FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Proceedings of the National Academy of Sciences of the United States of America2009; 106(51); 21754-21759; doi: 10.1073/pnas.0903672106

Revising the recent evolutionary history of equids using ancient DNA.

Abstract: The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.
Get Full Text
Publication Date: 2009-12-09 PubMed ID: 20007379PubMed Central: PMC2799835DOI: 10.1073/pnas.0903672106Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article
  • Research Support
  • Non-U.S. Gov't

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.

This research article explores the recent evolutionary history of the equid family, which includes horses and similar mammals. Using ancient DNA extracted from fossils, the researchers have found unexpected evolutionary patterns and two new species of equids, revising our understanding of this family’s history.

Understanding Equid Evolution Through Ancient DNA

  • The researchers examined the DNA extracted from fossils of 35 ancient equid specimens found in four different regions: South America, Europe, Southwest Asia, and South Africa.
  • Out of these samples, 22 provided between 87 and 688 base pairs of reproducible ancient DNA (aDNA) sequences from the mitochondrial DNA, which can provide insight into maternal lineage.
  • Through phylogenetic analysis (examining the relationship between different species), they identified two previously unknown equid species, a new South American variety of Hippidion (an extinct genus of horse) and another descendant of a basal lineage potentially related to Middle Pleistocene-era equids.

Revising Taxonomy and Extinction Timelines

  • The DNA from specimens of the extinct Cape zebra, known as Equus capensis, was found to form a separate clade within the modern plains zebra species, showing an unexpected relationship between these two groups. This clade also included the extinct quagga, suggesting that this group of zebras was more adaptable and varied than previously thought (termed ‘phenotypic plasticity’).
  • The research also revised previously accepted extinction timelines for two related equid groups, showing the value of aDNA in rectifying and updating historical records.

Proposition of a Rapid DNA Barcoding Approach

  • The researchers acknowledge that despite their findings, the current dataset is not able to answer all questions related to equid evolution and taxonomy. To assist in resolving this, they propose a rapid DNA barcoding approach.
  • This would involve quickly sequencing the DNA of various Late Pleistocene fossil equids that have been identified solely through morphological analysis (studying shape and form) to verify their taxonomic status. Such an approach could help clarify complex evolutionary and taxonomic questions.

Cite This Article

APA
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. (2009). Revising the recent evolutionary history of equids using ancient DNA. Proc Natl Acad Sci U S A, 106(51), 21754-21759. https://doi.org/10.1073/pnas.0903672106

Publication

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
NlmUniqueID: 7505876
Country: United States
Language: English
Volume: 106
Issue: 51
Pages: 21754-21759

Researcher Affiliations

Orlando, Ludovic
  • Institut de Génomique Fonctionnelle de Lyon, Université de Lyon 1, Ecole Normale Supérieure de Lyon, and Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, 69364 Lyon Cédex 07, France. ludovic.orlando@ens-lyon.fr
Metcalf, Jessica L
    Alberdi, Maria T
      Telles-Antunes, Miguel
        Bonjean, Dominique
          Otte, Marcel
            Martin, Fabiana
              Eisenmann, Véra
                Mashkour, Marjan
                  Morello, Flavia
                    Prado, Jose L
                      Salas-Gismondi, Rodolfo
                        Shockey, Bruce J
                          Wrinn, Patrick J
                            Vasil'ev, Sergei K
                              Ovodov, Nikolai D
                                Cherry, Michael I
                                  Hopwood, Blair
                                    Male, Dean
                                      Austin, Jeremy J
                                        Hänni, Catherine
                                          Cooper, Alan

                                            MeSH Terms

                                            • Animals
                                            • Biological Evolution
                                            • DNA / genetics
                                            • Fossils
                                            • Horses / classification
                                            • Horses / genetics
                                            • Molecular Sequence Data

                                            Conflict of Interest Statement

                                            The authors declare no conflict of interest.

                                            References

                                            This article includes 69 references
                                            1. Huxley TH. Address delivered at the anniversary meeting of the Geological Society of London, February 18. Proceedings of the Geological Society of London 1870 pp. 16–38.
                                            2. Gould SJ. Hen's Teeth and Horse's Toe: Further Reflections in Natural History. 1994.
                                            3. Simpson GG. Horses. 1951.
                                            4. Macfadden BJ. Evolution. Fossil horses--evidence for evolution.. Science 2005 Mar 18;307(5716):1728-30.
                                              pubmed: 15774746doi: 10.1126/science.1105458google scholar: lookup
                                            5. Azzaroli A. Phylogeny of the genus Equus L. Palaeontogr Ital 2002;89:11–16.
                                            6. Groves CP, Willoughby DP. Studies on the taxonomy and phylogeny of the genus Equus. Mammalia 1981;45:321–354.
                                            7. Oakenfull EA, Lim HN, Ryder OA. A survey of equid mitochondrial DNA: Implications for the evolution, genetic diversity and conservation of Equus. Cons Genet 2000;1:341–353.
                                            8. Groves CP, Bell CH. New investigations on the taxonomy of the zebras genus Equus, subgenus. Hippotigris. Mammal Biol 2004;69:182–196.
                                            9. Lorenzen ED, Arctander P, Siegismund HR. High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites.. Mol Ecol 2008 Jun;17(12):2812-24.
                                              pubmed: 18466230doi: 10.1111/j.1365-294x.2008.03781.xgoogle scholar: lookup
                                            10. Eisenmann V. Evolutionary characters and phylogeny of the genus Equus (Mammalia, Perissodactyla) (Translated from French). CR Acad Sci Paris D 1979;288:497–500.
                                            11. Leonard JA, Rohland N, Glaberman S, Fleischer RC, Caccone A, Hofreiter M. A rapid loss of stripes: the evolutionary history of the extinct quagga.. Biol Lett 2005 Sep 22;1(3):291-5.
                                              pmc: PMC1617154pubmed: 17148190doi: 10.1098/rsbl.2005.0323google scholar: lookup
                                            12. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M. Genetic analyses from ancient DNA.. Annu Rev Genet 2004;38:645-79.
                                              pubmed: 15568989doi: 10.1146/annurev.genet.37.110801.143214google scholar: lookup
                                            13. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. DNA sequences from the quagga, an extinct member of the horse family.. Nature 1984 Nov 15-21;312(5991):282-4.
                                              pubmed: 6504142doi: 10.1038/312282a0google scholar: lookup
                                            14. Vilà C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H. Widespread origins of domestic horse lineages.. Science 2001 Jan 19;291(5503):474-7.
                                              pubmed: 11161199doi: 10.1126/science.291.5503.474google scholar: lookup
                                            15. Orlando L, Eisenmann V, Reynier F, Sondaar P, Hänni C. Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis.. J Mol Evol 2003;57 Suppl 1:S29-40.
                                              pubmed: 15008401doi: 10.1007/s00239-003-0005-4google scholar: lookup
                                            16. 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.
                                              pmc: PMC1159165pubmed: 15974804doi: 10.1371/journal.pbio.0030241google scholar: lookup
                                            17. 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.
                                              pubmed: 16780426doi: 10.1111/j.1365-294x.2006.02922.xgoogle scholar: lookup
                                            18. 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.
                                              pubmed: 18398561doi: 10.1007/s00239-008-9100-xgoogle scholar: lookup
                                            19. MacFadden BJ. Pleistocene horses from Tarija, Bolivia, and validity of the genus Onohippidium (Mammalia: Equidae). J Vertebr Paleontol 1997;17:199–218.
                                            20. Reguero MA, Candela AM, Alonso RN. Biochronology and biostratigraphy of the Uquia Formation (Pliocene–early Pleistocene, NW Argentina) and its significance in the Great American Biotic Interchange. J S Am Earth Sci 2007;23:1–16.
                                            21. Alberdi MT, Prado JL, Prieto A. Considerations on the paper "Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis'', by Ludovic Orlando, Véra Eisenmann, Frédéric Reynier, Paul Sondaar, Catherine Hänni.. J Mol Evol 2005 Jul;61(1):145-7.
                                              pubmed: 15980958doi: 10.1007/s00239-004-0216-3google scholar: lookup
                                            22. Azzaroli A. The genus Equus in North America—The Pleistocene species. Palaeont Ital 1998;85:1–60.
                                            23. Eisenmann V. Equus capensis (Mammalia, Perissodactyla) from Elandsfontein. Palaeont Afr 2000;36:91–96.
                                            24. Churcher CS. The extinct Cape zebra. Sagittarius 1986;1:4–5.
                                            25. Thackeray JF. Zebras from Wonderwerk cave, northern Cape Province, South Africa: Attempts to distinguish Equus burchelli and E quagga. South African J Sci 1988;84:99–101.
                                            26. Smith CI, Chamberlain AT, Riley MS, Stringer C, Collins MJ. The thermal history of human fossils and the likelihood of successful DNA amplification.. J Hum Evol 2003 Sep;45(3):203-17.
                                              pubmed: 14580590doi: 10.1016/s0047-2484(03)00106-4google scholar: lookup
                                            27. Hofreiter M, Jaenicke V, Serre D, von Haeseler A, Pääbo S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA.. Nucleic Acids Res 2001 Dec 1;29(23):4793-9.
                                              pmc: PMC96698pubmed: 11726688doi: 10.1093/nar/29.23.4793google scholar: lookup
                                            28. Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions.. Nucleic Acids Res 2007;35(17):5717-28.
                                              pmc: PMC2034480pubmed: 17715147doi: 10.1093/nar/gkm588google scholar: lookup
                                            29. Cooper A, Poinar HN. Ancient DNA: do it right or not at all.. Science 2000 Aug 18;289(5482):1139.
                                              pubmed: 10970224doi: 10.1126/science.289.5482.1139bgoogle scholar: lookup
                                            30. Orlando L, Hänni C, Douady CJ. Mammoth and elephant phylogenetic relationships: Mammut americanum, the missing outgroup.. Evol Bioinform Online 2007 Mar 29;3:45-51.
                                              pmc: PMC2674638pubmed: 19430604
                                            31. Rohland N, Malaspinas AS, Pollack JL, Slatkin M, Matheus P, Hofreiter M. Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup.. PLoS Biol 2007 Aug;5(8):e207.
                                              pmc: PMC1925134pubmed: 17676977doi: 10.1371/journal.pbio.0050207google scholar: lookup
                                            32. Prado JL, Alberdi MT. A cladistic analysis of the horses of the tribe equine. J Paleontol 1996;39:663–680.
                                            33. Shockey BJ. New Pleistocene cave faunas of the Andes of central Perú: Radiocarbon ages and the survival of low latitude, Pleistocene DNA. Palaeontologia Electronica 2009;12(3):15A.
                                            34. Alberdi MT, Prado JL. Review of the genus Hippidion Owen, 1869 (Mammalia: Perissodactyla) from the Pleistocene of South America. Zool J Linn Soc 1993;108:1–22.
                                            35. Alberdi MT, Prado JL. Comments on Pleistocene horses from Tarija, Bolivia, and the validity of the genus Onohippidium (Mammalia: Equidae), by B. J. MacFadden. J Vert Palaeontol 1998;18:669–672.
                                            36. Ibaraki M. Closing of the Central American Seaway and Neogene coastal upwelling along the Pacific coast of South America. Tectonophysics 1997;281:99–104.
                                            37. Alberdi MT, Prado JL, Ortiz Jaureguizar E. Patterns of body size changes in fossil and living Equini (Perissodactyla). Biol J Linn Soc 1995;54:349–370.
                                            38. Eisenmann V, Brink JS. Koffiefontein quaggas and true Cape quaggas: The importance of basic skull morphology. South Afric J Sci 2000;96:529–533.
                                            39. Vasiliev SK, Derevianko AP, Markin SV. Large mammal fauna of the Sartan period from the northwestern Altai. Arch Ethn Anthropol Eurasia 2006;2:2–22.
                                            40. Eisenmann V. Pliocene and pleistocene equids: Paleontology versus molecular biology. 2006 pp. 71–89.
                                            41. Eisenmann V, Howe J, Pichardo M. Old World hemiones and New World slender species (Mammalia, Equidae). Palaeovertebrata in press.
                                            42. Antunes MT. The Zebro (Equidae) and its extinction in Portugal, with an appendix on the noun zebro and the modern zebra. 2006 pp. 210–235.
                                            43. Bonifay MF. Equus hydruntinus Regalia minor n. ssp. from the caves of Lunel-Viel (Hérault, France). Beihefte Tübinger Atlas Vorderen Orients Reihe A 1991;19:178–216.
                                            44. Wilms C. The extinction of the European wild ass (Translated from German). Germania 1989;67:143–148.
                                            45. Burke A, Eisenmann V, Ambler G. The systematic position of Equus hydruntinus, an extinct species of Pleistocene equid. Quat Res 2003;59:459–469.
                                            46. Ryder OA, Chemnick LG. Chromosomal and molecular evolution in Asiatic wild asses.. Genetica 1990;83(1):67-72.
                                              pubmed: 2090563doi: 10.1007/bf00774690google scholar: lookup
                                            47. Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AW, Bray SC, O'Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.. BMC Evol Biol 2008 Jul 28;8:220.
                                              pmc: PMC2518930pubmed: 18662376doi: 10.1186/1471-2148-8-220google scholar: lookup
                                            48. Oakenfull EA, Clegg JB. Phylogenetic relationships within the genus Equus and the evolution of alpha and theta globin genes.. J Mol Evol 1998 Dec;47(6):772-83.
                                              pubmed: 9847419doi: 10.1007/pl00006436google scholar: lookup
                                            49. Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I, Binladen J, Willerslev E, Hansen AJ, Baryshnikov GF, Burns JA, Davydov S, Driver JC, Froese DG, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, Cooper A. Rise and fall of the Beringian steppe bison.. Science 2004 Nov 26;306(5701):1561-5.
                                              pubmed: 15567864doi: 10.1126/science.1101074google scholar: lookup
                                            50. Barnett R, Shapiro B, Barnes I, Ho SY, Burger J, Yamaguchi N, Higham TF, Wheeler HT, Rosendahl W, Sher AV, Sotnikova M, Kuznetsova T, Baryshnikov GF, Martin LD, Harington CR, Burns JA, Cooper A. Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity.. Mol Ecol 2009 Apr;18(8):1668-77.
                                              pubmed: 19302360doi: 10.1111/j.1365-294x.2009.04134.xgoogle scholar: lookup
                                            51. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A. Dynamics of Pleistocene population extinctions in Beringian brown bears.. Science 2002 Mar 22;295(5563):2267-70.
                                              pubmed: 11910112doi: 10.1126/science.1067814google scholar: lookup
                                            52. Bunce M, Worthy TH, Ford T, Hoppitt W, Willerslev E, Drummond A, Cooper A. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis.. Nature 2003 Sep 11;425(6954):172-5.
                                              pubmed: 12968178doi: 10.1038/nature01871google scholar: lookup
                                            53. Huynen L, Millar CD, Scofield RP, Lambert DM. Nuclear DNA sequences detect species limits in ancient moa.. Nature 2003 Sep 11;425(6954):175-8.
                                              pubmed: 12968179doi: 10.1038/nature01838google scholar: lookup
                                            54. Wood B, Lonergan N. The hominin fossil record: taxa, grades and clades.. J Anat 2008 Apr;212(4):354-76.
                                              pmc: PMC2409102pubmed: 18380861doi: 10.1111/j.1469-7580.2008.00871.xgoogle scholar: lookup
                                            55. Wood B, Collard M. The human genus.. Science 1999 Apr 2;284(5411):65-71.
                                              pubmed: 10102822doi: 10.1126/science.284.5411.65google scholar: lookup
                                            56. Knapp M, Rohland N, Weinstock J, Baryshnikov G, Sher A, Nagel D, Rabeder G, Pinhasi R, Schmidt HA, Hofreiter M. First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns.. Mol Ecol 2009 Mar;18(6):1225-38.
                                              pubmed: 19226321doi: 10.1111/j.1365-294x.2009.04088.xgoogle scholar: lookup
                                            57. Hofreiter M. Long DNA sequences and large data sets: Investigating the Quaternary via ancient DNA. Quat Sci Rev 2008;27:2586–2592.
                                            58. Hofreiter M, Stewart J. Ecological change, range fluctuations and population dynamics during the Pleistocene.. Curr Biol 2009 Jul 28;19(14):R584-94.
                                              pubmed: 19640497doi: 10.1016/j.cub.2009.06.030google scholar: lookup
                                            59. Loreille O, Orlando L, Patou-Mathis M, Philippe M, Taberlet P, Hänni C. Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages.. Curr Biol 2001 Feb 6;11(3):200-3.
                                              pubmed: 11231157doi: 10.1016/s0960-9822(01)00046-xgoogle scholar: lookup
                                            60. Orlando L, Darlu P, Toussaint M, Bonjean D, Otte M, Hänni C. Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence.. Curr Biol 2006 Jun 6;16(11):R400-2.
                                              pubmed: 16753548doi: 10.1016/j.cub.2006.05.019google scholar: lookup
                                            61. Rohland N, Hofreiter M. Ancient DNA extraction from bones and teeth.. Nat Protoc 2007;2(7):1756-62.
                                              pubmed: 17641642doi: 10.1038/nprot.2007.247google scholar: lookup
                                            62. Mateiu LM, Rannala BH. Bayesian inference of errors in ancient DNA caused by postmortem degradation.. Mol Biol Evol 2008 Jul;25(7):1503-11.
                                              pubmed: 18420593doi: 10.1093/molbev/msn095google scholar: lookup
                                            63. Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny.. Comput Appl Biosci 1996 Dec;12(6):543-8.
                                              pubmed: 9021275doi: 10.1093/bioinformatics/12.6.543google scholar: lookup
                                            64. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sunderland, MA: Sinauer Associates; 2000.
                                            65. R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing; 2007.
                                            66. Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies.. Mol Biol Evol 1999 Jan;16(1):37-48.
                                              pubmed: 10331250doi: 10.1093/oxfordjournals.molbev.a026036google scholar: lookup
                                            67. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees.. BMC Evol Biol 2007 Nov 8;7:214.
                                              pmc: PMC2247476pubmed: 17996036doi: 10.1186/1471-2148-7-214google scholar: lookup
                                            68. Eisenmann V. Extinct and extant horses (Equus sensu lato): Skulls and superior cheek teeth (Translated from French). Cah Paleont Paris: 1980.
                                            69. Geraads D. The Pleistocene hominid site of Ternifine, Algeria: New results on the environment, age, and human industries. Quaternary Res 1986;25:380–386.

                                            Citations

                                            This article has been cited 37 times.
                                            1. 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
                                            2. 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
                                            3. Bacon AM, Bourgon N, Welker F, Cappellini E, Fiorillo D, Tombret O, Thi Mai Huong N, Anh Tuan N, Sayavonkhamdy T, Souksavatdy V, Sichanthongtip P, Antoine PO, Duringer P, Ponche JL, Westaway K, Joannes-Boyau R, Boesch Q, Suzzoni E, Frangeul S, Patole-Edoumba E, Zachwieja A, Shackelford L, Demeter F, Hublin JJ, Dufour É. A multi-proxy approach to exploring Homo sapiens' arrival, environments and adaptations in Southeast Asia. Sci Rep 2021 Oct 26;11(1):21080.
                                              doi: 10.1038/s41598-021-99931-4pubmed: 34702921google scholar: lookup
                                            4. Boubli JP, Janiak MC, Porter LM, de la Torre S, Cortés-Ortiz L, Da Silva MNF, Rylands AB, Nash S, Bertuol F, Byrne H, Silva FE, Rohe F, de Vries D, Beck RMD, Ruiz-Gartzia I, Kuderna LFK, Marques-Bonet T, Hrbek T, Farias IP, Van Heteren AH, Roos C. Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum. Zool Res 2021 Nov 18;42(6):761-771.
                                              doi: 10.24272/j.issn.2095-8137.2021.143pubmed: 34643070google scholar: lookup
                                            5. Zecherle LJ, Nichols HJ, Bar-David S, Brown RP, Hipperson H, Horsburgh GJ, Templeton AR. Subspecies hybridization as a potential conservation tool in species reintroductions. Evol Appl 2021 May;14(5):1216-1224.
                                              doi: 10.1111/eva.13191pubmed: 34025762google scholar: lookup
                                            6. Cirilli O, Pandolfi L, Rook L, Bernor RL. Evolution of Old World Equus and origin of the zebra-ass clade. Sci Rep 2021 May 12;11(1):10156.
                                              doi: 10.1038/s41598-021-89440-9pubmed: 33980921google scholar: lookup
                                            7. Druzhkova AS, Makunin AI, Vorobieva NV, Vasiliev SK, Ovodov ND, Shunkov MV, Trifonov VA, Graphodatsky AS. Complete mitochondrial genome of an extinct Equus (Sussemionus) ovodovi specimen from Denisova cave (Altai, Russia). Mitochondrial DNA B Resour 2017 Feb 6;2(1):79-81.
                                              doi: 10.1080/23802359.2017.1285209pubmed: 33473722google scholar: lookup
                                            8. Andermann T, Faurby S, Turvey ST, Antonelli A, Silvestro D. The past and future human impact on mammalian diversity. Sci Adv 2020 Sep;6(36).
                                              doi: 10.1126/sciadv.abb2313pubmed: 32917612google scholar: lookup
                                            9. Badenhorst S, Steininger CM. The Equidae from Cooper's D, an early Pleistocene fossil locality in Gauteng, South Africa. PeerJ 2019;7:e6909.
                                              doi: 10.7717/peerj.6909pubmed: 31143541google scholar: lookup
                                            10. Yuan JX, Hou XD, Barlow A, Preick M, Taron UH, Alberti F, Basler N, Deng T, Lai XL, Hofreiter M, Sheng GL. Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China. PLoS One 2019;14(5):e0216883.
                                              doi: 10.1371/journal.pone.0216883pubmed: 31095634google scholar: lookup
                                            11. Heck L, Wilson LAB, Evin A, Stange M, Sánchez-Villagra MR. Shape variation and modularity of skull and teeth in domesticated horses and wild equids. Front Zool 2018;15:14.
                                              doi: 10.1186/s12983-018-0258-9pubmed: 29713365google scholar: lookup
                                            12. Rey-Iglesia A, Grandal-d'Anglade A, Campos PF, Hansen AJ. Mitochondrial DNA of pre-last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species. Ecol Evol 2017 Dec;7(24):10690-10700.
                                              doi: 10.1002/ece3.3553pubmed: 29299249google scholar: lookup
                                            13. 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.
                                              doi: 10.7554/eLife.29944pubmed: 29182148google scholar: lookup
                                            14. 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.0174216pubmed: 28422966google scholar: lookup
                                            15. Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M, Orlando L. The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2016 Oct;204(2):423-434.
                                              doi: 10.1534/genetics.116.194860pubmed: 27729493google scholar: lookup
                                            16. Famoso NA, Davis EB. On the relationship between enamel band complexity and occlusal surface area in Equids (Mammalia, Perissodactyla). PeerJ 2016;4:e2181.
                                              doi: 10.7717/peerj.2181pubmed: 27441119google scholar: lookup
                                            17. Metcalf JL, Turney C, Barnett R, Martin F, Bray SC, Vilstrup JT, Orlando L, Salas-Gismondi R, Loponte D, Medina M, De Nigris M, Civalero T, Fernández PM, Gasco A, Duran V, Seymour KL, Otaola C, Gil A, Paunero R, Prevosti FJ, Bradshaw CJ, Wheeler JC, Borrero L, Austin JJ, Cooper A. Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation. Sci Adv 2016 Jun;2(6):e1501682.
                                              doi: 10.1126/sciadv.1501682pubmed: 27386563google scholar: lookup
                                            18. Naundrup PJ, Svenning JC. A Geographic Assessment of the Global Scope for Rewilding with Wild-Living Horses (Equus ferus). PLoS One 2015;10(7):e0132359.
                                              doi: 10.1371/journal.pone.0132359pubmed: 26177104google scholar: lookup
                                            19. 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.2014.1058pubmed: 25762573google scholar: lookup
                                            20. 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.1412627111pubmed: 25453089google scholar: lookup
                                            21. Han L, Zhu S, Ning C, Cai D, Wang K, Chen Q, Hu S, Yang J, Shao J, Zhu H, Zhou H. Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys. BMC Evol Biol 2014 Nov 30;14:246.
                                              doi: 10.1186/s12862-014-0246-4pubmed: 25433485google scholar: lookup
                                            22. Nedoluzhko AV, Boulygina ES, Sokolov AS, Tsygankova SV, Gruzdeva NM, Rezepkin AD, Prokhortchouk EB. Analysis of the Mitochondrial Genome of a Novosvobodnaya Culture Representative using Next-Generation Sequencing and Its Relation to the Funnel Beaker Culture. Acta Naturae 2014 Apr;6(2):31-5.
                                              pubmed: 25093108
                                            23. Finno CJ, Bannasch DL. Applied equine genetics. Equine Vet J 2014 Sep;46(5):538-44.
                                              doi: 10.1111/evj.12294pubmed: 24802051google scholar: lookup
                                            24. Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT, Prado JL, Prieto A, Willerslev E, Orlando L. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS One 2013;8(10):e78575.
                                              doi: 10.1371/journal.pone.0078575pubmed: 24205269google scholar: lookup
                                            25. 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
                                            26. Wang X, Miller DC, Harman R, Antczak DF, Clark AG. Paternally expressed genes predominate in the placenta. Proc Natl Acad Sci U S A 2013 Jun 25;110(26):10705-10.
                                              doi: 10.1073/pnas.1308998110pubmed: 23754418google scholar: lookup
                                            27. MacFadden BJ. Dispersal of Pleistocene Equus (Family Equidae) into South America and calibration of GABI 3 based on evidence from Tarija, Bolivia. PLoS One 2013;8(3):e59277.
                                              doi: 10.1371/journal.pone.0059277pubmed: 23527150google scholar: lookup
                                            28. 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.0055950pubmed: 23437078google scholar: lookup
                                            29. McCallum J, Hall S, Lissone I, Anderson J, Huynen L, Lambert DM. Highly informative ancient DNA 'snippets' for New Zealand moa. PLoS One 2013;8(1):e50732.
                                              doi: 10.1371/journal.pone.0050732pubmed: 23341875google scholar: lookup
                                            30. 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: 10.1186/1471-2148-11-328pubmed: 22082251google scholar: lookup
                                            31. Pruvost M, Bellone R, Benecke N, Sandoval-Castellanos E, Cieslak M, Kuznetsova T, Morales-Muñiz A, O'Connor T, Reissmann M, Hofreiter M, Ludwig A. Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art. Proc Natl Acad Sci U S A 2011 Nov 15;108(46):18626-30.
                                              doi: 10.1073/pnas.1108982108pubmed: 22065780google scholar: lookup
                                            32. Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B, Hofreiter M. Discovery of lost diversity of paternal horse lineages using ancient DNA. Nat Commun 2011 Aug 23;2:450.
                                              doi: 10.1038/ncomms1447pubmed: 21863017google scholar: lookup
                                            33. Hofreiter M, Barnes I. Diversity lost: are all Holarctic large mammal species just relict populations?. BMC Biol 2010 Apr 21;8:46.
                                              doi: 10.1186/1741-7007-8-46pubmed: 20409351google scholar: lookup
                                            34. 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
                                            35. Castiglione GM, Chen X, Xu Z, Dbouk NH, Bose AA, Carmona-Berrio D, Chi EE, Zhou L, Boronina TN, Cole RN, Wu S, Liu AD, Liu TD, Lu H, Kalbfleisch T, Rinker D, Rokas A, Ortved K, Duh EJ. Running a genetic stop sign accelerates oxygen metabolism and energy production in horses. Science 2025 Mar 28;387(6741):eadr8589.
                                              doi: 10.1126/science.adr8589pubmed: 40146832google scholar: lookup
                                            36. Mondanaro A, Girardi G, Castiglione S, Timmermann A, Zeller E, Venugopal T, Serio C, Melchionna M, Esposito A, Di Febbraro M, Raia P. EutherianCoP. An integrated biotic and climate database for conservation paleobiology based on eutherian mammals. Sci Data 2025 Jan 13;12(1):6.
                                              doi: 10.1038/s41597-024-04181-4pubmed: 39805871google scholar: lookup
                                            37. Bard JBL. Modelling speciation: Problems and implications. In Silico Biol 2023;15(1-2):23-42.
                                              doi: 10.3233/ISB-220253pubmed: 36502315google scholar: lookup
                                            Subscribe to our newsletter
                                            Join 99,780 horse owners like you who receive our email updates on horse health and nutrition.