1. Genetics and Genomics
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A new genus of horse from Pleistocene North America

  1. Peter D Heintzman  Is a corresponding author
  2. Grant D Zazula
  3. Ross DE MacPhee
  4. Eric Scott
  5. James A Cahill
  6. Brianna K McHorse
  7. Joshua D Kapp
  8. Mathias Stiller
  9. Matthew J Wooller
  10. Ludovic Orlando
  11. John Southon
  12. Duane G Froese
  13. Beth Shapiro  Is a corresponding author
  1. University of California, Santa Cruz, United States
  2. Tromsø University Museum, UiT - The Arctic University of Norway, Norway
  3. Government of Yukon, Canada
  4. American Museum of Natural History, United States
  5. Cogstone Resource Management, Incorporated, United States
  6. California State University San Bernardino, United States
  7. Harvard University, United States
  8. German Consortium for Translational Cancer Research, Germany
  9. University of Alaska Fairbanks, United States
  10. Natural History Museum of Denmark, Denmark
  11. Université Paul Sabatier, Université de Toulouse, France
  12. University of California, Irvine, United States
  13. University of Alberta, Canada
Research Article
Cite this article as: eLife 2017;6:e29944 doi: 10.7554/eLife.29944
8 figures, 6 tables, 31 data sets and 4 additional files

Figures

Figure 1 with 3 supplements
Phylogeny of extant and middle-late Pleistocene equids, as inferred from the Bayesian analysis of full mitochondrial genomes.

Purple node-bars illustrate the 95% highest posterior density of node heights and are shown for nodes with >0.99 posterior probability support. The range of divergence estimates derived from our nuclear genomic analyses is shown by the thicker, lime green node-bars ([Orlando et al., 2013]; this study). Nodes highlighted in the main text are labeled with boxed numbers. All analyses were calibrated using as prior information a caballine/non-caballine Equus divergence estimate of 4.0–4.5 Ma (Orlando et al., 2013) at node 3, and, in the mitochondrial analyses, the known ages of included ancient specimens. The thicknesses of nodes 2 and 3 represent the range between the median nuclear and mitochondrial genomic divergence estimates. Branches are coloured based on species provenance and the most parsimonious biogeographic scenario given the data, with gray indicating ambiguity. Fossil record occurrences for major represented groups (including South American Hippidion, New World stilt-legged equids, and Old World Sussemiones) are represented by the geographically coloured bars, with fade indicating uncertainty in the first appearance datum (after (Eisenmann et al., 2008; Forsten, 1992; O'Dea et al., 2016; Orlando et al., 2013) and references therein). The Asiatic ass species (E. kiang, E. hemionus) are not reciprocally monophyletic based on the analyzed mitochondrial genomes, and so the Asiatic ass clade is shown as ‘E. kiang + hemionus’. Daggers denote extinct taxa. NW: New World.

https://doi.org/10.7554/eLife.29944.003
Figure 1—source data 1

Bayesian time tree analysis results, with support and estimated divergence times for major nodes, and the tMRCAs for Haringtonhippus, E. asinus, and E. quagga summarized.

All analyses supported topology one in Appendix 2—figure 3. HPD: highest posterior density.

https://doi.org/10.7554/eLife.29944.007
Figure 1—source data 2

Statistics from the phylogenetic inference analyses of nuclear genomes using all four approaches.

(A) Read mapping statistics. (B) Relative transversion frequencies for approaches 1–3. (C) Relative private transversion frequencies for approach 4. DNA extraction 1: (Rohland et al., 2010); DNA extraction 2: (Dabney et al., 2013b); library preparation 1: (Meyer and Kircher, 2010; Heintzman et al., 2015); library preparation 2: (Meyer and Kircher, 2010; Vilstrup et al., 2013). In (C), data in length bins with fewer than 200,000 called sites are italicized.

https://doi.org/10.7554/eLife.29944.008
Figure 1—source data 3

Summary of nuclear genome data from all 17 NWSL equids pooled together and analyzed using approach four.

Minimum and maximum NWSL:Equus ratios between relative frequencies are in bold, and are used for the divergence estimates in Figure 1—figure supplement 3. Total and mean values are for the four longest bins only (90–99 to 120–129 bp). Mean values equally weight each length bin. bp: base pairs.

https://doi.org/10.7554/eLife.29944.009
Figure 1—figure supplement 1
An example maximum likelihood (ML) phylogeny of equid mitochondrial genomes.

This topology resulted from the analysis of mtDNA data set 3 (see Appendix 1) with all partitions and Hippidion included, and dog and ceratomorphs as outgroup (not shown). Numbers above branches are Bayesian posterior probability support values from equivalent MrBayes and BEAST analyses, with those below indicating ML bootstrap values calculated in RAxML, and are shown for major nodes. (A) Full phylogeny of the analyzed equid sequences. (B) The Haringtonhippus (NWSL equid) clade, with tips color coded by geographic origin: east Beringia, blue; contiguous USA, red (following Figure 3). Tips in bold were included in the BEAST analysis (see also Supplementary file 1).

https://doi.org/10.7554/eLife.29944.004
Figure 1—figure supplement 2
A comparison of relative private transversion frequencies between the nuclear genomes of a horse, donkey, and 17 NWSL equids.

A comparison of relative private transversion frequencies between the nuclear genomes of a caballine Equus (horse, E. caballus; green), a non-caballine Equus (donkey, E. asinus; red), and 17 NWSL equids (=Haringtonhippus francisci; blue) at different read lengths, with reads divided into 10 base pair (bp) bins. Analyses are based on alignment to the horse (A) or donkey (B) genome coordinates. To account for bins with low data content, we only display comparisons with at least 200,000 observable sites.

https://doi.org/10.7554/eLife.29944.005
Figure 1—figure supplement 3
Calculation of divergence date estimates from nuclear genome data.

Relative branch lengths are from Figure 1—source data 3. Minimum (darker blue) and maximum (lighter blue) estimates are shown for the NWSL equid branch.

https://doi.org/10.7554/eLife.29944.006
Figure 2 with 4 supplements
Morphological analysis of extant and middle-late Pleistocene equids.

(A) Crania of Haringtonhippus francisci, upper: LACM(CIT) 109/156450 from Nevada, lower: TMM 34–2518 from Texas. (B) From upper to lower, third metatarsals of: H. francisci (YG 401.268), E. lambei (YG 421.84), and E. cf. scotti (YG 198.1) from Yukon. Scale bar is 5 cm. (C) Principal component analysis of selected third metatarsals from extant and middle-late Pleistocene equids, showing clear clustering of stilt-legged (hemionine Equus (orange) and H. francisci (green)) from stout-legged (caballine Equus; blue) specimens (see also Figure 2—source data 1). Symbol shape denotes the specimen identification method (DNA: square, triangle: DNA/morphology, circle: morphology). The first and second principal components explain 95% of the variance.

https://doi.org/10.7554/eLife.29944.010
Figure 2—source data 1

Measurement data for (A) equid third metatarsals, which were used in the morphometrics analysis, and (B) other NWSL equid elements.

https://doi.org/10.7554/eLife.29944.015
Figure 2—figure supplement 1
The two crania assigned to H. francisci.

(A) LACM(CIT) 109/156450 from Nevada, identified through mitochondrial and nuclear palaeogenomic analysis. Upper: right side (reflected for comparison), lower: left side. (B) Part of the H. francisci holotype, TMM 34–2518 from Texas.

https://doi.org/10.7554/eLife.29944.011
Figure 2—figure supplement 2
Comparison between the limb bones of H. francisci, E. lambei, and E. cf. scotti from Yukon.

(A) Third metatarsals from H. francisci (upper; YG 401.268), E. lambei (middle; YG 421.84), and E. cf. scotti (lower; YG 198.1). (B) Third metacarpals from H. francisci (upper; YG 404.663), E. lambei (middle; YG 109.6), and E. cf. scotti (lower; YG 378.15). (C) Proximal fragments of radii from H. francisci (left; YG 303.1085), and E. lambei (right; YG 303.325). (D) First phalanges from H. francisci (left; YG 130.3), E. lambei (middle; YG 404.22), and E. cf. scotti (right; YG 168.1).

https://doi.org/10.7554/eLife.29944.012
Figure 2—figure supplement 3
An example equid metacarpal from Natural Trap Cave, Wyoming.

This specimen (KU 47800; JK260) was originally referred to Equus sp., but is here identified as H. francisci on the basis of mitochondrial and nuclear genome data. We note the relative slenderness of this specimen, which is comparable to YG 404.663 (H. francisci) from Yukon in Figure 2—figure supplement 2.

https://doi.org/10.7554/eLife.29944.013
Figure 2—figure supplement 4
An example femur of H. francisci from Gypsum Cave, Nevada.

This specimen (LACM(CIT)109/150708; JW277/JK166) was originally identified by Weinstock et al., 2005. List of Source data files.

https://doi.org/10.7554/eLife.29944.014
The geographic distribution of Haringtonhippus.

Blue circles are east Beringian localities (KL: Klondike region, Yukon Territory, Canada). Red circles are contiguous USA localities (NTC: Natural Trap Cave, Wyoming, USA; GC: Gypsum Cave, Nevada, USA; MHC: Mineral Hill Cave, Nevada, USA; DC: Dry Cave, New Mexico, USA [Barrón-Ortiz et al., 2017; Weinstock et al., 2005]). Orange circles are localities with tentatively assigned Haringtonhippus specimens only (FB: Fairbanks, Alaska, USA; ED: Edmonton, Alberta, Canada, USA; SJC: San Josecito Cave, Nuevo Leon, Mexico; (Barrón-Ortiz et al., 2017; Guthrie, 2003). The green-star-labeled HT is the locality of the francisci holotype, Wharton County, Texas, USA. This figure was drawn using Simplemappr (Shorthouse, 2010).

https://doi.org/10.7554/eLife.29944.016
Appendix 1—figure 1
An overview of the nuclear genome analysis pipeline.

A first reference genome sequence (red; step 1) is divided into 150 bp pseudo-reads, tiled every 75 bp for exactly 2 × genomic coverage (step 2). These pseudo-reads are then mapped to a second reference genome (blue; step 3), and a consensus sequence of the mapped pseudo-reads is called (step 4). Regions of the second reference genome that are not covered by the pseudo-reads are masked (step 5). For each NWSL equid sample, reads (orange) are mapped independently to the first reference consensus sequence (step 6a) and masked second reference genome (step 6b). Alignments from steps 6a and 6b are then merged (step 7). For alignment coordinates that have base calls for the first reference, second reference, and NWSL equid sample genomes, the relative frequencies of private transversion substitutions (yellow stars) for each genome are calculated (step 8). The co-ordinates from the second reference genome (blue) are used for each analysis.

https://doi.org/10.7554/eLife.29944.023
Appendix 2—figure 1
Characterization of ancient mitochondrial DNA damage patterns from nine equid samples.

H. francisci: (A–C) JK166 (LACM(CIT) 109/150807; Nevada), (D–F) JK207 (LACM(CIT) 109/156450; Nevada), (G–I) JK260 (KU 47800; Wyoming), (J–L) PH013 (YG 130.6; Yukon), (M–O) PH047 (YG 404.663; Yukon), (P–R) MS272 (YG 401.268; Yukon), (S–U) MS349 (YG 130.55; Yukon); E. cf. scotti: (V–X) PH055 (YG 198.1; Yukon); E. lambei: (Y–AA) MS316 (YG 328.54; Yukon). Every third panel: (A) to (Y) DNA fragment length distributions; (B) to (Z) proportion of cytosines that are deaminated at fragment ends (red: cytosine → thymine; blue: guanine → adenine); and (C) to (AA) mean base frequencies immediately upstream and downstream of the 5’ and 3’ ends of mapped reads.

https://doi.org/10.7554/eLife.29944.025
Appendix 2—figure 2
Characterization of ancient nuclear DNA damage patterns from six H. francisci samples.

(A–C) JK166 (LACM(CIT) 109/150807; Nevada), (D–F) JK260 (KU 47800; Wyoming), (G–I) PH013 (YG 130.6; Yukon), (J–L) PH036 (YG 76.2; Yukon), (M–O) MS349 (YG 130.55; Yukon), (P–R) MS439 (YG 401.387; Yukon). Every third panel: (A) to (P) DNA fragment length distributions; (B) to (Q) proportion of cytosines that are deaminated at fragment ends (red: cytosine → thymine; blue: guanine → adenine); and (C) to (R) mean base frequencies immediately upstream and downstream of the 5’ and 3’ ends of mapped reads.

https://doi.org/10.7554/eLife.29944.026
Appendix 2—figure 3
Seven phylogenetic hypotheses for the four major groups of equids with sequenced mitochondrial genomes.

These major groups are Hippidion, the New World stilt-legged equids (=Haringtonhippus), non-caballine Equus (asses, zebras, and E. ovodovi) and caballine Equus (horses). (A) imbalanced and (B) balanced hypotheses. The hypotheses presented in (C) and (D) are identical to (A) and (B), except that Hippidion is excluded. Node letters are referenced in Appendix 2—tables 12. We only list combinations that were recovered by our palaeogenomic, or previous palaeogenetic, analyses.

https://doi.org/10.7554/eLife.29944.027
Appendix 2—figure 4
A comparison of relative private transversion frequencies between the nuclear genomes of a caballine Equus (horse, E.

caballus; green), a non-caballine Equus (donkey, E. asinus; red), and the 17 New World-stilt legged (NWSL) equid samples (=Haringtonhippus francisci; blue), using approach three (Appendix 1), with samples ordered by increasing mean mapped read length. Analyses are based on alignment to the horse (A) or donkey (B) genome coordinates.

https://doi.org/10.7554/eLife.29944.031

Tables

Appendix 1—table 1
Selected models of molecular evolution for partitions of the first five mtDNA genome alignment data sets.

All lengths are in base pairs. Reduced length excludes the Coding3 and CR partitions. For all RAxML analyses the GTR model was implemented. *The TrN model was selected, but this cannot be implemented in MrBayes and so the HKY model was used. EPA: evolutionary placement algorithm; CR: control region.

https://doi.org/10.7554/eLife.29944.020
Data setPartitionTotal length
Coding1Coding2Coding3rRNAstRNAsCRAllReduced
1. White rhino outgroupLength3803380338032579152910661658311714
ModelGTR + I + GHKY + I + GGTR + I + GGTR + I + GHKY + I + GHKY*+I + G
2. Malayan tapir outgroupLength3803380338032585153010651658911721
ModelGTR + I + GHKY + I + GGTR + I + GGTR + I + GHKY + I + GHKY*+G
3. Dog + ceratomorphs outgroupsLength38033803380326151540N/A1556411761
ModelGTR + I + GHKY + I + GGTR + I + GGTR + I + GHKY + I + GN/A
4. EPALength3803380338032601153411181666211741
ModelGTR + I + GTrN + I + GGTR + I + GGTR + I + GHKY + I + GHKY + I + G
5. Equids onlyLength380238023802257115289711647611703
ModelTrN + I + GTrN + I + GGTR + GTrN + I + GHKY + IHKY + G
Appendix 1—table 2
Summary of the number and type of synapomorphic bases for each of the three examined equid genera.

A full list of these substitutions, and their position relative to the E. caballus reference mitochondrial genome (NC_001640), can be found in Appendix 1—table 2-Source data 1. *total includes a further five synapomorphic sites that have unique states in each genus.

https://doi.org/10.7554/eLife.29944.021
SubstitutionHippidionHaringtonhippusEquus
 Transition33814766
 Transversion43224
 Insertion240
 Deletion300
Total*39117875
Appendix 1—table 2—source data 1

A compilation of all 634 putative synapomorphic sites in the mitochondrial genome for Hippidion, Haringtonhippus, and Equus (A), with a comparison to the published MS272 mitochondrial genome sequence at the 140 sites with a base state that matches one of the three genera (B).

The horse reference mtDNA has Genbank accession NC_001640.1.

https://doi.org/10.7554/eLife.29944.022
Appendix 2—table 1
Topological shape and support values for the best supported trees.

These results are from the Bayesian and maximum likelihood (ML) analyses of mtDNA data sets 1–3, including either the all or reduced partition sets, and with Hippidion sequences either included or excluded. Topology numbers and node letters refer to those outlined in Appendix 2—figure 3. Bayesian posterior probability support of >0.99 and ML bootstrap support of >95% are in bold for nodes A and B. *support for nodes that are consistent with topology one in Appendix 2—figure 3. NCs: non-caballines.

https://doi.org/10.7554/eLife.29944.028
OutgroupPartitionsHippidion?TipsAnalysis methodTopologySupport
Node ANode BHippidionNWSLNCsCaballines
White rhino
 (Data set 1)
AllExcluded63Bayesian1/2/30.996*N/AN/A1.0001.0001.000
ML1/2/371*N/AN/A10099100
Included69Bayesian20.7511.000*1.0001.0001.0001.000
ML164*96*100100100100
ReducedExcluded63Bayesian1/2/31.000*N/AN/A1.0001.0001.000
ML1/2/3100*N/AN/A99100100
Included69Bayesian20.9481.000*1.0001.0001.0001.000
ML27398*10099100100
Malayan tapir
 (Data set 2)
AllExcluded63Bayesian5/70.971N/AN/A1.0001.0001.000
ML5/787N/AN/A1009999
Included69Bayesian60.8080.8671.0001.0001.0001.000
ML65563100100100100
ReducedExcluded63Bayesian1/2/30.675*N/AN/A1.0001.0001.000
ML4/628N/AN/A1009698
Included69Bayesian30.6850.864*1.0001.0001.0001.000
ML37069100100100100
Dog + ceratomorphs
 (Data set 3)
AllExcluded71Bayesian1/2/30.598*N/AN/A1.0001.0001.000
ML4/659N/AN/A100100100
Included77Bayesian11.000*1.000*1.0001.0001.0001.000
ML194*96*100100100100
ReducedExcluded71Bayesian1/2/30.999*N/AN/A1.0001.0001.000
ML1/2/397*N/AN/A100100100
Included77Bayesian11.000*1.000*1.0001.0001.0001.000
ML199*100*100100100100
Appendix 2—table 2
The a posteriori phylogenetic placement likelihood for eight ceratomorph (rhino and tapir) outgroups.

These analyses used a ML evolutionary placement algorithm, whilst varying the partition set used (all or reduced), and either including or excluding Hippidion sequences. Likelihoods >0.95 are in bold. Topology numbers refer to those outlined in Appendix 2—figure 3. Genbank accession numbers are given in parentheses after outgroup names.

https://doi.org/10.7554/eLife.29944.029
PartitionsOutgroupHippidion?IncludedExcluded
Topology12361/2/34/65/7
 AllTapirus terrestris (AJ428947)0.4560.3170.2050.0180.5490.3130.139
Tapirus indicus (NC023838)0.2750.1050.2250.3890.0500.9080.042
Coelodonta antiquitatis (NC012681)0.9980.2480.4510.301
Dicerorhinus sumatrensis (NC012684)0.9810.0090.1550.5530.292
Rhinoceros unicornis (NC001779)0.9980.5290.3340.137
Rhinoceros sondaicus (NC012683)0.9890.0060.7320.1960.072
Ceratotherium simum (NC001808)0.4480.4990.0530.9490.0180.033
Diceros bicornis (NC012682)0.9170.0650.0180.8510.0730.076
 ReducedTapirus terrestris (AJ428947)0.4100.3910.1990.9870.012
Tapirus indicus (NC023838)0.5360.2980.1660.995
Coelodonta antiquitatis (NC012681)0.4110.5540.0351.000
Dicerorhinus sumatrensis (NC012684)0.9830.0151.000
Rhinoceros unicornis (NC001779)0.9981.000
Rhinoceros sondaicus (NC012683)0.8950.1021.000
Ceratotherium simum (NC001808)0.2960.7041.000
Diceros bicornis (NC012682)0.9961.000
Appendix 2—table 3
The a posteriori phylogenetic placement likelihood for 21 published equid mitochondrial sequences.

These analyses used the ML evolutionary placement algorithm, whilst varying the partition set used (all or reduced), and either including or excluding Hippidion sequences. Sample names are given in parentheses after the species or group name. Localities are given for NWSL equids only. Likelihoods >0.95 are in bold. *Equus includes only caballines and non-caballine equids (NCE). **For EQ04 from Alberta, other placement likelihood values for the Hippidion included/excluded partitions were: Within caballines: 0.003/0.002, Sister to caballines: 0.002/0.002, Within NCE: 0.246/0.245, Sister to NCE: 0.004/0.003. No placements were returned for ‘within Hippidion’. bp: base pairs.

https://doi.org/10.7554/eLife.29944.030
Hippidion?PartitionPublished sampleSequence length (bp)LocalityPlacement
Sister to E. ovodoviSister to HippidionWithin NWSLSister to NWSLSister to Equus*Other**
IncludedAllE. ovodovi (ACAD2305)6881.000
E. ovodovi (ACAD2302)6881.000
E. ovodovi (ACAD2303)6881.000
H. devillei (ACAD3615)476N/A1.000
H. devillei (ACAD3625)543N/A1.000
H. devillei (ACAD3627)543N/A1.000
H. devillei (ACAD3628)543N/A0.999
H. devillei (ACAD3629)476N/A0.999
NWSL equid (JW125)720Klondike, YTN/A0.996
NWSL equid (JW126)720Klondike, YTN/A0.999
IncludedAllNWSL equid (EQ01)620Dry Cave, NMN/A0.7350.256
NWSL equid (EQ03)117Dry Cave, NMN/A0.0020.9740.0110.003
NWSL equid (EQ04)117Edmonton, ABN/A0.0040.7030.0140.0070.255
NWSL equid (EQ09)620Natural Trap Cave, WYN/A0.9810.014
NWSL equid (EQ13)620Natural Trap Cave, WYN/A0.992
NWSL equid (EQ16)464Dry Cave, NMN/A0.8540.138
NWSL equid (EQ22)620Natural Trap Cave, WYN/A0.999
NWSL equid (EQ30)393San Josecito Cave, MX-NLN/A0.7920.198
NWSL equid (EQ41)398Natural Trap Cave, WYN/A0.997
NWSL equid (JW328)mitogenomeMineral Hill Cave, NVN/A1.000
NWSL equid (MS272)mitogenomeKlondike, YTN/A1.000
ReducedNWSL equid (JW328)mitogenomeMineral Hill Cave, NVN/A0.996
NWSL equid (MS272)mitogenomeKlondike, YTN/A1.000
ExcludedAllE. ovodovi (ACAD2305)6881.000N/AN/A
E. ovodovi (ACAD2302)6881.000N/AN/A
E. ovodovi (ACAD2303)6881.000N/AN/A
NWSL equid (JW125)720Klondike, YTN/AN/A0.996N/A
NWSL equid (JW126)720Klondike, YTN/AN/A0.999N/A
NWSL equid (EQ01)620Dry Cave, NMN/AN/A0.7310.259N/A
NWSL equid (EQ03)117Dry Cave, NMN/AN/A0.9800.010N/A
NWSL equid (EQ04)117Edmonton, ABN/AN/A0.7210.013N/A0.252
NWSL equid (EQ09)620Natural Trap Cave, WYN/AN/A0.9870.008N/A
NWSL equid (EQ13)620Natural Trap Cave, WYN/AN/A0.993N/A
NWSL equid (EQ16)464Dry Cave, NMN/AN/A0.8440.148N/A
NWSL equid (EQ22)620Natural Trap Cave, WYN/AN/A0.999N/A
NWSL equid (EQ30)393San Josecito Cave, MX-NLN/AN/A0.7880.203N/A
NWSL equid (EQ41)398Natural Trap Cave, WYN/AN/A0.995N/A
NWSL equid (JW328)mitogenomeMineral Hill Cave, NVN/AN/A1.000N/A
NWSL equid (MS272)mitogenomeKlondike, YTN/AN/A1.000N/A
ReducedNWSL equid (JW328)mitogenomeMineral Hill Cave, NVN/AN/A0.995N/A
NWSL equid (MS272)mitogenomeKlondike, YTN/AN/A1.000N/A
Appendix 2—table 4
Sex determination analysis of 17 NWSL equids.

Chromosome ratio is the relative mapping frequency ratio between all autosomes and the X-chromosome. Males are inferred if the ratio is 0.45–0.55 and females if the ratio is 0.9–1.1.

https://doi.org/10.7554/eLife.29944.032
SampleMuseum accessionChromosome ratioInferred sex
 AF037YG 402.2350.48male
 JK166LACM(CIT) 109/1508070.93female
 JK167LACM(CIT) 109/1492910.91female
 JK207LACM(CIT) 109/1564500.92female
 JK260KU 478000.95female
 JK276KU 536780.91female
 MS341YG 303.10850.50male
 MS349YG 130.550.48male
 MS439YG 401.3870.98female
 PH008YG 404.2050.90female
 PH013YG 130.60.87probable female
 PH014YG 303.3710.46male
 PH015YG 404.6620.44probable male
 PH021YG 29.1690.83probable female
 PH023YG 160.80.91female
 PH036YG 76.20.81probable female
 PH047YG 404.6630.88probable female
Appendix 2—table 4—source data 1

Data from the sex determination analyses of 17 NWSL equids, based on alignment to the horse genome (EquCab2).

https://doi.org/10.7554/eLife.29944.033

Data availability

The following data sets were generated
  1. 1
    Nuclear DNA sequences from 17 Haringtonhippus francisci fossils
    1. Heintzman PD
    2. Cahill JA
    3. Kapp JD
    4. Stiller M
    5. Shapiro B
    (2017)
    Publicly available at NCBI Short Read Archive (accession no: PRJNA384940).
  2. 2
    Mitochondrial genome sequence from YG 303.371
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168317).
  3. 3
    Mitochondrial genome sequence from YG 133.16
    1. Heintzman PD
    2. Stiller M
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168318).
  4. 4
    Mitochondrial genome sequence from YG 29.169
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168319).
  5. 5
    Mitochondrial genome sequence from YG 401.387
    1. Heintzman PD
    2. Stiller M
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168320).
  6. 6
    Mitochondrial genome sequence from YG 404.663
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168321).
  7. 7
    Mitochondrial genome sequence from YG 328.54
    1. Heintzman PD
    2. Stiller M
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168322).
  8. 8
    Mitochondrial genome sequence from YG 378.5
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168323).
  9. 9
    Mitochondrial genome sequence from YG 404.478
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168324).
  10. 10
    Mitochondrial genome sequence from YG 402.235
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168325).
  11. 11
    Mitochondrial genome sequence from YG 130.55
    1. Heintzman PD
    2. Stiller M
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168326).
  12. 12
    Mitochondrial genome sequence from YG 198.1
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168327).
  13. 13
    Mitochondrial genome sequence from YG 303.1085
    1. Heintzman PD
    2. Stiller M
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168328).
  14. 14
    Mitochondrial genome sequence from YG 130.6
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168329).
  15. 15
    Mitochondrial genome sequence from YG 417.13
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168330).
  16. 16
    Mitochondrial genome sequence from YG 76.2
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168331).
  17. 17
    Mitochondrial genome sequence from YG 160.8
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168332).
  18. 18
    Mitochondrial genome sequence from YG 404.662
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168333).
  19. 19
    Mitochondrial genome sequence from YG 404.480
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168334).
  20. 20
    Mitochondrial genome sequence from YG 401.235
    1. Heintzman PD
    2. Stiller M
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168335).
  21. 21
    Mitochondrial genome sequence from YG 404.205
    1. Heintzman PD
    2. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:KT168336).
  22. 22
    Mitochondrial genome sequence from LACM(CIT) 109 / 150807
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134655).
  23. 23
    Mitochondrial genome sequence from LACM(CIT) 109 / 149291
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134656).
  24. 24
    Mitochondrial genome sequence from LACM(CIT) 109 / 156450
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134657).
  25. 25
    Mitochondrial genome sequence from KU 47800
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134658).
  26. 26
    Mitochondrial genome sequence from KU 62055
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134659).
  27. 27
    Mitochondrial genome sequence from KU 33418
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134660).
  28. 28
    Mitochondrial genome sequence from KU 53678
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134661).
  29. 29
    Mitochondrial genome sequence from KU 50817
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134662).
  30. 30
    Mitochondrial genome sequence from KU 62158
    1. Heintzman PD
    2. Kapp JD
    3. Shapiro B
    (2017)
    Publicly available at NCBI GenBank (accession no:MF134663).
  31. 31
    Data from: A new genus of horse from Pleistocene North America
    1. Heintzman PD
    2. McHorse BK
    3. Shapiro B
    (2017)
    Available at Dryad Digital Repository under a CC0 Public Domain Dedication.

Additional files

Supplementary file 1

Metadata for all samples used in the mitochondrial and nuclear genomic analyses, with the francisci holotype included for reference.

*mtDNA coverage is based on the iterative assembler or as previously published. **New mtDNA genome sequence, coverage, and radiocarbon data are reported for MS272.

https://doi.org/10.7554/eLife.29944.017
Transparent reporting form
https://doi.org/10.7554/eLife.29944.018
Appendix 1—table 2—source data 1

A compilation of all 634 putative synapomorphic sites in the mitochondrial genome for Hippidion, Haringtonhippus, and Equus (A), with a comparison to the published MS272 mitochondrial genome sequence at the 140 sites with a base state that matches one of the three genera (B).

The horse reference mtDNA has Genbank accession NC_001640.1.

https://doi.org/10.7554/eLife.29944.022
Appendix 2—table 4—source data 1

Data from the sex determination analyses of 17 NWSL equids, based on alignment to the horse genome (EquCab2).

https://doi.org/10.7554/eLife.29944.033

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