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eLife2017; 6; e29944; doi: 10.7554/eLife.29944

A new genus of horse from Pleistocene North America.

Abstract: The extinct 'New World stilt-legged', or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group . We therefore propose a new genus, , for the sole species . Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event.
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Publication Date: 2017-11-28 PubMed ID: 29182148PubMed Central: PMC5705217DOI: 10.7554/eLife.29944Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't
  • Research Support
  • N.I.H.
  • Extramural
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research examines the extinct ‘New World stilt-legged’, or NWSL, equids which are a group of Pleistocene horses that were endemic to North America. Through the use of complete mitochondrial and partial nuclear genomes, the study finds that these equids belonged to a single species that falls outside of previously known groups, leading to the proposal of a new genus.

Genomic Analysis of NWSL Equids

  • The research focused on the NWSL equids – Pleistocene horses native to North America, which have slender distal limb bones similar to those of Asiatic asses, like the Persian onager.
  • Earlier genetic studies suggested that these horses may be closely related to caballine horses rather than Asiatic asses.
  • The scientists obtained complete mitochondrial genomes and partial nuclear genomes from NWSL equid remains found in different location across North America.

Defining a New Genus

  • Even though there have been several species of NWSL equid named in the past, the genetic analysis performed in this study supports the hypothesis that all these equids belonged to a single species that existed between the middle and late Pleistocene epoch.
  • The genetics of this species show they do not fit within any previously known group (or “crown group”), suggesting that they belong to a newfound genus.
  • The researchers propose the name “Haringtonhippus francisci” for this new genus and sole species.

Implications For Understanding Pleistocene Extinction

  • By integrating genomic (genetic) and phenomic (physical traits) approaches, the study enables a refined system for classifying extinct megafauna (large animals).
  • This new understanding could allow for a more comprehensive comprehension of the full extent of the Pleistocene extinction event, which saw the disappearance of numerous large mammal species.

Cite This Article

APA
Heintzman PD, Zazula GD, MacPhee R, Scott E, Cahill JA, McHorse BK, Kapp JD, Stiller M, Wooller MJ, Orlando L, Southon J, Froese DG, Shapiro B. (2017). A new genus of horse from Pleistocene North America. Elife, 6, e29944. https://doi.org/10.7554/eLife.29944

Publication

eLife
ISSN: 2050-084X
NlmUniqueID: 101579614
Country: England
Language: English
Volume: 6
PII: e29944

Researcher Affiliations

Heintzman, Peter D
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.
  • Tromsø University Museum, UiT - The Arctic University of Norway, Tromsø, Norway.
Zazula, Grant D
  • Yukon Palaeontology Program, Government of Yukon, Whitehorse, Canada.
MacPhee, Ross DE
  • Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, United States.
Scott, Eric
  • Cogstone Resource Management, Incorporated, Riverside, United States.
  • California State University San Bernardino, San Bernardino, United States.
Cahill, James A
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.
McHorse, Brianna K
  • Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, United States.
Kapp, Joshua D
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.
Stiller, Mathias
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.
  • Department of Translational Skin Cancer Research, German Consortium for Translational Cancer Research, Essen, Germany.
Wooller, Matthew J
  • College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, United States.
  • Alaska Stable Isotope Facility, Water and Environmental Research Center, University of Alaska Fairbanks, Fairbanks, United States.
Orlando, Ludovic
  • Centre for GeoGenetics, Natural History Museum of Denmark, København K, Denmark.
  • Université Paul Sabatier, Université de Toulouse, Toulouse, France.
Southon, John
  • Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, Irvine, United States.
Froese, Duane G
  • Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada.
Shapiro, Beth
  • Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States.
  • UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, United States.

MeSH Terms

  • Animals
  • Biometry
  • DNA / chemistry
  • DNA / genetics
  • Fossils
  • Genotype
  • Horses / anatomy & histology
  • Horses / classification
  • Horses / genetics
  • North America
  • Phenotype
  • Sequence Analysis, DNA

Grant Funding

  • S10 RR027303 / NCRR NIH HHS
  • S10 RR029668 / NCRR NIH HHS

Conflict of Interest Statement

No competing interests declared.

References

This article includes 98 references
  1. Allen WR, Short RV. Interspecific and extraspecific pregnancies in equids: anything goes.. J Hered 1997 Sep-Oct;88(5):384-92.
    doi: 10.1093/oxfordjournals.jhered.a023123pubmed: 9378914google scholar: lookup
  2. Arnason U, Adegoke JA, Gullberg A, Harley EH, Janke A, Kullberg M. Mitogenomic relationships of placental mammals and molecular estimates of their divergences.. Gene 2008 Sep 15;421(1-2):37-51.
    doi: 10.1016/j.gene.2008.05.024pubmed: 18590805google scholar: lookup
  3. Azzaroli A, Voorhies MR. The Genus Equus in North America. The blancan species.. Palaeontographia Italica 1993;80:175–198.
  4. Azzaroli A. Ascent and decline of monodactyl equids: a case for prehistoric overkill.. Annales Zoologici Fennici 1992;28:151–163.
  5. Azzaroli A. A synopsis of the Quaternary species of Equus in North America.. Bolletino Della Societa Palaeontologica Italiana 1995;34:205–221.
  6. Barrón-Ortiz CI, Rodrigues AT, Theodor JM, Kooyman BP, Yang DY, Speller CF. Cheek tooth morphology and ancient mitochondrial DNA of late Pleistocene horses from the western interior of North America: Implications for the taxonomy of North American Late Pleistocene Equus.. PLoS One 2017;12(8):e0183045.
    doi: 10.1371/journal.pone.0183045pmc: PMC5560644pubmed: 28817644google scholar: lookup
  7. Beaumont W, Beverly R, Southon J, Taylor RE. Bone preparation at the KCCAMS laboratory.. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 2010;268:906–909.
    doi: 10.1016/j.nimb.2009.10.061google scholar: lookup
  8. Bennett DK. Stripes Do Not a Zebra Make, Part I: A Cladistic Analysis of Equus.. Systematic Zoology 1980;29:272–287.
    doi: 10.2307/2412662google scholar: lookup
  9. Bennett EA, Champlot S, Peters J, Arbuckle BS, Guimaraes S, Pruvost M, Bar-David S, Davis SJM, Gautier M, Kaczensky P, Kuehn R, Mashkour M, Morales-Muñiz A, Pucher E, Tournepiche JF, Uerpmann HP, Bălăşescu A, Germonpré M, Gündem CY, Hemami MR, Moullé PE, Ötzan A, Uerpmann M, Walzer C, Grange T, Geigl EM. Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA.. PLoS One 2017;12(4):e0174216.
    doi: 10.1371/journal.pone.0174216pmc: PMC5396879pubmed: 28422966google scholar: lookup
  10. Berger SA, Krompass D, Stamatakis A. Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood.. Syst Biol 2011 May;60(3):291-302.
    doi: 10.1093/sysbio/syr010pmc: PMC3078422pubmed: 21436105google scholar: lookup
  11. Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S. Targeted retrieval and analysis of five Neandertal mtDNA genomes.. Science 2009 Jul 17;325(5938):318-21.
    doi: 10.1126/science.1174462pubmed: 19608918google scholar: lookup
  12. Burke A, Eisenmann V, Ambler GK. The systematic position of Equus hydruntinus, an extinct species of Pleistocene equid☆.. Quaternary Research 2003;59:459–469.
    doi: 10.1016/S0033-5894(03)00059-0google scholar: lookup
  13. Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, Mitrovica JX, Hostetler SW, McCabe AM. The Last Glacial Maximum.. Science 2009 Aug 7;325(5941):710-4.
    doi: 10.1126/science.1172873pubmed: 19661421google scholar: lookup
  14. Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, Valdiosera C, García N, Pääbo S, Arsuaga JL, Meyer M. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.. Proc Natl Acad Sci U S A 2013 Sep 24;110(39):15758-63.
    doi: 10.1073/pnas.1314445110pmc: PMC3785785pubmed: 24019490google scholar: lookup
  15. Dabney J, Meyer M, Pääbo S. Ancient DNA damage.. Cold Spring Harb Perspect Biol 2013 Jul 1;5(7).
    doi: 10.1101/cshperspect.a012567pmc: PMC3685887pubmed: 23729639google scholar: lookup
  16. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing.. Nat Methods 2012 Jul 30;9(8):772.
    doi: 10.1038/nmeth.2109pmc: PMC4594756pubmed: 22847109google scholar: lookup
  17. Der Sarkissian C, Vilstrup JT, Schubert M, Seguin-Orlando A, Eme D, Weinstock J, Alberdi MT, Martin F, Lopez PM, Prado JL, Prieto A, Douady CJ, Stafford TW, Willerslev E, Orlando L. Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids.. Biol Lett 2015 Mar;11(3).
    doi: 10.1098/rsbl.2014.1058pmc: PMC4387498pubmed: 25762573google scholar: lookup
  18. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7.. Mol Biol Evol 2012 Aug;29(8):1969-73.
    doi: 10.1093/molbev/mss075pmc: PMC3408070pubmed: 22367748google scholar: lookup
  19. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput.. Nucleic Acids Res 2004;32(5):1792-7.
    doi: 10.1093/nar/gkh340pmc: PMC390337pubmed: 15034147google scholar: lookup
  20. Eisenmann V, Alberdi MT, deGiuli C, Staesche U. Methodology.. In: Woodburne M, Sondaar P, editors. Studying Fossil Horses. Vol. 1. Leiden: E. J. Brill; 1988. pp. 1–71.
  21. Eisenmann V, Howe J, Pichardo M. Old World hemiones and New World slender species (Mammalia, Equidae). Palaeovertebrata 2008;36:159–233.
    doi: 10.18563/pv.36.1-4.159-233google scholar: lookup
  22. Eisenmann V, Sergej V. Unexpected finding of a new Equus species (Mammalia, Perissodactyla) belonging to a supposedly extinct subgenus in late Pleistocene deposits of Khakassia (Southwestern Siberia). Geodiversitas 2011;33:519–530.
    doi: 10.5252/g2011n3a5google scholar: lookup
  23. Eisenmann V. L’Environnement Des Hominidés Au Plio- Pléistocène. Indications paléoécologiques fournies par les Equus (Mammalia, Perissodactyla) Plio-Pléistocènes d’Afrique. 1985; pp. 57–79.
  24. Eisenmann V. Origins, dispersals, and migrations of Equus (Mammalia, Perissodactyla). CFS Courier Forschungsinstitut Senckenberg 1992;153:161–170.
  25. Eisenmann V. In: Advances in Vertebrate Paleontology: Hen to Panta ; a Tribute to Constantin Rădulescu and Petre Mihai Samson. Petculescu A, Stiuca E, editors. Bucharest: 2003. pp. 31–40.
  26. Enk J, Devault A, Widga C, Saunders J, Szpak P, Southon J, Rouillard J-M, Shapiro B, Golding GB, Zazula G, Froese D, Fisher DC, MacPhee RDE, Poinar H. Mammuthus population dynamics in late Pleistocene North America: divergence, phylogeography, and introgression.. Frontiers in Ecology and Evolution 2016;4.
    doi: 10.3389/fevo.2016.00042google scholar: lookup
  27. Forsten A. Middle Pleistocene replacement of stenonid horses by caballoid horses — ecological implications.. Palaeogeography, Palaeoclimatology, Palaeoecology 1988;65:23–33.
    doi: 10.1016/0031-0182(88)90109-5google scholar: lookup
  28. Forsten A. Mitochondrial-DNA time-table and the evolution of Equus: comparison of molecular and palaeontological evidence.. Annales Zoologici Fennici 1992;28:301–309.
  29. Forsten A. Climate and the evolution of Equus (Perissodactyla, Equidae) in the Plio-Pleistocene of Eurasia.. Acta Zoologica Cracoviensia 1996;39:161–166.
  30. Froese D, Stiller M, Heintzman PD, Reyes AV, Zazula GD, Soares AE, Meyer M, Hall E, Jensen BJ, Arnold LJ, MacPhee RD, Shapiro B. Fossil and genomic evidence constrains the timing of bison arrival in North America.. Proc Natl Acad Sci U S A 2017 Mar 28;114(13):3457-3462.
    doi: 10.1073/pnas.1620754114pmc: PMC5380047pubmed: 28289222google scholar: lookup
  31. Froese DG, Zazula GD, Westgate JA, Preece SJ, Sanborn PT, Reyes AV, Pearce NJG. The Klondike goldfields and Pleistocene environments of Beringia.. GSA Today 2009;19:4.
    doi: 10.1130/GSATG54A.1google scholar: lookup
  32. Goebel T, Waters MR, O'Rourke DH. The late Pleistocene dispersal of modern humans in the Americas.. Science 2008 Mar 14;319(5869):1497-502.
    doi: 10.1126/science.1153569pubmed: 18339930google scholar: lookup
  33. Graham RW, Belmecheri S, Choy K, Culleton BJ, Davies LJ, Froese D, Heintzman PD, Hritz C, Kapp JD, Newsom LA, Rawcliffe R, Saulnier-Talbot É, Shapiro B, Wang Y, Williams JW, Wooller MJ. Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska.. Proc Natl Acad Sci U S A 2016 Aug 16;113(33):9310-4.
    doi: 10.1073/pnas.1604903113pmc: PMC4995940pubmed: 27482085google scholar: lookup
  34. Green RE, Vohr SH, Rice ES. tri-aln-report.. 4404df2Github 2015 https://github.com/Paleogenomics/Chrom-Compare.
  35. Groves CP, Willoughby DP. Studies on the taxonomy and phylogeny of the genus Equus. 1. Subgeneric classification of the recent species.. Mammalia 1981;45.
    doi: 10.1515/mamm.1981.45.3.321google scholar: lookup
  36. Guthrie RD. Rapid body size decline in Alaskan Pleistocene horses before extinction.. Nature 2003 Nov 13;426(6963):169-71.
    doi: 10.1038/nature02098pubmed: 14614503google scholar: lookup
  37. Guthrie RD. New carbon dates link climatic change with human colonization and Pleistocene extinctions.. Nature 2006 May 11;441(7090):207-9.
    doi: 10.1038/nature04604pubmed: 16688174google scholar: lookup
  38. Harington CR, Clulow FV. Pleistocene mammals from Gold Run Creek, Yukon Territory.. Canadian Journal of Earth Sciences 1973;10:697–759.
    doi: 10.1139/e73-069google scholar: lookup
  39. Harington CR. PhD Thesis: Pleistocene mammals of the Yukon Territory.. Edmonton: University of Alberta; 1977.
  40. Harington CR. Pleistocene vertebrates of the Yukon Territory.. Quaternary Science Reviews 2011;30:2341–2354.
    doi: 10.1016/j.quascirev.2011.05.020google scholar: lookup
  41. Hay OP. Contributions to the knowledge of the mammals of the Pleistocene of North America.. Proceedings of the United States National Museum 1915;48:515–575.
    doi: 10.5479/si.00963801.48-2086.515google scholar: lookup
  42. Heintzman PD, Zazula GD, Cahill JA, Reyes AV, MacPhee RD, Shapiro B. Genomic Data from Extinct North American Camelops Revise Camel Evolutionary History.. Mol Biol Evol 2015 Sep;32(9):2433-40.
    doi: 10.1093/molbev/msv128pubmed: 26037535google scholar: lookup
  43. Heintzman PD, Zazula GD, MacPhee R, Scott E, Cahill JA, McHorse BK, Kapp JD, Stiller M, Wooller MJ, Orlando L, Southon J, Froese DG, Shapiro B. A new genus of horse from Pleistocene North America.. Elife 2017 Nov 28;6.
    pmc: PMC5705217pubmed: 29182148doi: 10.7554/elife.29944google scholar: lookup
  44. Hibbard CW. Equus (Asinus) calobatus Troxell and associated vertebrates from the Pleistocene of Kansas.. Transactions of the Kansas Academy of Science 1953;56:111–126.
    doi: 10.2307/3626201google scholar: lookup
  45. Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.. Bioinformatics 2013 Jul 1;29(13):1682-4.
    doi: 10.1093/bioinformatics/btt193pmc: PMC3694634pubmed: 23613487google scholar: lookup
  46. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18655-60.
    doi: 10.1073/pnas.1412627111pmc: PMC4284605pubmed: 25453089google scholar: lookup
  47. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.. Bioinformatics 2012 Jun 15;28(12):1647-9.
    doi: 10.1093/bioinformatics/bts199pmc: PMC3371832pubmed: 22543367google scholar: lookup
  48. Kim KS, Lee SE, Jeong HW, Ha JH. The complete nucleotide sequence of the domestic dog (Canis familiaris) mitochondrial genome.. Mol Phylogenet Evol 1998 Oct;10(2):210-20.
    doi: 10.1006/mpev.1998.0513pubmed: 9878232google scholar: lookup
  49. Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform.. Nucleic Acids Res 2012 Jan;40(1):e3.
    doi: 10.1093/nar/gkr771pmc: PMC3245947pubmed: 22021376google scholar: lookup
  50. Koch PL, Barnosky AD. Late quaternary extinctions: state of the debate.. Annual Review of Ecology, Evolution, and Systematics 2006;37:215–250.
    doi: 10.1146/annurev.ecolsys.34.011802.132415google scholar: lookup
  51. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2.. Nat Methods 2012 Mar 4;9(4):357-9.
    doi: 10.1038/nmeth.1923pmc: PMC3322381pubmed: 22388286google scholar: lookup
  52. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform.. Bioinformatics 2010 Mar 1;26(5):589-95.
    doi: 10.1093/bioinformatics/btp698pmc: PMC2828108pubmed: 20080505google scholar: lookup
  53. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools.. Bioinformatics 2009 Aug 15;25(16):2078-9.
    doi: 10.1093/bioinformatics/btp352pmc: PMC2723002pubmed: 19505943google scholar: lookup
  54. Linnaeus C. Systema Naturae Per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, Cum Characteribus, Differentiis, Synonymis, Locis .. Salvius: Holmiæ; 1758.
  55. Lippold S, Matzke NJ, Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.. BMC Evol Biol 2011 Nov 14;11:328.
    doi: 10.1186/1471-2148-11-328pmc: PMC3247663pubmed: 22082251google scholar: lookup
  56. Lundelius EL, Stevens MS. Equus francisci Hay, a small stilt-legged horse, middle Pleistocene of Texas.. Journal of Palaeontology 1970;44:148–153.
  57. Luo Y, Chen Y, Liu F, Jiang C, Gao Y. Mitochondrial genome sequence of the Tibetan wild ass (Equus kiang).. Mitochondrial DNA 2011 Feb;22(1-2):6-8.
    doi: 10.3109/19401736.2011.588221pubmed: 21732718google scholar: lookup
  58. Macdonald ML, Toohey LM, Skinner MF. The Species, Genera, and Tribes of the Living and Extinct Horses of the World 1758-1966.. 1992.
  59. MacFadden BJ. Fossil Horses: Systematics, Palaeobiology, and Evolution of the Family Equidae.. Cambridge University Press; 1992.
  60. MacFadden BJ. Evolution of Tertiary Mammals of North America. Equidae. 1998; pp. 537–559.
  61. Martin FM, Borrero LA. Climate change, availability of territory, and Late Pleistocene human exploration of Ultima Esperanza, South Chile.. Quaternary International 2017;428:86–95.
    doi: 10.1016/j.quaint.2015.06.023google scholar: lookup
  62. Martin FM, Todisco D, Rodet J, San Román M, Morello F, Prevosti F, Stern C, Borrero LA. Nuevas excavaciones en cueva del medio: procesos de formación de la cueva y avances en los estudios de interacción entre cazadores-recolectores y fauna extinta (Pleistoceno final, Patagonia Meridional). Magallania 2015;43:165–189.
    doi: 10.4067/S0718-22442015000100010google scholar: lookup
  63. Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing.. Cold Spring Harb Protoc 2010 Jun;2010(6):pdb.prot5448.
    doi: 10.1101/pdb.prot5448pubmed: 20516186google scholar: lookup
  64. Muangkram Y, Wajjwalku W, Kaolim N, Buddhakosai W, Kamolnorranath S, Siriaroonrat B, Tipkantha W, Dongsaard K, Maikaew U, Sanannu S. The complete mitochondrial genome of the Asian tapirs (Tapirus indicus): the only extant Tapiridae species in the old world.. Mitochondrial DNA A DNA Mapp Seq Anal 2016;27(1):413-5.
    doi: 10.3109/19401736.2014.898283pubmed: 24621216google scholar: lookup
  65. O'Dea A, Lessios HA, Coates AG, Eytan RI, Restrepo-Moreno SA, Cione AL, Collins LS, de Queiroz A, Farris DW, Norris RD, Stallard RF, Woodburne MO, Aguilera O, Aubry MP, Berggren WA, Budd AF, Cozzuol MA, Coppard SE, Duque-Caro H, Finnegan S, Gasparini GM, Grossman EL, Johnson KG, Keigwin LD, Knowlton N, Leigh EG, Leonard-Pingel JS, Marko PB, Pyenson ND, Rachello-Dolmen PG, Soibelzon E, Soibelzon L, Todd JA, Vermeij GJ, Jackson JB. Formation of the Isthmus of Panama.. Sci Adv 2016 Aug;2(8):e1600883.
    doi: 10.1126/sciadv.1600883pmc: PMC4988774pubmed: 27540590google scholar: lookup
  66. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. Nature 2013 Jul 4;499(7456):74-8.
    doi: 10.1038/nature12323pubmed: 23803765google scholar: lookup
  67. Orlando L, Male D, Alberdi MT, Prado JL, Prieto A, Cooper A, Hänni C. Ancient DNA clarifies the evolutionary history of American Late Pleistocene equids.. J Mol Evol 2008 May;66(5):533-8.
    doi: 10.1007/s00239-008-9100-xpubmed: 18398561google scholar: lookup
  68. Orlando L, Mashkour M, Burke A, Douady CJ, Eisenmann V, Hänni C. Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed by morphological and genetical analyses of fossils.. Mol Ecol 2006 Jul;15(8):2083-93.
    doi: 10.1111/j.1365-294X.2006.02922.xpubmed: 16780426google scholar: lookup
  69. Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R, Shockey BJ, Wrinn PJ, Vasil'ev SK, Ovodov ND, Cherry MI, Hopwood B, Male D, Austin JJ, Hänni C, Cooper A. Revising the recent evolutionary history of equids using ancient DNA.. Proc Natl Acad Sci U S A 2009 Dec 22;106(51):21754-9.
    doi: 10.1073/pnas.0903672106pmc: PMC2799835pubmed: 20007379google scholar: lookup
  70. Quinn JH. Pleistocene Equidae of Texas. Bureau of Economic Geology Vol. 33. University of Texas; 1957. pp. 1–51.
    doi: 10.23867/ri0033dgoogle scholar: lookup
  71. R Development Core Team . R Foundation for Statistical Computing. Vienna, Austria: 2008. http://www.R-project.org
  72. Reimer PJ, Bard E, Bayliss A, Beck JW, Blackwell PG, Ramsey CB, Buck CE, Cheng H, Edwards RL, Friedrich M, Grootes PM, Guilderson TP, Haflidason H, Hajdas I, Hatté C, Heaton TJ, Hoffmann DL, Hogg AG, Hughen KA, Kaiser KF, Kromer B, Manning SW, Niu M, Reimer RW, Richards DA, Scott EM, Southon JR, Staff RA, Turney CSM, van der Plicht J. IntCal13 and marine13 radiocarbon age calibration curves 0–50,000 years cal BP.. Radiocarbon 2013;55:1869–1887.
    doi: 10.2458/azu_js_rc.55.16947google scholar: lookup
  73. Rohland N, Siedel H, Hofreiter M. A rapid column-based ancient DNA extraction method for increased sample throughput.. Mol Ecol Resour 2010 Jul;10(4):677-83.
    doi: 10.1111/j.1755-0998.2009.02824.xpubmed: 21565072google scholar: lookup
  74. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.. Syst Biol 2012 May;61(3):539-42.
    doi: 10.1093/sysbio/sys029pmc: PMC3329765pubmed: 22357727google scholar: lookup
  75. Rybczynski N, Gosse JC, Harington CR, Wogelius RA, Hidy AJ, Buckley M. Mid-Pliocene warm-period deposits in the High Arctic yield insight into camel evolution.. Nat Commun 2013;4:1550.
    doi: 10.1038/ncomms2516pmc: PMC3615376pubmed: 23462993google scholar: lookup
  76. Ryder OA, Epel NC, Benirschke K. Chromosome banding studies of the Equidae.. Cytogenet Cell Genet 1978;20(1-6):332-50.
    doi: 10.1159/000130862pubmed: 648186google scholar: lookup
  77. Sandom C, Faurby S, Sandel B, Svenning JC. Global late Quaternary megafauna extinctions linked to humans, not climate change.. Proc Biol Sci 2014 Jul 22;281(1787).
    doi: 10.1098/rspb.2013.3254pmc: PMC4071532pubmed: 24898370google scholar: lookup
  78. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets.. Bioinformatics 2011 Mar 15;27(6):863-4.
    doi: 10.1093/bioinformatics/btr026pmc: PMC3051327pubmed: 21278185google scholar: lookup
  79. Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L. Improving ancient DNA read mapping against modern reference genomes.. BMC Genomics 2012 May 10;13:178.
    doi: 10.1186/1471-2164-13-178pmc: PMC3468387pubmed: 22574660google scholar: lookup
  80. Scott E. Biodiversity Response to Climate Change in the Middle Pleistocene. Pliocene and Pleistocene horses from Porcupine Cave. 2004; pp. 264–279.
  81. Seguin-Orlando A, Gamba C, Sarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen ED, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW Jr, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Shapiro B, Willerslev E, Prokhortchouk E, Orlando L. Pros and cons of methylation-based enrichment methods for ancient DNA.. Sci Rep 2015 Jul 2;5:11826.
    doi: 10.1038/srep11826pmc: PMC4488743pubmed: 26134828google scholar: lookup
  82. Shockey BJ, Salas-Gismondi R, Baby P, Guyot J-L, Baltazar MC, Huaman L, Flynn JJ. New Pleistocene cave faunas of the Andes of central Peru: radiocarbon ages and the survival of low latitude, Pleistocene DNA.. Palaeontologia Electronica 2009;12:15A.
  83. Shorthouse DP. SimpleMappr. An Online Tool to Produce Publication-Quality Point Maps.. [2017]; 2010 http://www.simplemappr.net.
  84. Skinner MF, Hibbard CW. Early Pleistocene pre-glacial and glacial rocks and faunas of North-Central Nebraska.. Bulletin of the American Museum of Natural History 1972;148:1–148.
  85. St. John J. SeqPrep.. b5606ddGithub 2013 https://github.com/jstjohn/SeqPrep.
  86. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.. Bioinformatics 2014 May 1;30(9):1312-3.
    doi: 10.1093/bioinformatics/btu033pmc: PMC3998144pubmed: 24451623google scholar: lookup
  87. Steiner CC, Ryder OA. Characterization of Prdm9 in equids and sterility in mules.. PLoS One 2013;8(4):e61746.
    doi: 10.1371/journal.pone.0061746pmc: PMC3632555pubmed: 23613924google scholar: lookup
  88. Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. Mitochondrial phylogenomics of modern and ancient equids.. PLoS One 2013;8(2):e55950.
    doi: 10.1371/journal.pone.0055950pmc: PMC3577844pubmed: 23437078google scholar: lookup
  89. Weinstock J, Willerslev E, Sher A, Tong W, Ho SY, Rubenstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Xulong L, Cooper A. Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective.. PLoS Biol 2005 Aug;3(8):e241.
    doi: 10.1371/journal.pbio.0030241pmc: PMC1159165pubmed: 15974804google scholar: lookup
  90. Welker F, Collins MJ, Thomas JA, Wadsley M, Brace S, Cappellini E, Turvey ST, Reguero M, Gelfo JN, Kramarz A, Burger J, Thomas-Oates J, Ashford DA, Ashton PD, Rowsell K, Porter DM, Kessler B, Fischer R, Baessmann C, Kaspar S, Olsen JV, Kiley P, Elliott JA, Kelstrup CD, Mullin V, Hofreiter M, Willerslev E, Hublin JJ, Orlando L, Barnes I, MacPhee RD. Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.. Nature 2015 Jun 4;522(7554):81-4.
    doi: 10.1038/nature14249pubmed: 25799987google scholar: lookup
  91. Willerslev E, Gilbert MT, Binladen J, Ho SY, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, Schuster SC. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.. BMC Evol Biol 2009 May 11;9:95.
    doi: 10.1186/1471-2148-9-95pmc: PMC2694787pubmed: 19432984google scholar: lookup
  92. Winans MC. Revision of North American Fossil Species of the Genus Equus (Mammalia: Perissodactyla: Equidae). Dissertation.. Austin: Univ. of Texas; 1985. p. 264.
  93. Xu X, Arnason U. The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region.. Gene 1994 Oct 21;148(2):357-62.
    pubmed: 7958969doi: 10.1016/0378-1119(94)90713-7google scholar: lookup
  94. Xu X, Arnason U. The complete mitochondrial DNA sequence of the white rhinoceros, Ceratotherium simum, and comparison with the mtDNA sequence of the Indian rhinoceros, Rhinoceros unicornis.. Mol Phylogenet Evol 1997 Apr;7(2):189-94.
    doi: 10.1006/mpev.1996.0385pubmed: 9126560google scholar: lookup
  95. Xu X, Gullberg A, Arnason U. The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs.. J Mol Evol 1996 Nov;43(5):438-46.
    doi: 10.1007/BF02337515pubmed: 8875857google scholar: lookup
  96. Xu X, Janke A, Arnason U. The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the Phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea).. Mol Biol Evol 1996 Nov;13(9):1167-73.
    doi: 10.1093/oxfordjournals.molbev.a025681pubmed: 8896369google scholar: lookup
  97. Zazula GD, MacPhee RD, Metcalfe JZ, Reyes AV, Brock F, Druckenmiller PS, Groves P, Harington CR, Hodgins GW, Kunz ML, Longstaffe FJ, Mann DH, McDonald HG, Nalawade-Chavan S, Southon JR. American mastodon extirpation in the Arctic and Subarctic predates human colonization and terminal Pleistocene climate change.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18460-5.
    doi: 10.1073/pnas.1416072111pmc: PMC4284604pubmed: 25453065google scholar: lookup
  98. Zazula GD, MacPhee RDE, Southon J, Nalawade-Chavan S, Reyes AV, Hewitson S, Hall E. A case of early Wisconsinan “over-chill”: New radiocarbon evidence for early extirpation of western camel (Camelops hesternus) in eastern Beringia.. Quaternary Science Reviews 2017;171:48–57.
    doi: 10.1016/j.quascirev.2017.06.031google scholar: lookup

Citations

This article has been cited 15 times.
  1. Musiał AD, Ropka-Molik K, Stefaniuk-Szmukier M, Myćka G, Bieniek A, Yasynetska N. Characteristic of Przewalski horses population from Askania-Nova reserve based on genetic markers. Mol Biol Rep 2023 Aug;50(8):7121-7126.
    doi: 10.1007/s11033-023-08581-4pubmed: 37365410google scholar: lookup
  2. Landry Z, Roloson MJ, Fraser D. Investigating the reliability of metapodials as taxonomic Indicators for Beringian horses. J Mamm Evol 2022;29(4):863-875.
    doi: 10.1007/s10914-022-09626-4pubmed: 36438779google scholar: lookup
  3. Cirilli O, Machado H, Arroyo-Cabrales J, Barrón-Ortiz CI, Davis E, Jass CN, Jukar AM, Landry Z, Marín-Leyva AH, Pandolfi L, Pushkina D, Rook L, Saarinen J, Scott E, Semprebon G, Strani F, Villavicencio NA, Kaya F, Bernor RL. Evolution of the Family Equidae, Subfamily Equinae, in North, Central and South America, Eurasia and Africa during the Plio-Pleistocene. Biology (Basel) 2022 Aug 24;11(9).
    doi: 10.3390/biology11091258pubmed: 36138737google scholar: lookup
  4. Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. Elife 2022 May 11;11.
    doi: 10.7554/eLife.73346pubmed: 35543411google scholar: lookup
  5. Stephan T, Burgess SM, Cheng H, Danko CG, Gill CA, Jarvis ED, Koepfli KP, Koltes JE, Lyons E, Ronald P, Ryder OA, Schriml LM, Soltis P, VandeWoude S, Zhou H, Ostrander EA, Karlsson EK. Darwinian genomics and diversity in the tree of life. Proc Natl Acad Sci U S A 2022 Jan 25;119(4).
    doi: 10.1073/pnas.2115644119pubmed: 35042807google scholar: lookup
  6. Nedoluzhko AV, Sharko FS, Boulygina ES, Tsygankova SV, Slobodova NV, Gruzdeva NM, Rastorguev SM, Spasskaya NN, Maschenko EN. The complete mitochondrial genome of the extinct Pleistocene horse (Equus cf. lenensis) from Kotelny Island (New Siberian Islands, Russia) and its phylogenetic assessment. Mitochondrial DNA B Resour 2019 Dec 13;5(1):243-245.
    doi: 10.1080/23802359.2019.1699877pubmed: 33366505google scholar: lookup
  7. Meltzer DJ. Overkill, glacial history, and the extinction of North America's Ice Age megafauna. Proc Natl Acad Sci U S A 2020 Nov 17;117(46):28555-28563.
    doi: 10.1073/pnas.2015032117pubmed: 33168739google scholar: lookup
  8. Günther T, Nettelblad C. The presence and impact of reference bias on population genomic studies of prehistoric human populations. PLoS Genet 2019 Jul;15(7):e1008302.
    doi: 10.1371/journal.pgen.1008302pubmed: 31348818google scholar: lookup
  9. Novak BJ. De-Extinction. Genes (Basel) 2018 Nov 13;9(11).
    doi: 10.3390/genes9110548pubmed: 30428542google scholar: lookup
  10. Weingarten A, Häusler M, Serangeli J, Verheijen I, Reiter E, Radzevičiūtė R, Stoessel A, Krause J, Spyrou MA, Conard NJ, Nieselt K, Posth C. Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen. Nat Ecol Evol 2025 Dec;9(12):2248-2258.
    doi: 10.1038/s41559-025-02859-5pubmed: 41034648google scholar: lookup
  11. Günther T, Goldberg A, Schraiber JG. Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias. G3 (Bethesda) 2025 Oct 8;15(10).
    doi: 10.1093/g3journal/jkaf172pubmed: 40737495google scholar: lookup
  12. Hill MG, Widga CC, Surovell TA, Wilson KM, Allaun SA, Litynski ML, Titcomb J. An update on Aenocyon dirus in the interior of North America: new records, radiocarbon dates, ZooMS spectra, and isotopic data for an iconic late Pleistocene carnivore. PeerJ 2025;13:e19219.
    doi: 10.7717/peerj.19219pubmed: 40231072google scholar: lookup
  13. Du W, Sun Q, Hu S, Yu P, Kan S, Zhang W. Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses. Sci Rep 2025 Feb 25;15(1):6803.
    doi: 10.1038/s41598-025-91564-1pubmed: 40000832google scholar: lookup
  14. Chatters JC, Potter BA, Fiedel SJ, Morrow JE, Jass CN, Wooller MJ. Mammoth featured heavily in Western Clovis diet. Sci Adv 2024 Dec 6;10(49):eadr3814.
    doi: 10.1126/sciadv.adr3814pubmed: 39630905google scholar: lookup
  15. Vincelette AR, Renders E, Scott KM, Falkingham PL, Janis CM. Hipparion tracks and horses' toes: the evolution of the equid single hoof. R Soc Open Sci 2023 Jun;10(6):230358.
    doi: 10.1098/rsos.230358pubmed: 37351494google scholar: lookup
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