FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Nature communications2011; 2; 450; doi: 10.1038/ncomms1447

Discovery of lost diversity of paternal horse lineages using ancient DNA.

Abstract: Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA from eight ancient wild horses and one 2,800-year-old domesticated horse. Both ancient and modern domestic horses form a separate branch from the ancient wild horses, with the Przewalski horse at its base. Our methodology establishes the feasibility of re-sequencing long ancient nuclear DNA fragments and demonstrates the power of ancient Y chromosome DNA sequence data to provide insights into the evolutionary history of populations.
© 2011 Macmillan Publishers Limited. All rights reserved.
Get Full Text
Publication Date: 2011-08-23 PubMed ID: 21863017DOI: 10.1038/ncomms1447Google 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 explores the historical diversity of paternal horse lineages, which has been lost in modern horses, by analyzing ancient DNA. Contrary to the lack of diversity in today’s male horse DNA, the study finds significant diversity in paternal lineages from ancient wild and domesticated horses.

Research Overview

  • The research revolves around the discrepancy between the abundant genetic diversity seen in female-inherited mitochondrial DNA of modern domestic horses and the virtually non-existent sequence diversity in the male-inherited Y chromosome. Several theories exist to explain this difference, but these require knowledge about the diversity present in both maternal and paternal lineages prior to horse domestication.
  • Because wild horses are nearly extinct, ancient DNA studies are the only method available to assess this ancestral diversity. This study uses technology that allows for the sequencing of long ancient nuclear DNA fragments to examine the Y chromosomal DNA of ancient horses.

Methodology and Findings

  • Researchers sequenced 4 kb (kilobases) of Y chromosomal DNA from eight ancient wild horses and one 2,800-year-old domesticated horse to investigate the ancestral diversity in ancient male horses. The vast diversity found in these samples contrasts with the minimal diversity seen in modern male horse Y chromosomes.
  • The results indicated that both ancient and modern domestic horses form a unique branch separate from that of ancient wild horses. The Przewalski horse, considered the last truly wild horse species in the world, formed the base of this branch. This suggests that the lack of diversity in modern horse Y chromosomes could be attributed to the domestication process, rather than being a trait of all horses.

Implications of the Study

  • The methodology used in this study demonstrates the feasibility of re-sequencing long ancient nuclear DNA fragments. This is significant because it opens the possibility of researching other extinct or near extinct species with similar methods.
  • Furthermore, the study shows the potential of ancient Y chromosome DNA sequence data in providing important insights into the evolutionary history of species.

Cite This Article

APA
Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B, Hofreiter M. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nat Commun, 2, 450. https://doi.org/10.1038/ncomms1447

Publication

Nature communications
ISSN: 2041-1723
NlmUniqueID: 101528555
Country: England
Language: English
Volume: 2
Pages: 450

Researcher Affiliations

Lippold, Sebastian
  • Research Group Molecular Ecology, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. sebastian_lippold@eva.mpg.de
Knapp, Michael
    Kuznetsova, Tatyana
      Leonard, Jennifer A
        Benecke, Norbert
          Ludwig, Arne
            Rasmussen, Morten
              Cooper, Alan
                Weinstock, Jaco
                  Willerslev, Eske
                    Shapiro, Beth
                      Hofreiter, Michael

                        MeSH Terms

                        • Animals
                        • DNA, Mitochondrial / genetics
                        • Evolution, Molecular
                        • Female
                        • Genetic Variation
                        • Horses / classification
                        • Horses / genetics
                        • Male
                        • Molecular Sequence Data
                        • Phylogeny
                        • Y Chromosome / genetics

                        Grant Funding

                        • Wellcome Trust

                        References

                        This article includes 49 references
                        1. 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
                        2. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence.. PLoS Biol 2006 May;4(5):e88.
                          pubmed: 16683862doi: 10.1371/journal.pbio.0040088google scholar: lookup
                        3. Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C, Weber J, Olek K. Mitochondrial DNA and the origins of the domestic horse.. Proc Natl Acad Sci U S A 2002 Aug 6;99(16):10905-10.
                          pubmed: 12130666doi: 10.1073/pnas.152330099google scholar: lookup
                        4. Jobling MA, Tyler-Smith C. The human Y chromosome: an evolutionary marker comes of age.. Nat Rev Genet 2003 Aug;4(8):598-612.
                          pubmed: 12897772doi: 10.1038/nrg1124google scholar: lookup
                        5. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
                          pubmed: 19892987doi: 10.1126/science.1178158google scholar: lookup
                        6. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees.. BMC Evol Biol 2007 Nov 8;7:214.
                          pubmed: 17996036doi: 10.1186/1471-2148-7-214google scholar: lookup
                        7. Schwarz C, Debruyne R, Kuch M, McNally E, Schwarcz H, Aubrey AD, Bada J, Poinar H. New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains.. Nucleic Acids Res 2009 Jun;37(10):3215-29.
                          pubmed: 19321502doi: 10.1093/nar/gkp159google scholar: lookup
                        8. Meadows JR, Hawken RJ, Kijas JW. Nucleotide diversity on the ovine Y chromosome.. Anim Genet 2004 Oct;35(5):379-85.
                          pubmed: 15373741doi: 10.1111/j.1365-2052.2004.01180.xgoogle scholar: lookup
                        9. Meyer M, Briggs AW, Maricic T, Höber B, Höffner B, Krause J, Weihmann A, Pääbo S, Hofreiter M. From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing.. Nucleic Acids Res 2008 Jan;36(1):e5.
                          pubmed: 18084031doi: 10.1093/nar/gkm1095google scholar: lookup
                        10. Oakenfull EA, Ryder OA. Mitochondrial control region and 12S rRNA variation in Przewalski's horse (Equus przewalskii).. Anim Genet 1998 Dec;29(6):456-9.
                          pubmed: 9883508doi: 10.1046/j.1365-2052.1998.296380.xgoogle scholar: lookup
                        11. Shapiro B, Ho SY, Drummond AJ, Suchard MA, Pybus OG, Rambaut A. A Bayesian phylogenetic method to estimate unknown sequence ages.. Mol Biol Evol 2011 Feb;28(2):879-87.
                          pubmed: 20889726doi: 10.1093/molbev/msq262google scholar: lookup
                        12. 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
                        13. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers.. Methods Mol Biol 2000;132:365-86.
                          pubmed: 10547847doi: 10.1385/1-59259-192-2:365google scholar: lookup
                        14. Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M. Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA.. Genome Res 2009 Oct;19(10):1843-8.
                          pubmed: 19635845doi: 10.1101/gr.095760.109google scholar: lookup
                        15. Greminger MP, Krützen M, Schelling C, Pienkowska-Schelling A, Wandeler P. The quest for Y-chromosomal markers - methodological strategies for mammalian non-model organisms.. Mol Ecol Resour 2010 May;10(3):409-20.
                          pubmed: 21565040doi: 10.1111/j.1755-0998.2009.02798.xgoogle scholar: lookup
                        16. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.. Bioinformatics 2009 Jun 1;25(11):1451-2.
                          pubmed: 19346325doi: 10.1093/bioinformatics/btp187google scholar: lookup
                        17. Bowling AT, Zimmermann W, Ryder O, Penado C, Peto S, Chemnick L, Yasinetskaya N, Zharkikh T. Genetic variation in Przewalski's horses, with special focus on the last wild caught mare, 231 Orlitza III.. Cytogenet Genome Res 2003;102(1-4):226-34.
                          pubmed: 14970708doi: 10.1159/000075754google scholar: lookup
                        18. Luo SJ, Johnson WE, David VA, Menotti-Raymond M, Stanyon R, Cai QX, Beck T, Yuhki N, Pecon-Slattery J, Smith JL, O'Brien SJ. Development of Y chromosome intraspecific polymorphic markers in the Felidae.. J Hered 2007;98(5):400-13.
                          pubmed: 17646273doi: 10.1093/jhered/esm063google scholar: lookup
                        19. 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.
                          pubmed: 21565072doi: 10.1111/j.1755-0998.2009.02824.xgoogle scholar: lookup
                        20. Natanaelsson C, Oskarsson MC, Angleby H, Lundeberg J, Kirkness E, Savolainen P. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.. BMC Genet 2006 Oct 6;7:45.
                          pubmed: 17026745doi: 10.1186/1471-2156-7-45google scholar: lookup
                        21. McGahern AM, Edwards CJ, Bower MA, Heffernan A, Park SD, Brophy PO, Bradley DG, MacHugh DE, Hill EW. Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses.. Anim Genet 2006 Oct;37(5):498-502.
                          pubmed: 16978181doi: 10.1111/j.1365-2052.2006.01506.xgoogle scholar: lookup
                        22. Outram AK, Stear NA, Bendrey R, Olsen S, Kasparov A, Zaibert V, Thorpe N, Evershed RP. The earliest horse harnessing and milking.. Science 2009 Mar 6;323(5919):1332-5.
                          pubmed: 19265018doi: 10.1126/science.1168594google scholar: lookup
                        23. Römpler H, Dear PH, Krause J, Meyer M, Rohland N, Schöneberg T, Spriggs H, Stiller M, Hofreiter M. Multiplex amplification of ancient DNA.. Nat Protoc 2006;1(2):720-8.
                          pubmed: 17406302doi: 10.1038/nprot.2006.84google scholar: lookup
                        24. Hellborg L, Ellegren H. Low levels of nucleotide diversity in mammalian Y chromosomes.. Mol Biol Evol 2004 Jan;21(1):158-63.
                          pubmed: 14595096doi: 10.1093/molbev/msh008google scholar: lookup
                        25. Ramírez O, Ojeda A, Tomàs A, Gallardo D, Huang LS, Folch JM, Clop A, Sánchez A, Badaoui B, Hanotte O, Galman-Omitogun O, Makuza SM, Soto H, Cadillo J, Kelly L, Cho IC, Yeghoyan S, Pérez-Enciso M, Amills M. Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds.. Mol Biol Evol 2009 Sep;26(9):2061-72.
                          pubmed: 19535739doi: 10.1093/molbev/msp118google scholar: lookup
                        26. Emlen ST, Oring LW. Ecology, sexual selection, and the evolution of mating systems.. Science 1977 Jul 15;197(4300):215-23.
                          pubmed: 327542doi: 10.1126/science.327542google scholar: lookup
                        27. Sundqvist AK, Björnerfeldt S, Leonard JA, Hailer F, Hedhammar A, Ellegren H, Vilà C. Unequal contribution of sexes in the origin of dog breeds.. Genetics 2006 Feb;172(2):1121-8.
                          pubmed: 16219789doi: 10.1534/genetics.105.042358google scholar: lookup
                        28. Suchard MA, Weiss RE, Sinsheimer JS. Bayesian selection of continuous-time Markov chain evolutionary models.. Mol Biol Evol 2001 Jun;18(6):1001-13.
                          pubmed: 11371589doi: 10.1093/oxfordjournals.molbev.a003872google scholar: lookup
                        29. Ishida N, Oyunsuren T, Mashima S, Mukoyama H, Saitou N. Mitochondrial DNA sequences of various species of the genus Equus with special reference to the phylogenetic relationship between Przewalskii's wild horse and domestic horse.. J Mol Evol 1995 Aug;41(2):180-8.
                          pubmed: 7666447doi: 10.1007/BF00170671google scholar: lookup
                        30. Ling Y, Ma Y, Guan W, Cheng Y, Wang Y, Han J, Jin D, Mang L, Mahmut H. Identification of Y chromosome genetic variations in Chinese indigenous horse breeds.. J Hered 2010 Sep-Oct;101(5):639-43.
                          pubmed: 20497969doi: 10.1093/jhered/esq047google scholar: lookup
                        31. Lei CZ, Su R, Bower MA, Edwards CJ, Wang XB, Weining S, Liu L, Xie WM, Li F, Liu RY, Zhang YS, Zhang CM, Chen H. Multiple maternal origins of native modern and ancient horse populations in China.. Anim Genet 2009 Dec;40(6):933-44.
                          pubmed: 19744143doi: 10.1111/j.1365-2052.2009.01950.xgoogle scholar: lookup
                        32. Geraldes A, Rogel-Gaillard C, Ferrand N. High levels of nucleotide diversity in the European rabbit (Oryctolagus cuniculus) SRY gene.. Anim Genet 2005 Aug;36(4):349-51.
                          pubmed: 16026347doi: 10.1111/j.1365-2052.2005.01300.xgoogle scholar: lookup
                        33. Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H. Limited number of patrilines in horse domestication.. Nat Genet 2004 Apr;36(4):335-6.
                          pubmed: 15034578doi: 10.1038/ng1326google scholar: lookup
                        34. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution.. Bioinformatics 1998;14(9):817-8.
                          pubmed: 9918953doi: 10.1093/bioinformatics/14.9.817google scholar: lookup
                        35. 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.
                          pubmed: 20007379doi: 10.1073/pnas.0903672106google scholar: lookup
                        36. Kent WJ. BLAT--the BLAST-like alignment tool.. Genome Res 2002 Apr;12(4):656-64.
                          pubmed: 11932250doi: 10.1101/gr.229202google scholar: lookup
                        37. Wallner B, Brem G, Müller M, Achmann R. Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus.. Anim Genet 2003 Dec;34(6):453-6.
                          pubmed: 14687077doi: 10.1046/j.0268-9146.2003.01044.xgoogle scholar: lookup
                        38. Cunningham EP, Dooley JJ, Splan RK, Bradley DG. Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses.. Anim Genet 2001 Dec;32(6):360-4.
                          pubmed: 11736806doi: 10.1046/j.1365-2052.2001.00785.xgoogle scholar: lookup
                        39. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome.. Science 2010 May 7;328(5979):710-722.
                          pubmed: 20448178doi: 10.1126/science.1188021google scholar: lookup
                        40. Götherström A, Anderung C, Hellborg L, Elburg R, Smith C, Bradley DG, Ellegren H. Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe.. Proc Biol Sci 2005 Nov 22;272(1579):2345-50.
                          pubmed: 16243693doi: 10.1098/rspb.2005.3243google scholar: lookup
                        41. Lira J, Linderholm A, Olaria C, Brandström Durling M, Gilbert MT, Ellegren H, Willerslev E, Lidén K, Arsuaga JL, Götherström A. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses.. Mol Ecol 2010 Jan;19(1):64-78.
                          pubmed: 19943892doi: 10.1111/j.1365-294X.2009.04430.xgoogle scholar: lookup
                        42. Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castaños P, Cieslak M, Lippold S, Llorente L, Malaspinas AS, Slatkin M, Hofreiter M. Coat color variation at the beginning of horse domestication.. Science 2009 Apr 24;324(5926):485.
                          pubmed: 19390039doi: 10.1126/science.1172750google scholar: lookup
                        43. Lau AN, Peng L, Goto H, Chemnick L, Ryder OA, Makova KD. Horse domestication and conservation genetics of Przewalski's horse inferred from sex chromosomal and autosomal sequences.. Mol Biol Evol 2009 Jan;26(1):199-208.
                          pubmed: 18931383doi: 10.1093/molbev/msn239google scholar: lookup
                        44. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences.. Mol Biol Evol 2005 May;22(5):1185-92.
                          pubmed: 15703244doi: 10.1093/molbev/msi103google scholar: lookup
                        45. Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform.. Nat Protoc 2008;3(2):267-78.
                          pubmed: 18274529doi: 10.1038/nprot.2007.520google scholar: lookup
                        46. Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A. Origin and history of mitochondrial DNA lineages in domestic horses.. PLoS One 2010 Dec 20;5(12):e15311.
                          pubmed: 21187961doi: 10.1371/journal.pone.0015311google scholar: lookup
                        47. Wallner B, Piumi F, Brem G, Müller M, Achmann R. Isolation of Y chromosome-specific microsatellites in the horse and cross-species amplification in the genus Equus.. J Hered 2004 Mar-Apr;95(2):158-64.
                          pubmed: 15073232doi: 10.1093/jhered/esh020google scholar: lookup
                        48. Keyser-Tracqui C, Blandin-Frappin P, Francfort HP, Ricaut FX, Lepetz S, Crubézy E, Samashev Z, Ludes B. Mitochondrial DNA analysis of horses recovered from a frozen tomb (Berel site, Kazakhstan, 3rd Century BC).. Anim Genet 2005 Jun;36(3):203-9.
                          pubmed: 15932398doi: 10.1111/j.1365-2052.2005.01316.xgoogle scholar: lookup
                        49. Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences.. Brief Bioinform 2008 Jul;9(4):299-306.
                          pubmed: 18417537doi: 10.1093/bib/bbn017google scholar: lookup

                        Citations

                        This article has been cited 40 times.
                        1. Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, Shah MK, Nishibori M, Kazymbet P, Bakhtin M, Zhunushov A, Paul RC, Dashnyam B, Nozawa K, Almarzook S, Brockmann GA, Reissmann M, Antczak DF, Miller DC, Sadeghi R, von Butler-Wemken I, Kostaras N, Han H, Manglai D, Abdurasulov A, Sukhbaatar B, Ropka-Molik K, Stefaniuk-Szmukier M, Lopes MS, da Câmara Machado A, Kalashnikov VV, Kalinkova L, Zaitev AM, Novoa-Bravo M, Lindgren G, Brooks S, Rosa LP, Orlando L, Juras R, Kunieda T, Wallner B. Refining the evolutionary tree of the horse Y chromosome. Sci Rep 2023 Jun 2;13(1):8954.
                          doi: 10.1038/s41598-023-35539-0pubmed: 37268661google scholar: lookup
                        2. Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022 Dec 2;13(12).
                          doi: 10.3390/genes13122272pubmed: 36553539google scholar: lookup
                        3. Delsol N, Stucky BJ, Oswald JA, Reitz EJ, Emery KF, Guralnick R. Analysis of the earliest complete mtDNA genome of a Caribbean colonial horse (Equus caballus) from 16th-century Haiti. PLoS One 2022;17(7):e0270600.
                          doi: 10.1371/journal.pone.0270600pubmed: 35895670google scholar: lookup
                        4. Hong JH, Oh CS, Kim S, Kang IU, Shin DH. Genetic analysis of mitochondrial DNA from ancient Equus caballus bones found at archaeological site of Joseon dynasty period capital area. Anim Biosci 2022 Aug;35(8):1141-1150.
                          doi: 10.5713/ab.21.0500pubmed: 35240033google scholar: lookup
                        5. Wang L, Sheng G, Preick M, Hu S, Deng T, Taron UH, Barlow A, Hu J, Xiao B, Sun G, Song S, Hou X, Lai X, Hofreiter M, Yuan J. Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys. Front Genet 2021;12:759831.
                          doi: 10.3389/fgene.2021.759831pubmed: 34721545google scholar: lookup
                        6. Klecel W, Martyniuk E. From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management. Animals (Basel) 2021 Jun 22;11(7).
                          doi: 10.3390/ani11071859pubmed: 34206575google scholar: lookup
                        7. Liu S, Fu C, Yang Y, Zhang Y, Ma H, Xiong Z, Ling Y, Zhao C. Current genetic conservation of Chinese indigenous horses revealed with Y-chromosomal and mitochondrial DNA polymorphisms. G3 (Bethesda) 2021 Feb 9;11(2).
                          doi: 10.1093/g3journal/jkab008pubmed: 33604674google scholar: lookup
                        8. Guimaraes S, Arbuckle BS, Peters J, Adcock SE, Buitenhuis H, Chazin H, Manaseryan N, Uerpmann HP, Grange T, Geigl EM. Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age. Sci Adv 2020 Sep;6(38).
                          doi: 10.1126/sciadv.abb0030pubmed: 32938680google scholar: lookup
                        9. Ford BM, Cornellas A, Leonard JA, Weir RD, Russello MA. Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation. Ecol Evol 2020 Aug;10(15):8345-8357.
                          doi: 10.1002/ece3.6541pubmed: 32788984google scholar: lookup
                        10. Liu S, Yang Y, Pan Q, Sun Y, Ma H, Liu Y, Wang M, Zhao C, Wu C. Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers. Front Genet 2020;11:467.
                          doi: 10.3389/fgene.2020.00467pubmed: 32508879google scholar: lookup
                        11. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019 Dec;50(6):569-597.
                          doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
                        12. Castaneda C, Juras R, Khanshour A, Randlaht I, Wallner B, Rigler D, Lindgren G, Raudsepp T, Cothran EG. Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines. Genes (Basel) 2019 Aug 20;10(8).
                          doi: 10.3390/genes10080629pubmed: 31434327google scholar: lookup
                        13. Kvist L, Niskanen M, Mannermaa K, Wutke S, Aspi J. Genetic variability and history of a native Finnish horse breed. Genet Sel Evol 2019 Jul 1;51(1):35.
                          doi: 10.1186/s12711-019-0480-8pubmed: 31262246google scholar: lookup
                        14. Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines. Sci Rep 2019 Apr 15;9(1):6095.
                          doi: 10.1038/s41598-019-42640-wpubmed: 30988347google scholar: lookup
                        15. Ma H, Wang S, Zeng G, Guo J, Guo M, Dong X, Hua G, Liu Y, Wang M, Ling Y, Ding X, Zhao C, Wu C. The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data. Genes (Basel) 2019 Mar 21;10(3).
                          doi: 10.3390/genes10030241pubmed: 30901931google scholar: lookup
                        16. Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA, Love CC, Varner DD, Bellott DW, Murphy WJ, Chowdhary BP, Raudsepp T. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nat Commun 2018 Jul 27;9(1):2945.
                          doi: 10.1038/s41467-018-05290-6pubmed: 30054462google scholar: lookup
                        17. Ma H, Wu Y, Xiang H, Yang Y, Wang M, Zhao C, Wu C. Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences. PeerJ 2018;6:e4896.
                          doi: 10.7717/peerj.4896pubmed: 29868288google scholar: lookup
                        18. Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. Improved de novo genomic assembly for the domestic donkey. Sci Adv 2018 Apr;4(4):eaaq0392.
                          doi: 10.1126/sciadv.aaq0392pubmed: 29740610google scholar: lookup
                        19. Wutke S, Sandoval-Castellanos E, Benecke N, Döhle HJ, Friederich S, Gonzalez J, Hofreiter M, Lõugas L, Magnell O, Malaspinas AS, Morales-Muñiz A, Orlando L, Reissmann M, Trinks A, Ludwig A. Decline of genetic diversity in ancient domestic stallions in Europe. Sci Adv 2018 Apr;4(4):eaap9691.
                          doi: 10.1126/sciadv.aap9691pubmed: 29675468google scholar: lookup
                        20. Khaudov AD, Duduev AS, Kokov ZA, Amshokov KK, Zhekamukhov MK, Zaitsev AM, Reissmann M. Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers. Open Vet J 2018;8(1):40-46.
                          doi: 10.4314/ovj.v8i1.7pubmed: 29445620google scholar: lookup
                        21. Hirata D, Mano T, Abramov AV, Baryshnikov GF, Kosintsev PA, Murata K, Masuda R. Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations. Zoological Lett 2017;3:21.
                          doi: 10.1186/s40851-017-0084-5pubmed: 29214050google scholar: lookup
                        22. Bitocchi E, Rau D, Bellucci E, Rodriguez M, Murgia ML, Gioia T, Santo D, Nanni L, Attene G, Papa R. Beans (Phaseolus ssp.) as a Model for Understanding Crop Evolution. Front Plant Sci 2017;8:722.
                          doi: 10.3389/fpls.2017.00722pubmed: 28533789google scholar: lookup
                        23. Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2017 Jan 1;66(1):e1-e29.
                          doi: 10.1093/sysbio/syw059pubmed: 28173586google scholar: lookup
                        24. Wutke S, Benecke N, Sandoval-Castellanos E, Döhle HJ, Friederich S, Gonzalez J, Hallsson JH, Hofreiter M, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M, Ruttkay M, Trinks A, Ludwig A. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci Rep 2016 Dec 7;6:38548.
                          doi: 10.1038/srep38548pubmed: 27924839google scholar: lookup
                        25. 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
                        26. Reissmann M, Musa L, Zakizadeh S, Ludwig A. Distribution of coat-color-associated alleles in the domestic horse population and Przewalski's horse. J Appl Genet 2016 Nov;57(4):519-525.
                          doi: 10.1007/s13353-016-0352-7pubmed: 27194311google scholar: lookup
                        27. Cardinali I, Lancioni H, Giontella A, Capodiferro MR, Capomaccio S, Buttazzoni L, Biggio GP, Cherchi R, Albertini E, Olivieri A, Cappelli K, Achilli A, Silvestrelli M. An Overview of Ten Italian Horse Breeds through Mitochondrial DNA. PLoS One 2016;11(4):e0153004.
                          doi: 10.1371/journal.pone.0153004pubmed: 27054850google scholar: lookup
                        28. Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L. Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse. Curr Biol 2015 Oct 5;25(19):2577-83.
                          doi: 10.1016/j.cub.2015.08.032pubmed: 26412128google scholar: lookup
                        29. Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):E5661-9.
                          doi: 10.1073/pnas.1416991111pubmed: 25512547google scholar: lookup
                        30. Yin X, Guo M, Gu Q, Wu X, Wei P, Wang X. Antiviral potency and functional analysis of tetherin orthologues encoded by horse and donkey. Virol J 2014 Aug 27;11:151.
                          doi: 10.1186/1743-422X-11-151pubmed: 25158826google scholar: lookup
                        31. Bellucci E, Bitocchi E, Ferrarini A, Benazzo A, Biagetti E, Klie S, Minio A, Rau D, Rodriguez M, Panziera A, Venturini L, Attene G, Albertini E, Jackson SA, Nanni L, Fernie AR, Nikoloski Z, Bertorelle G, Delledonne M, Papa R. Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean. Plant Cell 2014 May;26(5):1901-1912.
                          doi: 10.1105/tpc.114.124040pubmed: 24850850google scholar: lookup
                        32. Brandariz-Fontes C, Leonard JA, Vega-Pla JL, Backström N, Lindgren G, Lippold S, Rico C. Y-chromosome analysis in Retuertas horses. PLoS One 2013;8(5):e64985.
                          doi: 10.1371/journal.pone.0064985pubmed: 23741439google scholar: lookup
                        33. Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds. PLoS One 2013;8(4):e60015.
                          doi: 10.1371/journal.pone.0060015pubmed: 23573227google scholar: lookup
                        34. Wall JD, Slatkin M. Paleopopulation genetics. Annu Rev Genet 2012;46:635-49.
                          doi: 10.1146/annurev-genet-110711-155557pubmed: 22994357google scholar: lookup
                        35. Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, Hanks BK, Li S, Lomitashvili D, Ochir-Goryaeva M, Sizonov GV, Soyonov V, Manica A. Reconstructing the origin and spread of horse domestication in the Eurasian steppe. Proc Natl Acad Sci U S A 2012 May 22;109(21):8202-6.
                          doi: 10.1073/pnas.1111122109pubmed: 22566639google scholar: lookup
                        36. Kayser M. Editors' pick: of horses and genes'. Investig Genet 2012 Feb 17;3:4.
                          doi: 10.1186/2041-2223-3-4pubmed: 22340794google scholar: lookup
                        37. Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MC, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt HJ, Torroni A. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):2449-54.
                          doi: 10.1073/pnas.1111637109pubmed: 22308342google scholar: lookup
                        38. 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
                        39. Saldaña CL, Justo S, Murga L, Vásquez HV, Maicelo JL, Arbizu CI, Bardales W. Mitochondrial genome assembly of the Peruvian Paso horse through PacBio long-read sequencing. Sci Rep 2025 Dec 21;16(1):85.
                          doi: 10.1038/s41598-025-29107-xpubmed: 41423464google scholar: lookup
                        40. Sharif MB, Mohaseb AF, Orlando L, Saliari K, Kunst GK, Czeika S, Mashkour M, Cucchi T, Peters J, Trixl S, Mohandesan E. Late Iron Age and Roman equine breeding north of the Alps: Genetic insights and cultural implications. iScience 2025 Sep 19;28(9):113224.
                          doi: 10.1016/j.isci.2025.113224pubmed: 40837235google scholar: lookup
                        Subscribe to our newsletter
                        Join 99,911 horse owners like you who receive our email updates on horse health and nutrition.