook University, Townsville, Australia
    2. Evolutionary Studies Institute and the National Centre for Excellence in PalaeoSciences, University of the Witwatersrand, Wits, South Africa
    Contribution
    PHGMD, Conceptualization, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing—original draft, Project administration, Writing—review and editing
    For correspondence
    1. paul.dirks@jcu.edu.au
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon 0000-0002-1582-1405
  2. Eric M Roberts

    1. Department of Geoscience, James Cook University, Townsville, Australia
    2. Evolutionary Studies Institute and the National Centre for Excellence in PalaeoSciences, University of the Witwatersrand, Wits, South Africa
    Contribution
    EMR, Conceptualization, Formal analysis, Supervision, Funding acquisition, Investigation, Visualization, Methodology, Project administration, Writing—review and editing
    Competing interests
    The authors declare that no competing interests exist.
  3. Hannah Hilbert-Wolf

    1. Department of Geoscience, James Cook University, Townsville, Australia
    Contribution
    HH-W, Formal analysis, Validation, Investigation, Writing—review and editing, Visualisation (U-Th; geochemistry; sample preparation)
    Competing interests
    The authors declare that no competing interests exist.
  4. Jan D Kramers

    1. Department of Geology, University of Johannesburg, Johannesburg, South Africa
    Contribution
    JDK, Resources, Formal analysis, Validation, Investigation, Writing (U-Th, OSL, geochemistry)
    Competing interests
    The authors declare that no competing interests exist.
  5. John Hawks

    1. Evolutionary Studies Institute and the National Centre for Excellence in PalaeoSciences, University of the Witwatersrand, Wits, South Africa
    2. Department of Anthropology, University of Wisconsin-Madison, Madison, United States
    Contribution
    JHa, Conceptualization, Visualization, Writing—review and editing
    Competing interests
    The authors declare that no competing interests exist.
  6. Anthony Dosseto

    1. School of Earth and Environmental Sciences, University of Wollongong, Wollongong, Australia
    Contribution
    AD, Formal analysis, Investigation (U-Th)
    Competing interests
    The authors declare that no competing interests exist.
  7. Mathieu Duval

    1. Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
    2. Geochronology, Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
    Contribution
    MD, Resources, Formal analysis, Validation, Investigation, Writing—review and editing, Visualisation (ESR)
    Competing interests
    The authors declare that no competing interests exist.
  8. Marina Elliott

    1. Evolutionary Studies Institute and the National Centre for Excellence in PalaeoSciences, University of the Witwatersrand, Wits, South Africa
    Contribution
    MEl, Supervision, Investigation, Visualisation (archaeology, speleology)
    Competing interests
    The authors declare that no competing interests exist.
  9. Mary Evans

    1. School of Geosciences, University of the Witwatersrand, Wits, South Africa
    Contribution
    MEv, Formal analysis, Investigation (OSL)
    Competing interests
    The authors declare that no competing interests exist.
  10. Rainer Grün

    1. Australian Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
    2. Research School of Earth Sciences, The Australian National University, Canberra, Australia
    Contribution
    RG, Formal analysis, Validation, Investigation, Resources (ESR)
    Competing interests
    The authors declare that no competing interests exist.
  11. John Hellstrom

    1. School of Earth Sciences, The University of Melbourne, Parkville, Australia
    Contribution
    JHe, Formal analysis, Investigation (U-Th)
    Competing interests
    The authors declare that no competing interests exist.
  12. Andy IR Herries

    1. The Australian Archaeomagnetism Laboratory, Department of Archaeology and History, La Trobe University, Melbourne, Australia
    Contribution
    AIRH, Formal analysis, Investigation, Writing (Palaeomagnetism)
    Competing interests
    The authors declare that no competing interests exist.
  13. Renaud Joannes-Boyau

    1. Geoarchaeology and Archaeometry Research Group, Department of GeoScience, Southern Cross University, Lismore, Australia
    Contribution
    RJ-B, Formal analysis, Validation, Investigation, Writing—review and editing, Visualisation (ESR)
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon 0000-0002-0452-486X
  14. Tebogo V Makhubela

    1. Department of Geology, University of Johannesburg, Johannesburg, South Africa
    Contribution
    TVM, Formal analysis, Investigation (geochemistry)
    Competing interests
    The authors declare that no competing interests exist.
  15. Christa J Placzek

    1. Department of Geoscience, James Cook University, Townsville, Australia
    Contribution
    CJP, Formal analysis, Investigation (U-Th)
    Competing interests
    The authors declare that no competing interests exist.
  16. Jessie Robbins

    1. Department of Geoscience, James Cook University, Townsville, Australia
    Contribution
    JR, Investigation (field sedimentology)
    Competing interests
    The authors declare that no competing interests exist.
  17. Carl Spandler

    1. Department of Geoscience, James Cook University, Townsville, Australia
    Contribution
    CS, Validation, Writing—review and editing
    Competing interests
    The authors declare that no competing interests exist.
  18. Jelle Wiersma

    1. Department of Geoscience, James Cook University, Townsville, Australia
    Contribution
    JWi, Investigation (field sedimentology)
    Competing interests
    The authors declare that no competing interests exist.
  19. Jon Woodhead

    1. School of Earth Sciences, The University of Melbourne, Parkville, Australia
    Contribution
    JWo, Formal analysis, Investigation, Resources (U-Th)
    Competing interests
    The authors declare that no competing interests exist.
  20. Lee R Berger

    1. Evolutionary Studies Institute and the National Centre for Excellence in PalaeoSciences, University of the Witwatersrand, Wits, South Africa
    Contribution
    LRB, Conceptualization, Resources, Funding acquisition, Project administration, Writing—review and editing
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon 0000-0002-0367-7629

Funding

Australian Research Council (DP140104282)

  • Paul H G M Dirks
  • Eric M Roberts
  • Hannah Hilbert-Wolf
  • Jan D Kramers
  • Carl Spandler
  • Lee R Berger

Australian Research Council (FT 120100399)

  • Andy IR Herries

Australian Research Council (DP140100919)

  • Renaud Joannes-Boyau

Marie Curie International Outgoing Fellowship (PIOF-GA-2013-626474)

  • Mathieu Duval

Australian Research Council (FT150100215)

  • Matthieu Duval

National Geographic Society

  • Lee R Berger

National Research Foundation

  • Lee R Berger

Lyda Hill Foundation

  • Lee R Berger

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

We would like to thank Chris Stringer and four anonymous reviewers for their constructive comments that have greatly helped improve this paper. We would also like to thank the many funding agencies that supported various aspects of this work. In particular we would like to thank the National Geographic Society, the National Research Foundation and the Lyda Hill Foundation for significant funding of the discovery, recovery and initial analysis of this material. Further support was provided by ARC (DP140104282: PHGMD, ER, JK, HHW; FT 120100399: AH). The ESR dosimetry study undertaken by CENIEH and Griffith University has been supported by a Marie Curie International Outgoing Fellowship (under REA Grant Agreement n° PIOF-GA-2013–626474) of the European Union's Seventh Framework Programme (FP7/2007-2013) and an Australian Research Council Future Fellowship (FT150100215). ESR and U-series dating undertaken at SCU were supported by ARC (DP140100919: RJB). We would also like to thank the University of the Witwatersrand, the Evolutionary Studies Institute and the South African National Centre of Excellence in PalaeoSciences for hosting many of the authors while studying the material, and allowing original material to be made available for dating. We would like to thank the South African Heritage Resource Agency for the necessary permits to work on the Rising Star site; the Jacobs family and later the Lee Berger Foundation for granting access. The assistance of members of the Speleological Exploration Club, in various safety aspects within the cave during excavations is gratefully acknowledged. Zenobia Jacobs and Bert Roberts of the University of Wollongong are thanked for helping with initial OSL tests for single grain analyses and for helpful discussions. We would also like to thank Wilma Lawrence, Bonita De Klerk, Natasha Barbolini, Merrill van der Walt, Wayne Crichton and Justin Mukanku for their assistance during all phases of the project. RG and MD thank Les Kinsley, ANU, for his invaluable help to keep the Neptune in tune. ME would like to thank Stephan Woodborne (iThemba LABS, Gauteng) for his help in unravelling the spectrometer results related to OSL and ESR dating.

Reviewing Editor

  1. George H Perry, Reviewing Editor, Pennsylvania State University, United States

Publication history

  1. Received: December 13, 2016
  2. Accepted: April 25, 2017
  3. Version of Record published: May 9, 2017 (version 1)

Copyright

© 2017, Dirks et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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