Evidence for deliberate burial of the dead by Homo naledi

Reviewer #1 (Public Review):

The discovery of Homo naledi fossils and the rising star cave system is unquestionably important for paleoanthropology. The fossils themselves hold a wealth of information about the diversity and complexity of morphological and evolutionary change on the hominin family tree. It is a truly amazing find and important site and it is important that information about this site continues to be produced so that more can be known. It is equally important that the papers produced from the site be fully reviewed for scientific rigor. I hope to assist with this to the best of my ability.

In its current form the paper, "Evidence for the deliberate burial of the dead by Homo naledi," does not meet the standards of our field. The paper is hard to follow. It lacks key citations, contextual background information to inform the reader about the geological and depositional structure of the caves, and concise understandable descriptions of the methods and the significance of the results.

The main point of the paper is to describe three possible burial features. The working hypothesis is that the features are intentional burials, and the authors seek to support this hypothesis throughout rather than test it. The authors do this by noting mineralogical differences in sediment and possible bowl-shaped sedimentological distinctions where fossil bones occur. As stated above, this evidence needs to be elaborated on the in text, contextualized, and edited for clarity. In addition, throughout the paper, the authors only consider two depositional scenarios for burial and body decomposition: 1) a body was intentionally buried in a pit that was dug into the cave sediments, and then buried in sediment (without detailing in the main text what sediment was used to backfill the pit); and 2) the body was left in a natural pit and decayed in the open. A major problem with only considering these two scenarios for body decomposition is that previous reports about cave geology and sedimentology show that it is a dynamic system involving erosion, sediment slumping and drainage, and contraction of clay, which is a major component of the sediment, etc. The authors are very clear that flooding is not a viable option for the movement of skeletal elements in the cave. However, they do not mention other processes such as erosion or sediment slumping, that are known to occur and could be responsible for moving sediment and fossils in each chamber of the cave. They also do not consider carnivore involvement which has been suggested by Val (2016) and Egeland et al. (2018). Such processes could naturally transport bodies, shift them around, and sediment erosion could bury them. The articulation of some skeletal elements is a major argument for intentional burial, yet within the cave substructure, articulated bones are often commingled with disarticulated elements from the same or different individuals. This same situation exists in the features included in this paper. It does appear that some skeletal material was covered in sediment before decomposition and remains in articulation, but bodies decompose at different rates, and can decompose slowly, especially in environments that lack insects (see Simmons et al. 2010 Journal of Forensic Sciences https://doi-org.aurarialibrary.idm.oclc.org/10.1111/j.1556-4029.2009.01206.x). Wiersma et al., 2019 describe the cave system as very humid, but dry due to little standing water, mildly acidic, with an average temperature today of 18{degree sign}C and a minimum of 12{degree sign}C over the last million years. The starting null hypothesis should be that the bodies were naturally covered in sediment. Intentional burial requires extraordinary circumstances and requires multiple lines of solid evidence to support the hypothesis. In testing for natural burial processes, the rate of body decomposition should be reconstructed given the environmental parameters of the cave.

In keeping with supporting their starting hypothesis that Homo naledi intentionally buried individuals in the cave, the authors conclude that "A parsimonious explanation for this configuration of skeletal remains is that these remains may be a palimpsest of burials that have sequentially disrupted each other. In this hypothesis, early burials were disturbed when pits were dug for subsequent burials. Other occurrences of remains outside of the Dinaledi Chamber and Hill Antechamber (Hawks et al., 2017; Brophy et al., 2021) are discussed as possible evidence of mortuary practices in SI 4.2. Instances where parts of individuals occur in remote narrow passages cannot be explained as a result of carnivore or water transport (Elliott et al., 2021; Brophy et al., 2021), making it necessary to consider that H. naledi may have placed these partial remains in these locations, possibly representing a form of funerary caching." After reviewing the evidence presented in the current manuscript, it is not clear why this is a parsimonious explanation. The authors have repeatedly described how incredibly challenging it is to get into and out of this cave system and all of its chambers. How could any species, even small bodied species, drag/pull/shove dead bodies through small crevasses, shove or drop them down a narrow shoot, continue to move through the hill antechamber to the Dineledi chamber and bury bodies? It is not impossible but given the previously published descriptions of the dynamic process of sedimentation movement in the cave it is certainly not a parsimonious explanation. To support this will take many more lines of evidence than presented here such as micromorphological analysis of the overall cave system and each feature (discussed in the supplementary information but briefly), full detailed reconstruction of sediment, water, fossil, and debris movement throughout the cave system coupled with reconstructions of body decomposition rates. Scientifically precise computer-generated reconstructions of all of this are possible working with specialists affiliated with National Geographic. An analysis also needs to start by testing a null hypothesis, not deciding on the conclusion and setting out to "prove" it.

Reviewer #2 (Public Review):

In this study (Berger et al.), geological and fossil data from the Rising Star Cave System in South Africa are presented to provide evidence for intentional burials of Homo naledi individuals. The authors focus on describing and interpreting what they refer to as "delimited burial features." These features include two located on the floor of the Dinaledi Chamber (referred to as 'Dinaledi Features' 1 and 2) and one from the floor of the Hill Antechamber.

'Dinaledi Feature 1' consists of a collection of 108 skeletal elements recovered from sub-unit 3b deposits. These remains are believed to primarily represent the remains of a single adult individual, along with at least one additional juvenile individual. Although additional anatomical elements associated with 'Dinaledi Feature 1' are mentioned, they are not described as they remain unexcavated. The study states that the spatial arrangement of the skeletal remains is indicative of the primary burial of a fleshed body. On the other hand, 'Dinaledi Feature 2' is not extensively discussed, and its complete extent was not thoroughly investigated.

Regarding the Hill Antechamber feature, it was divided into three separate plaster jackets for removal from the excavation. Through micro-CT and medical CT scans of these plaster jackets, a total of 90 skeletal elements and 51 dental elements were identified. From these data, three individuals were identified, along with a fourth individual described as significantly younger. Individuals 1 and 2 are classified as juveniles.

I feel that there is a significant amount of missing information in the study presented here, which fails to convince me that the human remains described represent primary burials, i.e. singular events where the bodies are placed in their final resting places. Insufficient evidence is provided to differentiate between natural processes and intentional funerary practices. In my opinion, the study should include a section that distinguishes between taphonomic changes and deliberate human modifications of the remains and their context, as well as reconstruct the sequence and timeline of events surrounding death and deposition. A deliberate burial involves a complex series of changes, including decomposition of soft tissues, disruption of articulations between bones, and the sequence of skeletonization. While the geological information is detailed, the archaeothanatological reasoning (see below) is largely absent and, when presented, it lacks clarity and unambiguousness.

My main concern is that the study does not apply or cite the basic principles of archaeothanatology, which combines taphonomy, anatomy, and knowledge of human decomposition to interpret the arrangement of human bones within the Dinaledi Chamber and the Hill Antechamber. Archaeothanatology has been developed since the 1970s (see Duday et al., 1990; Boulestin and Duday, 2005; Duday and Guillon, 2006) and has been widely used by archaeologists and osteologists to reconstruct various aspects such as the original treatment of the body, associated mortuary practices, the sequence of body decomposition, and the factors influencing changes in the skeleton within the burial.

Specifically, the study lacks a description of the relative sequence of joint disarticulation during decomposition and the spatial displacement of bones. A detailed assessment of the anatomical relationships of bones, both articulated and disarticulated, as well as the direction and extent of bone displacement, is missing. For instance, while it is mentioned that "many elements are in articulation or sequential anatomical position," a comprehensive list of these articulated elements and their classification (as labile or not) is not provided.

Furthermore, the patterns described are not illustrated in sufficient detail. If Homo naledi was deliberately buried, it would be crucial to present illustrations depicting the individuals in their burial positions, as well as the representation and proportions of the larger and smaller anatomical elements for each individual. While Figure 2B provides an overall view of 'Dinaledi Feature 1,' it is challenging to determine the relationships of bones, whether articulated or disarticulated, in Figures 2C or 2D. Such information is essential to determine whether the bones are in a primary or secondary position, differentiate between collective and multiple burials, ascertain the body's stage of decomposition at the time of burial, identify postmortem and post-depositional manipulation of the body and grave (e.g., intentional removal of bodies/body parts), and establish whether burial occurred immediately after death or was delayed.

Moreover, the study does not address bone displacements within secondary voids created after the decomposition of soft tissues, nor does it provide assessments of the position of bones within or outside of the original body volume. Factors such as variations in soft tissue volume between individuals of different sizes/corpulence, and the progressive filling (i.e., sediment continually fills newly formed voids) or delayed filling (causing the 'flattening' of the ribcage and 'hyper-flexed' burials, for instance) of secondary open spaces with sediment over time should also be discussed.

In conclusion, while I acknowledge the importance of investigating potential deliberate burials in Homo naledi, I do not think that in its present form, the evidence presented in this study is as robust as it should be.

Reviewer #3 (Public Review):

This paper provides new information on the Dinaledi Chamber at the Rising Star Cave System. In short, a previously excavated area was expanded and resulted in the discovery of a cluster of bones appearing to be of one individual, a second similar cluster, and a third cluster with articulated elements (though with several individuals). Two of these clusters are argued to be intentionally buried individuals (the third one has not been investigated) and thus Homo naledi not only placed conspecifics in deep and hard to reach parts of caves but also buried them (apparently in shallow graves). This would be the oldest evidence of intentional burial. The main issue with the paper is that the purported burials were not fully excavated. Two are still in the ground, and one was removed in blocks but left unexcavated. As burials are mostly about sediments, it means the authors are lacking important lines of evidence. Instead, they bring other lines of argument as outlined below. While their preferred scenario is possible, there are important issues with the evidence as presented and they are severely hampered by the lack of detailed archaeological and geoarchaeological information both from the specific skeletal contexts and more generally from the chamber (because in fact the amount of excavation conducted here is still quite limited in scope). I also found that while the presentations of the various specialists in the team was quite good, the integration of these contributions into the main text was not. In particular, the geology of the cave system and the chamber need (especially what is known of the depositional and post-depositional processes) need to be better integrated into the presentation of the archaeology and the interpretation of the finds.

Often times the presence of articulated or mostly articulated skeletons is used to argue for intentional burial. This argument, however, is based on the premise that if not buried, these skeletons would have otherwise become disarticulated. Normally disarticulation would happen as a result of subsequent use of the site by hominins (e.g. purported burials in Neandertal cave sites) or by carnivores scavenging the body. Indeed this latter point is why bodies are buried so deeply in many Western societies (i.e. beyond the reach and smell of carnivores). Bodies can also be disarticulated by natural processes of deposit and erosion.

However, here in the case of the Dinaledi Chamber, we apparently don't have any of these other processes. The chamber was not used by carnivores and it was not a living area where H. naledi would have frequently returned and cleared out the space. As for depositional processes, it is more complex, but it is clear from Wiersma et al. that there is a steady, constant movement of these sediments towards drains. They also think that this process can account for the mix of articulated and non-articulated elements in the cave. Importantly, that same paper makes the argument that the formation of these sediments is not the result of water movement and that the cave has been dry since the formation of this deposit. So bodies lying on the surface and slowly covered by the formation of the deposit and slowly moving towards the drains could perhaps account for the pattern observed, meaning burial is not needed to account for articulations (note that more information on fabrics would be good in this context - orientation analysis of surface finds or of excavated finds is either completely lacking or minimal - see figure 13b and c report orientations on 79 bones of unknown context that appear to show perhaps elevated plunge angles and some slightly patterning in bearing but there is no associated statistics or text explaining the significance).

So, unless the team can provide some process that would have otherwise disarticulated these skeletons after the bodies arrived here and decomposed, their articulated state is not evidence of burial (no more than finding an articulated or mostly articulated bear skeleton deep in a European cave would suggest that it was buried).

As for the elemental analysis, what I understood from the paper is that the sediment associated with bones is different from the sediment not associated with bones. It is therefore unsurprising that the sediment associated with the reported skeletons clusters with sediments with bones. The linking argument for why this makes this sediment pit fill is unclear to me. Perhaps it is there, but as written I didn't follow it.

What the elemental analysis could suggest, I think, is that there has not been substantial reworking of the sediments (as opposed to the creep suggested by Wiersma et al.) since the bones leached these minerals into the sediment. What I don't know, and what is not reported, is how long after deposition we can expect the soil chemistry to change. If this elemental analysis were extended in a systematic way across the chamber (both vertically and horizontally) after more extensive excavations, I could see it perhaps being useful for better understanding the site formation processes and depositional context. As it is now, I did not see the argument in support of a burial pit.

The other line of evidence here is that some bones are sediment supported. The argument here is that when a body decomposes, bones that were previously held in place by soft tissues will be free to move and will shift their position. How the bones shift will differ depending on whether the body is surrounded by matrix (as they argue here in an excavated burial pit) or whether it is in the open (say, for instance, in a coffin) (and there are other possibilities as well - for instance wrapped in a shroud). Experiments have also shown the order in which the tendons, for instance, decompose and therefore which bones are likely to be free to move first or last.

I will note that this literature is poorly cited. I think the only two papers cited for how bodies decompose are Roksandic 2002 and Mickleburgh and Wescott 2019. The former is a review paper that summarizes a great many contexts that are clearly not appropriate here, and it generally makes the point that it is difficult to sort out, and it notes that progressively filled is an additional alternative to not buried/buried. The other looks at experimental data of bodies decomposing without being buried. In the paper here, this citation is used to argue that the body must have been buried. I don't see the linking argument at all. And the cited paper is mostly about how complicated it is to figure this all out and how many variables are still unaccounted for (including the initial positioning of the body and the consumption of the body by insects - something that is attested to at Naledi - plus snails - see not just Val but also Wiersma et al. and I think the initial Dirk et al. paper).

So the team here instead simply speaks of how the body decomposes in burials as if it is known. For the Feature 1 skeleton, the authors note that the ribs are "apparently" sediment supported and that a portion of the partial cranium is vertical or subvertical and sediment supported. For both of these, the figures show it very poorly. We really have to take their word for it. Second, I would have liked to have seen some reference and comparison to the literature for how the ribs should be in sediment burial cases. For the cranium, seems like a broken cranium resting on a surface will have vertical aspects regardless of sediment support. To the contrary, the orientation of the cranium will change depending on whether there is sediment holding it in place or not. But that argument is not made here. It is very hard from the figures to have a detailed idea of how these skeletons are oriented in the sediments, to know which elements are in articulation, which are missing, etc.

In the case of the Hill Antechamber Feature, an additional argument is made about the orientation of the finds in relation to the natural stratigraphy in this location. The team argues that the skeleton is lying more horizontally than the sediments and that in fact the foot is lying against the slope. First, there is no documentation of the slope of the layers here (e.g. a stratigraphic profile with the layers marked or a fabric analysis). There is a photo in the SI that says it shows sloping, but it needs some work. Second, this skeleton was removed in three blocks and then scanned. So the position of the skeleton is being worked out separate from its context. This is doable, but I would have liked to have seen some mention of how the blocks were georeferenced in the field and then subsequently in the lab and of how the items inside the block (i.e. the data coming from the CT scanner) were then georeferenced. I can think of ways I would try to do this, but without some discussion of this critical issue, the argument presented in Figure 10c is difficult to evaluate. Further, even if we accept this work, it is hard for me to see how the alignment of the foot is 15 degrees opposite the slope (the figure in the SI is better). It is also hard to understand the argument that the sediment separating the lower limb from the torso means burial. The team gives the explanation that if the body was in an open pit it would have been flat with no separation. Maybe. I mean I guess if the pit was flat. But there is no evidence here of a pit (at all). And what if the body was stuffed down the chute and was resting on a slope and covered with additional sediments from the chute (or additional bodies) as it decomposed? It seems that this should be the starting point here rather than imagining a pit.

One of the key pieces of evidence for demonstrating deliberate burial is the recognition of a pit. Pits can be identified because of the rupture they create in the stratigraphy when older sediments are brought to the surface, mixed, and then refilled into the pit with a different color, texture, compaction, etc. In some homogenous sediments a pit can be hard to detect and in some instances post-depositional processes (e.g. burrowing) can blur the distinction between the pit and the surrounding sediments. But the starting point of any discussion of deliberate burial has to be the demonstration of a pit. And I don't see it here. It might just be that the figures need to be improved. But I am skeptical because the team has taken the view that these finds can't be excavated. While I appreciate the scanning work done on the Antechamber find, it is not the same as excavating. Same comment for Features 1 and 2.

In short, my view is that they have an extremely interesting dataset. That H. naledi buried their dead here can't be excluded based on the data, but neither is it supported here. My view is that this paper is premature and that more excavation and the use of geoarchaeological techniques (especially micromorphology) are required to sort this out (or go a long way towards sorting it out).

Reviewer #4 (Public Review):

Berger et al. 2023a argues that Homo naledi intentionally buried their dead within the Rising Star cave system by digging pits and covering the bodies with infilled sediment. The authors identified two burials: Dinaledi Feature 1 from the Dinaledi Chamber, and the Hill Antechamber Feature from the Hill Antechamber. The evolutionary and behavioral implications for such behavior are highly significant and would be the first instance of a relatively small-brained hominin engaging is complex behavior that is often found in association with Homo sapiens and Homo neanderthalensis. Thus, the scientific rigor to validate these findings should be of the highest quality, and thus, provide clear documentation of intentional burial. In an attempt to meet these standards, the authors stated a series of tests that would support their hypothesis of intentional burials in the Rising Star Cave system:

"The key observations are (1) the difference in sediment composition within the feature compared to surrounding sediment; (2) the disruption of stratigraphy; (3) the anatomical coherence of the skeletal remains; (4) the matrix-supported position of some skeletal elements; and (5) the compatibility of non-articulated material with decomposition and subsequent collapse." (page 5)

To find support for the first (1) test, the authors collected sediment samples from various locations within the Rising Star Cave system, including sediment from within and outside Dinaledi Feature 1. However:

• The authors did not select sediment samples from within the Hill Antechamber Feature, so this test was only used to assess Dinaledi Feature 1.

• The sediment samples were analyzed using x-ray diffraction (XRD) and x-ray fluorescence (XRF) to test the mineralogy and chemistry of the samples from within and outside the feature. The XRF results were presented as weighted percentages (not intensities) with no control source reported. The weighted percentages were analyzed using a principal components analysis (PCA) while the particle-size distribution was analyzed using GRADISTAT statistics package and the Folk and Ward Method to summarize "mean grain size, sorting, skewness and kurtosis in addition to the percentages of clay, silt and sand in each sample." (page 28).

• The PCA results were reported solely as a biplot without showing the PC scores projected into the loading space, which is unusual and does not present the data accurately. Instead, the authors present the scores of a single component (PC2, figure 3) because the authors interpreted this component as "distinctly delineates fossil-bearing sediments from sterile sediments based on the positive loadings of P and S" (Page 6). However, the supplementary table that reports XRF bulk chemistry results as a weighted percentage of minerals within each sample (SI Table 1) shows mostly an absence of data for both Na and S. Since Na is at the lower end of detection limits for the method, and S seems to just be absent from the list, the intentions of the authors for showing the inclusion of these elements in their PCA results is unclear. Given that this is the author's primary method for demonstrating a burial, this issue is particularly concerning and requires additional attention.

• Regardless of the missing data, this reviewer attempted to replicate the XRF PCA results using the data provided in SI Table 1 and was unsuccessful. The samples that were collected from within the feature (SB) cluster with samples collected from sterile sediments and other locations around the cave system. Thus, these results are not replicable as currently reported.

• Visual comparisons of sediment grain size, shape, and composition were qualitatively summarized. Grain size was plotted as a line graph and is buried as supplemental Figure S13 showing sample by color and area, but these results do not distinguish samples from WITHIN the burial compared to OUTSIDE the burial as the authors state in the methods as a primary goal.

To test the second (2) aim, the "stratigraphy" was primarily described in text.

• For Dinaledi Feature 1, the authors state that the layer around Feature 1 "is continuous in the profile immediately to the east of the feature; it is disrupted in the sediment profile at the southern extent of the feature (fig. 3b)." Upon examination of figure 3b, the image shows an incredibly small depiction of the south (?) profile view with an extremely large black box overlaying a large portion of the photograph containing a small 5 cm scale. Visually, there is no difference in the profile that would suggest a disruption in the form of a pit. The LORM (orange-red mud layer) does seem to become fragmentary, but no micromorphological analysis was conducted on this section to provide an evaluation of stratigraphic composition. Also, by only excavating a portion of the feature, the authors were unable to adequately demonstrate the full extent of this feature.

• The authors attempt to describe "a bowl-shaped concave layer of clasts and sediment-free voids make up the bottom of the feature" (page 13) and refer to figures and supplementary information that do not depict any stratigraphic profile. Moreover, the authors state that "the leg, foot, and adjacent [skeletal?] material cut across stratigraphy" indicating that the skeleton is orientated on a flat plane against the surrounding stratigraphy that is "30{degree sign} slope of floor and underlying strata" (page 51, fig. 10c captions). There is no mention of infilled sediment from a pit and how this relates to the skeleton or the slope of the floor. It is therefore extremely unclear what the authors are meaning to describe without any visual or micromorphological supplementation to demonstrate a "bowl-shaped concave layer".

The third (3) test was to evaluate the anatomical coherence of the skeletal remains using macro- and micro-CT (computed tomography) of the Hill Antechamber Feature that was removed during excavation. To visually assess the anatomy of the Dinaledi Feature 1 burial, the authors describe the spatial relationship of skeletal elements as they were being excavated but halted partway through the excavation.

• The authors do not provide any documentation (piece-plotting, 3D rendering of stages of excavation, etc.) of the elements that were removed from the Dinaledi Feature. Figure 4 and SI Fig. S22 show the spatial relationship between identifiable skeletal elements that remain in the Feature. However, in Fig. 4, it is unclear why the authors chose to plot 2023-2014 excavated material along with material reported here, and it's even more difficult to understand the anatomical positioning of the elements given their color and point size choices. Although, the authors do provide a 3D rendering of the unexcavated remains showing some skeletal cohesion, apart from the mandible and teeth being re-located near the pelvis (Fig. 9). That said, it is very difficult to visually confirm the elements from this model or understand the original placement of the skeleton.

• 3D renderings of the Hill Antechamber feature skeletal material is clearly shown in SI Fig. S26. Contrary to what the authors state in text, there is a rather wide dispersal and rearrangement of elements for a "burial" that is theoretically protected from scavengers and other agents that would aid in dispersing bone from the surface. The authors do not offer any alternatives to explain disturbance, such as human activity, which clearly took place.

• Moreover, there does not appear to be any intentional arrangement of limbs that may suggest symbolic orientation of the dead (another line of evidence often used to support intentional burial but omitted by the authors). Thus, skeletal cohesion is not enough evidence to support the hypothesis of an intentional burial.

The fourth (4) test was attempted by evaluating whether some elements were vertically aligned from 3D reconstructed models of Hill Antechamber Feature and a photogrammetric model of the Dinaledi Feature 1. The authors state that "the spatial arrangement of the skeletal remains is consistent with primary burial of the fleshed body" (page 8 in reference to Dinaledi Feature 1) without providing any evidence, qualitative or quantitative, that this is the case for either burial.

Since this reviewer was unable to understand the fifth (5) test as it was written by the authors, I am unable to comment on the evidence to support this test and will default to the other reviewers for evaluation of this claim.

In addition to a lack of evidence to support the claims of intentional burial, this paper was also written extremely poorly. For example, the authors often overused 'persuasive communication devices' (see eLife article, https://elifesciences.org/articles/88654) to mislead readers:

"During this excavation, we recognized that the developing evidence was suggestive of a burial, due to the spatial configuration of the feature and the evidence that the excavated material seemed to come from a single body." (page 5)

As an opening statement to introduce Dinaledi Feature 1, the authors state the interpretation and working hypothesis as fact before the authors present any evidence. This is known as "HARKing" and "gives the impression that a hypothesis was formulated before data were collected" (Corneille et al. 2023). This type of writing is pervasive throughout the manuscript and requires extensive editing. I recommend that the authors review the article provided by eLife (https://elifesciences.org/articles/88654) and carefully review the manuscript. Moreover, as this text demonstrates, the authors’ word choice is indicative of storytelling for a popular news article instead of a scientific paper. I highly suggest that the authors review the manuscript carefully and present the data prior to giving conclusions in a clear and concise manner.

Moreover, the writing structure is inconsistent. Information that should be included in results is included in the methods, text in the results should be in discussions, and so forth. This inconsistency is pervasive throughout the entire manuscript, making it incredibly difficult to adequately understand what the authors had done and how the results were interpreted.

Finally, the "artifact" that was described and visualized using CT models is just that - a digitally colored model. The object in question has not been analyzed. Until this object is removed from the dirt and physically analyzed, this information needs to be removed from the manuscript as there is nothing to report before the object is physically examined.

Overall, there is not enough evidence to support the claim that Homo naledi intentionally buried their dead inside the Rising Star Cave system. Unfortunately, the manuscript in its current condition is deemed incomplete and inadequate, and should not be viewed as finalized scholarship.

Author Response:

We would like to thank the eLife reviewers for the considerable time and effort they have invested to review these manuscripts. We have also benefited from a previous round of review of the manuscript describing the proposed burial features, which underwent two rounds of revisions in a high-impact journal over a period of approximately 8 months during 2022 and early 2023. Both sets of reviews have reflected mixed responses to the evidence we have presented, with one reviewer recommending acceptance with minor editorial revisions, two recommending acceptance with minor revisions and the fourth recommending rejection based upon similar arguments to those reflected by some of the reviewers in this current round of reviews in eLife. Ultimately the managing editor of this first journal took the decision that the review process could not be completed in a timely manner and rejected the manuscript although the submission here reflected our consideration of these reviewers suggestions.

We have chosen in this initial response to the eLife reviews to include some references to the previous anonymous reviews in order to illustrate differences of opinion and differences in revision suggestions within the review process. Our goal is to offer maximal insight into our decision-making process and to acknowledge the considerable time and effort put into the assessment of these manuscripts by reviewers (for eLife and in the case of the earlier review process). We hope that this approach will assist the readers, and reviewers, of our manuscripts in understanding why we are proceeding with certain decisions during the revision process.

This is a new process for us and the reviewers, and one way in which it significantly differs from more traditional review is that both the reviews and our reply will be public well in advance of our revisions to the manuscript. Indeed, considering the scope of the reviews, some of those revisions may take considerable time, although many can be accomplished fairly easily. Thus, we are not in a position to say that we have solved every issue raised by the reviewers. Instead, we will examine what appear to be the key critical issues raised regarding the data and the analyses and how we propose to address these as we revise the papers. We will also address several philosophical and ethical issues raised by the reviews and our proposal for dealing with these. More specific editorial and citational recommendations will be dealt with on a case-by-case basis, and we do not address these point-by-point in this reply. Please note, this response to the reviewers is not the revision of the manuscript and is only the initial opinion of the corresponding authors with some guidance from the larger group of authors of all three papers. Our final submitted revision will reflect the input of all authors included on those submissions.

We took the decision to submit three separate papers consciously. The two different categories of evidence, burials and engravings, involve different kinds of analysis and different (although overlapping) teams of researchers, and we recognized that each deserved their own presentation and assessment. Meanwhile, together they inform the context of H. naledi in a way that requires some synthetic discussion, in which both kinds of evidence are relevant, leading to a third paper. But the mutual relevance of these different kinds of evidence and their review by a common set of reviewers naturally raises cross-cutting issues, and the reviewers have cross-referenced the three articles. This has sometimes led to suggestions about one manuscript based on the contents of another. Considering the situation, we accepted the recommendation that it would be clearer to consider all three articles in a single reply. Thus, while each of the three papers will proceed separately during the revision process, it will be necessary to highlight across all three papers occasionally in our responses.

Scientific Issues:

In reading the reviews, we feel there are 9 critical points/assertions raised by one or more of the reviewers that present a problem for, or challenge to, our hypothesis that the observed evidence (bone accumulations and engravings) described in the Dinaledi subsystem are of intentional naledigenic origin. These are:

1. The evidence presented does not demonstrate a clear interruption of the floor sediments, thus failing to demonstrate excavated holes.

2. The sediments infilling the holes where the skeletal remains are found have not been demonstrated to originate from the disruption of the floor sediments and thus could be part of a natural geological process (e.g. water movement, slumping) or carnivore accumulations.

3. Previous geological interpretations by our research group have given alternative geological explanations for formation of the bony accumulations that contradict the present evidence presented here and result in alternative origins hypotheses.

4. Burial cannot be effectively assessed without complete excavation of the features and site.

5. The skeletal remains as presented do not conform clearly to typical body arrangement/positions associated with human (Homo sapiens) burials.

6. There is no evidence of grave goods or lithic scatters that are typically associated with human burials.

7. Humans may have been involved with the creation of either the Homo naledi bone accumulations, the engravings, or both.

8. Without a date of the engravings, the null hypothesis should be the engravings were created by Homo sapiens.

9. The null hypothesis for explanation of the skeletal remains in this situation should be “natural accumulation”.

Our analysis of the Dinaledi Feature 1 leads us to accept that the laminated orange-red mudstone (LORM) sedimentary layer is interrupted, indicating a non-natural intervention, and that the hole created by the interruption was then filled by both a fleshed body (and perhaps parts of other bodies) which were then covered by sediment that originated from the hole that was dug. We recognize that the four eLife reviewers are not convinced that our presentation is sufficient to establish this. Interestingly, this was not the universal opinion of earlier reviewers of the initial manuscript several of whom felt we had adequately supported this hypothesis. The lack of clarity in this current version of the burial manuscript is our responsibility. In the upcoming revision of this paper to be submitted, we will take the reviewers’ critiques to heart and add additional figures that illustrate better the disruption of the LORM and clarify the sedimentological data showing the material covering the skeletal remains in the hole are the disrupted sediments excavated from the same hole. We are proposing to isolate this most critical evidence for burial into a separate section in the revised submission based on the reviewers’ comments. The fact that the LORM layer is disrupted, a fleshed body was placed in the hole created by this disruption, and the body (and perhaps parts of other bodies) was/were then covered by the same sediments from the hole is the central feature of our hypothesis that the bone accumulations observed reflect a burial and not a natural process.

The possibility of fluvial transport or involvement in the subsystem is a topic that we have addressed extensively in past work, and it is clear from these reviews that we must enhance our current manuscript to discuss this issue at greater length. Our previous work (Dirks et al. 2015; Dirks et al. 2017) emphasized that fluvial transport of whole bodies into the subsystem was precluded by several lines of sedimentological evidence. We excavated a rich accumulation of skeletal remains, including articulated limbs and other elements in subvertical orientations inconsistent with slow sedimentary infill, which were difficult to explain without positing either a large and dense pile of bodies and/or sediment movement. We encountered fractured chunks of laminated orange-red mudstone (LORM) in random orientations within our excavation area, within and among skeletal remains, which directly refuted that the remains were inundated with water at the time of burial, and this limited the possibility of fluvial transport. Water flow sufficient to displace bodies or complete skeletal evidence would also transport large and course sediment, which is absent from the subsystem, and would sort the commingled skeletal material that we found by size, which we do not observe. But our excavation only covered less than a square meter at very limited depth, and this was the limit to our knowledge of subsurface sediment. We thus were left with uncertainty that led us to suggest the possibility of sediment slumping or movement into subsurface drains, although these were not observed near our excavation. Our current work expands our knowledge of the subsurface and presents an alternative explanation for the disposition of skeletal remains from our earlier excavation. But we acknowledge that this new explanation is vulnerable to our own previous published proposals, and we must do a better job of explaining how the new information addresses our previous suggestions. By not clearly creating a section where we explained how these previous hypotheses were now nullified by new evidence, we clearly confused the reviewers with our own previous work. We will revise the manuscript by enhancing the review of the significant geological evidence demonstrating that there is no significant fluvial action in the system and making it clear how the burial hypothesis provides a clearer explanation for the situation of skeletal remains from our previous excavation work.

One of the central issues raised by reviewers has been a perceived need to excavate these features completely, totally exhuming all skeletal remains from them. Reviewers have written that it is necessary to identify every skeletal element that is present and account for any missing elements. On this point, we have both ethical and scientific differences from these reviewers. We express our ethical concerns first. Many of the best-preserved possible burials ever discovered by archaeologists were subjected to total excavation and exhumation. Cases like La Chapelle-aux-Saints, La Ferrassie, and Skhūl were fully excavated at a time when data recording and excavation methods did not include the range of spatial and geomorphological approaches that later became routine. The judgment of early investigators that these situations were intentional burials was challenged by later workers, and the kind of information that might enable better tests had been irrevocably lost (Gargett 1999; Dibble et al. 2015; Rendu et al. 2014).

Later, improved excavation standards have not sufficed to remove uncertainty or debate about possible burials. For example, it was long presumed that well-preserved remains of young children were by themselves diagnostic of intentional burial, such as those from Dederiyeh, Border Cave, or Roc de Marsal. Such cases were also fully excavated, with adequate documentation of the positioning of skeletal remains and their surrounding stratigraphic situation, but such cases were later challenged on several bases and the complete exhumation of material has confused or precluded testing of new hypotheses (e.g. Gargett 1999). The case of Roc de Marsal is one in which data from the initial excavation combined with data from the initial excavation combined with re-excavation and geoarchaeological analysis led to a naturalistic interpretation of the skeletal material (Sandgathe et al. 2011; Goldberg et al. 2017). But even in this case, the researchers erred in their interpretation of the skeleton’s situation due to a lack of identification of parts of the infant’s skeleton (Gómez-Olivencia and García-Martinez 2019). That is to say, it is not only the burial hypothesis but other hypotheses that suffer from complete excavation. Researchers concerned with preserving all possible information have sometimes taken extraordinary measures to remove and study possible burials at high-resolution in the laboratory. Such was the case of the Shanidar IV burial removed from the site and transported in plaster jacket by Solecki, which led to the disruption and loss of internal stratigraphic information (Pomeroy et al. 2020). Arguably, the current state of the art is full excavation with partial preparation, such as that undertaken at Panga ya Saidi (Martinón-Torres et al. 2021). But again, any future attempt to reinterpret or test the hypothesis of burial must rely on the adequacy of documentation as the original context has been removed.

In our decision to leave material in place as much as possible, we are expanding upon standard practice to leave witness sections and unexcavated areas for future research. The situation is novel, representing possible burials by a nonhuman species, and that makes it doubly important in our opinion to be conservative in not fully exhuming the skeletal material from its context. We anticipate that many other researchers, including future investigators, will suggest additional methods to further test the hypothesis of burial, something that would be impossible if we had excavated the features in their entirety prior to publishing a description of our work. We believe strongly that our ethical responsibility is to publish the work and the most likely interpretation while leaving as much evidence in place as possible to enable further testing and replication. We welcome the suggestions of additional methods/analyses to test the H. naledi burial hypothesis.

This being said, we also observe that total exhumation would not resolve the concerns raised by the reviewers. The recommendation of total exhumation is in pursuit of a full account of all skeletal material present and its preservation and spatial situation, in order to demonstrate that they conform to body positions comparable to human burials. As has been highlighted in forensic casework, the excavation of an inhumation feature does not necessarily provide an accurate spatial or anatomical manifest of the stratigraphical relationships between the body, encapsulating matrix, and any cut present due to preservational, taphonomic and operational factors (Dirkmaat and Cabo, 2016; Hunter, 2014). In particular, in cases where skeletal elements are highly fragmented, friable, or degraded (such as through bioerosion) then complete excavation—even under controlled laboratory conditions—may destroy bone and severely limit skeletal identification (Henderson, 1997; Hochrein, 2002; Owsley and Compton, 1997), particularly in elements where the ratio of trabecular to cortical bone is high (Darwent and Lyman, 2002; Lyman, 1994). As such, non-invasive methods of 3D and 4D modelling (preservation in situ) are often considered preferable to complete necropsy or excavation (preservation by record) where appropriate (Bolliger and Thali, 2009; Dell’Unto and Landeschi, 2022; Randolph-Quinney et al., 2018; Silver, 2016).

The test of burial is not primarily positional, but taphonomic and geological. The position and number of bones can elaborate on process-driven questions of decay and destruction in the burial environment, or post-mortem modification, but are not singularly indicative of whether the remains were intentionally buried – the post-mortem narrative of all the processes affecting the cadaveric island is required (Knüsel and Robb, 2016). In previous cases, researchers have disputed or accepted the hypothesis of intentional hominin burial based upon assumptions about how modern humans or Neandertals would have positioned bodies, with the idea that some positions reflect ritual intent while others do not. But applying such assumptions is unjustifiable, particularly for a species like H. naledi, whose culture may have differed fundamentally from our own. Our work acknowledges that the present evidence does not enable a full reconstruction of the burial positions, but it does show that fleshed remains were encased in sediment prior to decomposition of soft tissue, and that subsequent spatial changes can be most parsimoniously explained by natural decomposition within sedimentary matrix contained within a burial feature (after Green, 2022; Mickleburgh and Wescott, 2018; Mickleburgh et al., 2022). If the argument is that extraordinary claims require extraordinary evidence, we feel that the evidence documents excavation and interment (and will do so more clearly in the revision) and the fact of the remains do not match a “typical” human burial in body positioning is not in itself evidence that these are not H. naledi burials.

We feel that the reviewers (in keeping with many palaeoanthropologists) have a clear idea of what they “think” a burial should look like in an idealised sense, but this platonic ideal of burial form is not matched by the extensive literature in archaeothanatology, funerary archaeology and forensic science which indicates enormous variability in the activity, morphology and post-mortem system experienced by the human body in cases of interment and body disposal (e.g. Aspöck, 2008; Boulestin and Duday, 2005 and 2006; Connelly et al., 2005; Channing and Randolph-Quinney, 2006; Cherryson, 2008; Donnelly et al., 1995; Finley, 2000; Hunter, 2014; Parker Pearson, 1999; Randolph-Quinney, 2013). Decades of experience in the identification, recovery and interpretation of clandestine, deviant, and non-formal burials indicates the platonic ideal is rare, and in many contexts, the exception (Cherryson, 2008; Parker Pearson, 1999). This variability is particularly relevant to morphological traits in burial context, such as the informal nature of the grave cut in plan and section, shallow burial depth, and initial disposition of body (placement) during the early post-mortem period. These might run counter to the expectations of reviewers or others referencing the fossil hominin record, but are well accepted within the communities of researchers investigating Holocene archaeological sites and forensic contexts.

It is encouraging to see reviewers beginning to incorporate the extensive (often experimentally derived) literature from archaeothanatology and forensic taphonomy in their deliberations, and we will be taking these comments on board going forward. In particular, we acknowledge reviewers’ comments and the need to construct a more detailed post-mortem narrative, accounting for joint disarticulation (labile versus persistent joints etc), displacement, and final disposition of elements within the burial space. As such we will incorporate the hierarchy of decomposition (rank order disarticulation), associations between regions of anatomical association, areas of disassociation, and the voids produced during decomposition (after Mickleburgh and Wescott, 2018; Mickleburgh et al., 2022) into our narrative. In doing so we acknowledge the tensions between the inductive archaeolothanatological narrative-driven approach (e.g. Duday, 2005 & 2009) versus robust decomposition data derived from human forensic taphonomic experimentation recently articulated by Schotsmans and colleagues (2022) - noting that we will highlight comparative data based on forensic experimental casework and actualistic modelling over inductive intuitive approaches which come with significant evidential shortcomings (Bristow et al. 2011).

Finally, from a taphonomic perspective it is worth pointing out to reviewers that we have already addressed the issue of lack of taphonomic evidence for carnivore involvement in the formation of the Dinaledi assemblage (Dirks, et al., 2016). Absence of any carnivore-induced bone surface modifications, patterns of skeletal part representation, and a total absence of any carnivore remains found within the Dinaledi chamber (following Kuhn and colleagues, 2010) lead us to reject carnivores as possible vectors of body accumulation within the Dinaledi Chamber and Hill Antechamber.

Reviewers suggest that without a date derived from geochronological methods, the engravings cannot be associated with H. naledi, and that it is possible (or probable) that the engravings were done in the recent past by H. sapiens. This suggestion neglects the context of the site. We have previously documented the structure and extremely limited accessibility of the Dinaledi subsystem. This subsystem was not recorded on maps of the documented Rising Star Cave system prior to our work and its discovery by our teams. Furthermore, there is no evidence of prehistoric human activity in the areas of the cave related to possible subterranean entrances There is no evidence that humans in the past typically ventured into such extreme spaces like those of Rising Star. It is clear from the presence of the remains of many individuals that H. naledi ventured into these spaces again and again. It is likely that H. naledi moved through these spaces more easily than humans do based on their physique. We show that the engravings overlay each other suggesting multiple engraving events. These engravings took time and effort and the only evidence for use of the Dinaledi subsystem by any hominin is by H. naledi. The context leads to the null hypothesis that H. naledi made the marks. In our revision, we will elaborate on this argument to clarify the evidence for our stance on this hypothesis. Several reviewers took issue with the title of the engraving paper as we did not insert a qualifier in front of the suggested date range for the engravings. We deliberately left out qualifying language so that the title took the form of a testable hypothesis rather than a weak assertation. Should future work find the engravings were not produced within this time range, then we will restate this hypothesis.

Finally, with regards to the engravings we have chosen to report them because they exist. Not reporting the presence of engraved marks on the walls of a cave above hypothesized burials would be tantamount to leaving relevant evidence out of the description of an archeological context. We recognize and state in our manuscript that these markings require substantial further study, including attempts at geochronological dating. But the current evidence is clearly relevant to the archaeological context of the subsystem. We take a similar stance with reporting the presence of the tool shaped artefact near the hand of the H. naledi skeleton in the Hill Antechamber. It is evident that this object requires further study, as we stated in our manuscript, but again omitting it from our study would be leaving out relevant evidence.

Some have suggested that the null hypothesis should be that all of these observed circumstances are of natural origin. Our team took this approach in our early investigation of the Dinaledi subsystem (Dirks et al. 2015). We adopted the null hypothesis that the geological processes involved in the accumulation of H. naledi skeletal remains were “natural” (e.g., non-naledigenic involvement), and we were able to reject many alternative explanations for the assemblage, including carnivore accumulation, “death trap” accumulation, and fluvial transport of bodies or bones (Dirks et al. 2015). This led us to the hypothesis that H. naledi were involved in bringing the bodies into the spaces where they were found. But we did not hypothesize their involvement in the formation of the deposit itself beyond bringing the bodies to the location.

This approach seems conservative. It followed the traditional view that small-brained hominins do not engage in cultural practices. But we recognize in hindsight that this null hypothesis approach did harm to our analyses. It impeded us from recognizing within our initial excavations of the puzzle box area and other excavations between 2014 – 2017 that we might be encountering remains that were intrusive in the sedimentary floor of the chamber. If we had approached the accumulation of a large number of hominins from the perspective of the null hypothesis being that the situation was likely cultural, we perhaps would have collected evidence in a slightly different manner. We certainly note that if the Dinaledi system had been full of the remains of modern humans, there would have been little doubt that the null hypothesis would have been that this was a cultural space and not a “natural space”. We therefore respectfully disagree with the reviewers who continue to support the idea that we should approach hominin excavations with the null hypothesis that they will be natural (specifically non-cultural) in origins. If excavations continue with this mindset we believe that potential cultural evidence is almost certain to be lost.

There has been a gradient across paleoanthropological excavations, archaeological work, and forensic investigation, with increasing precision of context. The reality is that the recording precision and frame of approach is typically different in most paleontological excavations than in those related to contemporary human remains. If anything comes from the present discussion of whether the Dinaledi system is a burial site for H. naledi or not, we hope that by taking seriously the possibility of deep cultural dynamics of hominins, we will encourage other teams to meet the highest standards of excavation in order to preserve potential cultural evidence. Given H. naledi’s cranial capacity we suggest that even very early hominin skeletal assemblages should be re-examined, if there is sufficient evidence or records available. These would include examples such as the A.L. 333 Au. afarensis site (the so called First Family site in Hadar Ethiopia), the Dikika infant skeleton, WT 15000 (Turkana Boy) and even A.L. 288 (Lucy) as such unusual taphonomic situations where skeletons are preserved cannot be simply explained away as “natural” in origin, based solely on the cranial capacity and assumed lack of cognitive and cultural complexity of the hominins as emphasized by us in Fuentes et al. (2023). We are not the first to observe that some very early hominin situations may represent early mortuary activity (Pettitt 2013), but we would advocate a step further. We suggest it may be damaging to take “natural accumulation” as the standard null hypothesis for hominin paleoanthropology, and that it is more conservative in practice to engage remains with the null hypothesis of possible cultural formation.

We are deeply grateful for the time and effort all of the 8 reviewers (across three reviews) have taken with this work. We also acknowledge the anonymous reviewers from previous submissions who’s opinions and comments will have made the final iterations of these manuscripts better for their efforts. As this process is rather public and includes commentary outside of the eLife forum, we ask that the efforts of all 37 authors and 8 reviewers involved be respected and that the discourse remain professional in all venues as we study this fascinating and quite complex occurrence. We appreciate also the efforts of members of the public who have engaged with this relatively new process where preprints are posted prior to the reviews allowing comments and interactions from colleagues and the public who are normally not part of the internal peer review process. We believe these interactions will make for better final papers. We feel we have met the standards of demonstrating burials in H. naledi and that the engraving are most likely associated with H. naledi. However, given the reviews we see many areas where our clarity and context, and analyses, were less strong than they can be. With the clarifications and additions taken on board through these review processes the final papers will be stronger and clearer. We, recognize that this is an ongoing process of scientific investigation and further work will allow continued, and possibly better, evaluation of these hypothesis and others.

Lee R Berger, Agustín Fuentes, John Hawks, Tebogo Makhubela

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