Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

1. Abad Ò.E., i Garra A.M., Bieto E.T.. Cantorella (Maldà, Urgell), un nou assentament a l’aire lliure del neolític final-calcolític i del bronze ple a la vall del Corb. Tribuna d'Arqueologia 2011:2011–2012.
2. Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlström T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, Harvig L, Baron J, Della Casa P, Dąbrowski P, Duffy PR, Ebel AV, Epimakhov A, Frei K, Furmanek M, Gralak T, Gromov A, Gronkiewicz S, Grupe G, Hajdu T, Jarysz R, Khartanovich V, Khokhlov A, Kiss V, Kolář J, Kriiska A, Lasak I, Longhi C, McGlynn G, Merkevicius A, Merkyte I, Metspalu M, Mkrtchyan R, Moiseyev V, Paja L, Pálfi G, Pokutta D, Pospieszny Ł, Price TD, Saag L, Sablin M, Shishlina N, Smrčka V, Soenov VI, Szeverényi V, Tóth G, Trifanova SV, Varul L, Vicze M, Yepiskoposyan L, Zhitenev V, Orlando L, Sicheritz-Pontén T, Brunak S, Nielsen R, Kristiansen K, Willerslev E. Population genomics of Bronze Age Eurasia.. Nature 2015 Jun 11;522(7555):167-72.
   pubmed: 26062507doi: 10.1038/nature14507google scholar: lookup
3. Anthony D.. The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. Princeton University Press; 2007.
4. Arbuckle B.S.. Pastoralism, Provisioning, and Power at Bronze Age Acemhöyük, Turkey. Am. Anthropol. 2012;114:462–476.
5. Barlow A., Hartmann S., Gonzalez J., Hofreiter M., Paijmans J.L.A.. Consensify: a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates. bioRxiv 2018.
6. Barrett J.H.B.. Being an islander: production and identity at Quoygrew, Orkney, AD 900-1600. McDonald Institute for Archaeological Research; 2012.
7. Barrett J.H., Slater A.. New Excavations at the Brough of Deerness: Power and Religion in Viking Age Scotland. J. North Atlantic 2009:81–94.
8. Benecke N.. On the beginning of horse husbandry in the southern Balkan Peninsula-the horse bones from Kirklareli-Kanhgecit (Turkish Thrace). In: Mashkour M., editor. Equids in Time and Space: Papers in Honour of Véra Eisenmann. Oxford; 2006.
9. Benjamini Y., Hochberg Y.. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J. R. Stat. Soc. Series B Stat. Methodol. 1995;57:289–300.
10. Bertašius M., Daugnora L.. Viking age horse graves from Kaunas region (Middle Lithuania). Int. J. Osteoarchaeol. 2001;11:387–399.
11. Biglari F., Taheri K.. The discovery of Upper Paleolithic remains at Mar Kuliyan and Mar Dalan Cave, Rawansar. Taq-E Bostan Publications; 2000. Essays on the Archaeology, Geology, Geography and Culture of Rawansar Area; pp. 7–27.
12. Blasco C., Rios P., Liesau C.. Yacimientos calcolíticos con campaniforme de la región de Madrid: nuevos estudios. Universidad Autónoma de Madrid Madrid; 2011.
13. Boeskorov G.G., Potapova O.R., Protopopov A.V., Plotnikov V.V., Maschenko E.N., Shchelchkova M.V., Petrova E.A., Kowalczyk R., van der Plicht J., Tikhonov A.N.. A study of a frozen mummy of a wild horse from the Holocene of Yakutia, East Siberia, Russia. Mammal Res. 2018;63:1–8.
14. Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. Patterns of damage in genomic DNA sequences from a Neandertal.. Proc Natl Acad Sci U S A 2007 Sep 11;104(37):14616-21.
    pmc: PMC1976210pubmed: 17715061doi: 10.1073/pnas.0704665104google scholar: lookup
15. Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA.. Nucleic Acids Res 2010 Apr;38(6):e87.
    pmc: PMC2847228pubmed: 20028723doi: 10.1093/nar/gkp1163google scholar: lookup
16. Brink S., Price N.. The Viking World. Routledge; 2008.
17. Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, Ovsyanikov N, Salamzade R, St John J, Stirling I, Slatkin M, Shapiro B. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution.. PLoS Genet 2013;9(3):e1003345.
    pmc: PMC3597504pubmed: 23516372doi: 10.1371/journal.pgen.1003345google scholar: lookup
18. Charlesworth B. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation.. Nat Rev Genet 2009 Mar;10(3):195-205.
    pubmed: 19204717doi: 10.1038/nrg2526google scholar: lookup
19. Corbin LJ, Blott SC, Swinburne JE, Vaudin M, Bishop SC, Woolliams JA. Linkage disequilibrium and historical effective population size in the Thoroughbred horse.. Anim Genet 2010 Dec;41 Suppl 2:8-15.
    pubmed: 21070270doi: 10.1111/j.1365-2052.2010.02092.xgoogle scholar: lookup
20. Cruz F, Vilà C, Webster MT. The legacy of domestication: accumulation of deleterious mutations in the dog genome.. Mol Biol Evol 2008 Nov;25(11):2331-6.
    pubmed: 18689870doi: 10.1093/molbev/msn177google scholar: lookup
21. 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.
    pmc: PMC5104162pubmed: 26412128doi: 10.1016/j.cub.2015.08.032google scholar: lookup
22. Drews R.. Early Riders: The Beginnings of Mounted Warfare in Asia and Europe. Routledge; 2004.
23. Durand EY, Patterson N, Reich D, Slatkin M. Testing for ancient admixture between closely related populations.. Mol Biol Evol 2011 Aug;28(8):2239-52.
    pmc: PMC3144383pubmed: 21325092doi: 10.1093/molbev/msr048google scholar: lookup
24. Dyson R.H.. The Iron Age architecture at Hasanlu: an essay. Expedition 1989;31:107.
25. Dyson R.H.. The Achaemenid painted pottery of Hasanlu IIIA. Anatolian Studies 1999;49:101–110.
26. Einarsson B.F.. The Settlement of Iceland, A Critical Approach: Granastaðair and the Ecological Heritage. Reykjavík: Hið íslenzka bókmentafélag. 1995.
27. Faostat F.A.O.. Statistical databases. Food and Agriculture Organization of the United Nations; 2009.
28. Felkel S, Vogl C, Rigler D, Jagannathan V, Leeb T, Fries R, Neuditschko M, Rieder S, Velie B, Lindgren G, Rubin CJ, Schlötterer C, Rattei T, Brem G, Wallner B. Asian horses deepen the MSY phylogeny.. Anim Genet 2018 Feb;49(1):90-93.
    pubmed: 29333704doi: 10.1111/age.12635google scholar: lookup
29. Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Bradley DG, Orlando L. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.. Mol Ecol Resour 2016 Mar;16(2):459-69.
    pubmed: 26401836doi: 10.1111/1755-0998.12470google scholar: lookup
30. Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski's horses.. Science 2018 Apr 6;360(6384):111-114.
    pubmed: 29472442doi: 10.1126/science.aao3297google scholar: lookup
31. Germonpré M.. Influence of climate on sexual segregation and cub mortality in Pleniglacial cave bear. The Future from the Past: Archaeozoology in Wildlife Conservation and Heritage Management (Proceedings of the 9th ICAZ Conference) Oxbow Books; 2004.
32. 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.
    pmc: PMC5100745pubmed: 20448178doi: 10.1126/science.1188021google scholar: lookup
33. Groves C.P.. Morphology, habitat, and taxonomy. In: Boyd L., Houpt K.A., editors. Przewalski’s Horse–The History and Biology of an Endangered Species. SUNY Press; 1994. pp. 39–60.
34. Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, Fu Q, Mittnik A, Bánffy E, Economou C, Francken M, Friederich S, Pena RG, Hallgren F, Khartanovich V, Khokhlov A, Kunst M, Kuznetsov P, Meller H, Mochalov O, Moiseyev V, Nicklisch N, Pichler SL, Risch R, Rojo Guerra MA, Roth C, Szécsényi-Nagy A, Wahl J, Meyer M, Krause J, Brown D, Anthony D, Cooper A, Alt KW, Reich D. Massive migration from the steppe was a source for Indo-European languages in Europe.. Nature 2015 Jun 11;522(7555):207-11.
    pmc: PMC5048219pubmed: 25731166doi: 10.1038/nature14317google scholar: lookup
35. Hall SJ. Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data.. Animal 2016 Nov;10(11):1778-1785.
    pubmed: 27160794doi: 10.1017/s1751731116000914google scholar: lookup
36. Haller BC, Messer PW. SLiM 2: Flexible, Interactive Forward Genetic Simulations.. Mol Biol Evol 2017 Jan;34(1):230-240.
    pubmed: 27702775doi: 10.1093/molbev/msw211google scholar: lookup
37. Hansman J., Stronach D.. A Sasanian Repository at Shahr-I Qūmis. JRAS 1970;102:142–155.
38. Hansman J., Stronach D., Bailey H.. Excavations at Shahr-I Qūmis. The Journal of Royal Asiatic Society of Great Britain and Ireland 1970;1:29–62.
39. Hill EW, Gu J, McGivney BA, MacHugh DE. Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance.. Anim Genet 2010 Dec;41 Suppl 2:56-63.
    pubmed: 21070277doi: 10.1111/j.1365-2052.2010.02104.xgoogle scholar: lookup
40. 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.
    pmc: PMC3694634pubmed: 23613487doi: 10.1093/bioinformatics/btt193google scholar: lookup
41. 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.
    pmc: PMC4284605pubmed: 25453089doi: 10.1073/pnas.1412627111google scholar: lookup
42. Jonvel R.. Démuin « Le village ». Rapport final d’opération. Autour du château médiéval (IXe-XVIe siècle). UnivArchéo, UPJV; Amiens: 2014.
43. Kamm J.A., Terhorst J., Durbin R., Song Y.S.. Efficiently inferring the demographic history of many populations with allele count data. bioRxiv 2018.
44. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified.. BMC Evol Biol 2006 Mar 24;6:29.
    pmc: PMC1435933pubmed: 16563161doi: 10.1186/1471-2148-6-29google scholar: lookup
45. Kelekna P.. The horse in human history. Cambridge University Press Cambridge; 2009.
46. Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data.. BMC Bioinformatics 2014 Nov 25;15(1):356.
    pmc: PMC4248462pubmed: 25420514doi: 10.1186/s12859-014-0356-4google scholar: lookup
47. Kosintsev P.A.. Bone remains from the settlement Belkaragay I. In: Beisenov A.Z., editor. Ancient Turgay and the Great Steppe: Part and Whole. Kostanay-Almaty; 2015. pp. 142–144.
48. Kosintsev P., Kuznetsov P.. Comment on “The Earliest Horse Harnessing and Milking.”. Tyragetia 2013;7:405–408.
49. Kousathanas A, Keightley PD. A comparison of models to infer the distribution of fitness effects of new mutations.. Genetics 2013 Apr;193(4):1197-208.
    pmc: PMC3606097pubmed: 23341416doi: 10.1534/genetics.112.148023google scholar: lookup
50. Kovalev A.A., Erdenebaatar D., Rukavishnikova I.V.. A ritual complex with deer stones at Uushigiin Uvur, Mongolia: composition and construction stages. Archaeol. Ethnol. Anthropol. Eurasia 2016;44:82–92.
51. Kristjansson T, Bjornsdottir S, Sigurdsson A, Andersson LS, Lindgren G, Helyar SJ, Klonowski AM, Arnason T. The effect of the 'Gait keeper' mutation in the DMRT3 gene on gaiting ability in Icelandic horses.. J Anim Breed Genet 2014 Dec;131(6):415-25.
    pubmed: 25073639doi: 10.1111/jbg.12112google scholar: lookup
52. Lang V.. Settlement Sites and Settlement in the Late Bronze and Early Iron Ages. University of Tartu Press; 2012. The Bronze and Early Iron Ages in Estonia; pp. 63–65.
53. Laurence R.. The Roads of Roman Italy: Mobility and Social Change. Routledge; 1999.
54. Lefort V, Desper R, Gascuel O. FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.. Mol Biol Evol 2015 Oct;32(10):2798-800.
    pmc: PMC4576710pubmed: 26130081doi: 10.1093/molbev/msv150google scholar: lookup
55. Leroi-Gourhan A.. L’art pariétal: langage de la préhistoire. Editions Jérôme Millon; 1958.
56. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.. Bioinformatics 2009 Jul 15;25(14):1754-60.
    pmc: PMC2705234pubmed: 19451168doi: 10.1093/bioinformatics/btp324google scholar: lookup
57. Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.. Proc Natl Acad Sci U S A 2015 Dec 15;112(50):E6889-97.
    pmc: PMC4687531pubmed: 26598656doi: 10.1073/pnas.1513696112google scholar: lookup
58. Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse.. Science 2017 Apr 28;356(6336):442-445.
    pubmed: 28450643doi: 10.1126/science.aam5298google scholar: lookup
59. Liesau C.. Arqueozoología del caballo en la antigua Iberia. Gladius 2005;25:187–206.
60. Liesau C.. Fauna in Living and Funerary Contexts of the 3rd Millennium BC in Central Iberia. In: Bartelheim M., Bueno P., Kunst M., editors. Key Resources and Sociocultural Developments in the Iberian Chalcolithic. Tübingen Publishing; 2017. pp. 107–128.
61. 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
62. 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.
    pmc: PMC3247663pubmed: 22082251doi: 10.1186/1471-2148-11-328google scholar: lookup
63. 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
64. Logvin A.V., Shevnina I.V.. Settlement Belkaragaj 1. In: Beisenov A.Z., editor. Ancient Rugay and the Great Steppe: Part and Whole. Kostanay-Almaty; 2015. pp. 122–144.
65. Lõugas L.. Post-glacial development of vertebrate fauna in Estonian water bodies: a palaeozoological study. Dissertationes Biologicae Universitatis Tartuensis Tartu University Press; 1997.
66. Mallory J.P., Adams D.Q.. Encyclopedia of Indo-European Culture. Taylor & Francis; 1997.
67. Marciniak S, Perry GH. Harnessing ancient genomes to study the history of human adaptation.. Nat Rev Genet 2017 Nov;18(11):659-674.
    pubmed: 28890534doi: 10.1038/nrg.2017.65google scholar: lookup
68. Martin SH, Davey JW, Jiggins CD. Evaluating the use of ABBA-BABA statistics to locate introgressed loci.. Mol Biol Evol 2015 Jan;32(1):244-57.
    pmc: PMC4271521pubmed: 25246699doi: 10.1093/molbev/msu269google scholar: lookup
69. McCue ME, Valberg SJ, Miller MB, Wade C, DiMauro S, Akman HO, Mickelson JR. Glycogen synthase (GYS1) mutation causes a novel skeletal muscle glycogenosis.. Genomics 2008 May;91(5):458-66.
    pmc: PMC2430182pubmed: 18358695doi: 10.1016/j.ygeno.2008.01.011google scholar: lookup
70. McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila.. Nature 1991 Jun 20;351(6328):652-4.
    pubmed: 1904993doi: 10.1038/351652a0google scholar: lookup
71. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.. Genome Res 2010 Sep;20(9):1297-303.
    pmc: PMC2928508pubmed: 20644199doi: 10.1101/gr.107524.110google scholar: lookup
72. 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.
    pubmed: 20516186doi: 10.1101/pdb.prot5448google scholar: lookup
73. Miller B., Allard F., Erdenebaatar D., Le C.. A Xiongnu tomb complex: Excavations at Gol Mod 2 Cemetery, Mongolia (2002–2005). Mongolian J. Anthropol. Arc. Ethnol. 2006;2:1–21.
74. Negahbān E.O.. Sagzabad Excavation Report. Iran 1974;12:216.
75. Nieto Espinet A.. Seguint les traces de la transhumància. Aproximació teòrica a partir dels resultats arqueozoològics de la fortalesa dels Vilars (Arbeca, Garrigues). Revista D’arqueologia de Ponent 2016;26:11–34.
76. Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Rojo Guerra MA, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D. The Beaker phenomenon and the genomic transformation of northwest Europe.. Nature 2018 Mar 8;555(7695):190-196.
    pmc: PMC5973796pubmed: 29466337doi: 10.1038/nature25738google scholar: lookup
77. Onar V., Pazvant G., Alpak H., İnce N.G., Armutak A., Kiziltan Z.S.. Animal skeletal remains of the Theodosius harbor: general overview. Turk. J. Vet. Anim. Sci. 2013;37:81–85.
78. 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.
    pubmed: 23803765doi: 10.1038/nature12323google scholar: lookup
79. 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
80. Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language.. Bioinformatics 2004 Jan 22;20(2):289-90.
    pubmed: 14734327doi: 10.1093/bioinformatics/btg412google scholar: lookup
81. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. Ancient admixture in human history.. Genetics 2012 Nov;192(3):1065-93.
    pmc: PMC3522152pubmed: 22960212doi: 10.1534/genetics.112.145037google scholar: lookup
82. Pearson JC, Lemons D, McGinnis W. Modulating Hox gene functions during animal body patterning.. Nat Rev Genet 2005 Dec;6(12):893-904.
    pubmed: 16341070doi: 10.1038/nrg1726google scholar: lookup
83. Pedersen CT, Lohmueller KE, Grarup N, Bjerregaard P, Hansen T, Siegismund HR, Moltke I, Albrechtsen A. The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.. Genetics 2017 Feb;205(2):787-801.
    pmc: PMC5289852pubmed: 27903613doi: 10.1534/genetics.116.193821google scholar: lookup
84. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data.. PLoS Genet 2012;8(11):e1002967.
    pmc: PMC3499260pubmed: 23166502doi: 10.1371/journal.pgen.1002967google scholar: lookup
85. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies.. Genome Res 2010 Jan;20(1):110-21.
    pmc: PMC2798823pubmed: 19858363doi: 10.1101/gr.097857.109google scholar: lookup
86. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses.. Am J Hum Genet 2007 Sep;81(3):559-75.
    pmc: PMC1950838pubmed: 17701901doi: 10.1086/519795google scholar: lookup
87. Ramsey C.B.. Bayesian Analysis of Radiocarbon Dates. Radiocarbon 2009;51:337–360.
88. Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E. The genome of a Late Pleistocene human from a Clovis burial site in western Montana.. Nature 2014 Feb 13;506(7487):225-9.
    pmc: PMC4878442pubmed: 24522598doi: 10.1038/nature13025google scholar: lookup
89. Rohland N, Harney E, Mallick S, Nordenfelt S, Reich D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130624.
    pmc: PMC4275898pubmed: 25487342doi: 10.1098/rstb.2013.0624google scholar: lookup
90. Schmid D., Peter M., Deschler-Erb S.. Crise, culte et immondices: le remplissage d’un puits au 3ème siècle à Augusta Raurica. In: Schatzmann R., Martin-Kilcher S., editors. L’Empire Romain En Mutation - Répercussions Sur Les Villes Dans La Deuxième Moitié Du 3e Siècle. éditions monique mergoil montagnac; 2011. pp. 125–132.
91. 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.
    pmc: PMC4284583pubmed: 25512547doi: 10.1073/pnas.1416991111google scholar: lookup
92. Schubert M, Ermini L, Der Sarkissian C, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.. Nat Protoc 2014 May;9(5):1056-82.
    pubmed: 24722405doi: 10.1038/nprot.2014.063google scholar: lookup
93. Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging.. BMC Res Notes 2016 Feb 12;9:88.
    pmc: PMC4751634pubmed: 26868221doi: 10.1186/s13104-016-1900-2google scholar: lookup
94. Schubert M., Mashkour M., Gaunitz C., Fages A., Seguin-Orlando A., Sheikhi S., Alfarhan A.H., Alquraishi S.A., Al-Rasheid K.A.S., Chuang R.. Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. J. Archaeol. Sci. 2017;72:147–157.
95. Sheikhi Seno S., Mashkour M., Sardari A.. Subsistence Economy of the Lapui settlement of Tepe Mehr Ali Fars on the basis of the archaeozoological analysis. J. Iran. Archaeol. 2012;2:39–60.
96. Skylitzes J., Wortley J.. John Skylitzes: A Synopsis of Byzantine History, 811–1057: Translation and Notes. Cambridge University Press; 2010.
97. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.. Bioinformatics 2014 May 1;30(9):1312-3.
    pmc: PMC3998144pubmed: 24451623doi: 10.1093/bioinformatics/btu033google scholar: lookup
98. Uerpmann H.-P.. Die Domestikation des Pferdes im Chalkolihikum West-und Mitteleuropas, mit 10 Textabbildungen. Madrider Mitteilungen 1990;31:109–153.
99. Vieira F.G., Lassalle F., Korneliussen T.S., Fumagalli M.. Improving the estimation of genetic distances from Next-Generation Sequencing data. Biol. J. Linn. Soc. Lond. 2016;117:139–149.
100. Vukičević T.T., Papeša A.R., Alić I., Kabalin A.E., Ostović M., Kužir S.. Contribution to understanding Avar burials with equids in Croatia: detailed archaeozoological analysis. Rev. Med. Vet. (Toulouse) 2017;168:73–80.
101. 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.
     pmc: PMC3785132pubmed: 19892987doi: 10.1126/science.1178158google scholar: lookup
102. Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer R, McCue M, Neuditschko M, Rieder S, Schlötterer C, Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions.. Curr Biol 2017 Jul 10;27(13):2029-2035.e5.
     pubmed: 28669755doi: 10.1016/j.cub.2017.05.086google scholar: lookup
103. Wang J, Vasaikar S, Shi Z, Greer M, Zhang B. WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit.. Nucleic Acids Res 2017 Jul 3;45(W1):W130-W137.
     pmc: PMC5570149pubmed: 28472511doi: 10.1093/nar/gkx356google scholar: lookup
104. Warmuth V, Eriksson A, Bower MA, Cañon J, Cothran G, Distl O, Glowatzki-Mullis ML, Hunt H, Luís C, do Mar Oom M, Yupanqui IT, Ząbek T, Manica A. European domestic horses originated in two holocene refugia.. PLoS One 2011 Mar 30;6(3):e18194.
     pmc: PMC3068172pubmed: 21479181doi: 10.1371/journal.pone.0018194google scholar: lookup
105. Williamson RJ, Josephs EB, Platts AE, Hazzouri KM, Haudry A, Blanchette M, Wright SI. Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora.. PLoS Genet 2014 Sep;10(9):e1004622.
     pmc: PMC4178662pubmed: 25255320doi: 10.1371/journal.pgen.1004622google scholar: lookup
106. Wilson Sayres MA, Lohmueller KE, Nielsen R. Natural selection reduced diversity on human y chromosomes.. PLoS Genet 2014 Jan;10(1):e1004064.
     pmc: PMC3886894pubmed: 24415951doi: 10.1371/journal.pgen.1004064google scholar: lookup
107. 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.
     pmc: PMC5906072pubmed: 29675468doi: 10.1126/sciadv.aap9691google scholar: lookup
108. 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
109. Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, Nie X, Wu H, Zhao M, Cao H, Zou J, Shan Y, Li S, Yang Q, Asan, Ni P, Tian G, Xu J, Liu X, Jiang T, Wu R, Zhou G, Tang M, Qin J, Wang T, Feng S, Li G, Huasang, Luosang J, Wang W, Chen F, Wang Y, Zheng X, Li Z, Bianba Z, Yang G, Wang X, Tang S, Gao G, Chen Y, Luo Z, Gusang L, Cao Z, Zhang Q, Ouyang W, Ren X, Liang H, Zheng H, Huang Y, Li J, Bolund L, Kristiansen K, Li Y, Zhang Y, Zhang X, Li R, Li S, Yang H, Nielsen R, Wang J, Wang J. Sequencing of 50 human exomes reveals adaptation to high altitude.. Science 2010 Jul 2;329(5987):75-8.
     pmc: PMC3711608pubmed: 20595611doi: 10.1126/science.1190371google scholar: lookup
110. Youn M., Kim J.C., Kim H.K., Tumen D., Navaan D., Erdene M.. Dating the Tavan Tolgoi Site, Mongolia: Burials of the Nobility from Genghis Khan’s Era. Radiocarbon 2007;49:685–691.

Citations

1. Kusliy MA, Yurlova AA, Neumestova AI, Vorobieva NV, Gutorova NV, Molodtseva AS, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Semibratov VP, Iderkhangai TO, Kovalev AA, Erdenebaatar D, Graphodatsky AS, Tishkin AA. Genetic History of the Altai Breed Horses: From Ancient Times to Modernity. Genes (Basel) 2023 Jul 26;14(8).
   doi: 10.3390/genes14081523pubmed: 37628575google scholar: lookup
2. Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits. Animals (Basel) 2023 Aug 8;13(16).
   doi: 10.3390/ani13162557pubmed: 37627349google scholar: lookup
3. Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia. Saudi J Biol Sci 2023 Sep;30(9):103741.
   doi: 10.1016/j.sjbs.2023.103741pubmed: 37575470google scholar: lookup
4. May-Davis S, Dzingle D, Saber E, Blades Eckelbarger P. Characterization of the Caudal Ventral Tubercle in the Sixth Cervical Vertebra in Modern Equus ferus caballus. Animals (Basel) 2023 Jul 22;13(14).
   doi: 10.3390/ani13142384pubmed: 37508161google scholar: lookup
5. Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T, Petersen JL, Orlando L. Imputed genomes of historical horses provide insights into modern breeding. iScience 2023 Jul 21;26(7):107104.
   doi: 10.1016/j.isci.2023.107104pubmed: 37416458google scholar: lookup
6. 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
7. Clavel P, Louis L, Sarkissian C, Thèves C, Gillet C, Chauvey L, Tressières G, Schiavinato S, Calvière-Tonasso L, Telmon N, Clavel B, Jonvel R, Tzortzis S, Bouniol L, Fémolant JM, Klunk J, Poinar H, Signoli M, Costedoat C, Spyrou MA, Seguin-Orlando A, Orlando L. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp. iScience 2023 May 19;26(5):106787.
   doi: 10.1016/j.isci.2023.106787pubmed: 37250315google scholar: lookup
8. Babarinde IA, Adeola AC, Djagoun CAMS, Nneji LM, Okeyoyin AO, Niba G, Wanzie NK, Oladipo OC, Adebambo AO, Bello SF, Ng'ang'a SI, Olaniyi WA, Okoro VMO, Adedeji BE, Olatunde O, Ayoola AO, Matouke MM, Wang YY, Sanke OJ, Oseni SO, Nwani CD, Murphy RW. Population structure and evolutionary history of the greater cane rat (Thryonomys swinderianus) from the Guinean Forests of West Africa. Front Genet 2023;14:1041103.
   doi: 10.3389/fgene.2023.1041103pubmed: 36923796google scholar: lookup
9. Boitard S, Liaubet L, Paris C, Fève K, Dehais P, Bouquet A, Riquet J, Mercat MJ. Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines. Genet Sel Evol 2023 Mar 2;55(1):13.
   doi: 10.1186/s12711-023-00789-zpubmed: 36864379google scholar: lookup
10. Liu X, Seguin-Orlando A, Chauvey L, Tressières G, Schiavinato S, Tonasso-Calvière L, Aury JM, Perdereau A, Wagner S, Clavel P, Estrada O, Pan J, Ma Y, Enk J, Devault A, Klunk J, Lepetz S, Clavel B, Jiang L, Wincker P, Collin YRH, Sarkissian C, Orlando L. DNA methylation-based profiling of horse archaeological remains for age-at-death and castration. iScience 2023 Mar 17;26(3):106144.
    doi: 10.1016/j.isci.2023.106144pubmed: 36843848google scholar: lookup
11. He Z, Dai X, Lyu W, Beaumont M, Yu F. Estimating Temporally Variable Selection Intensity from Ancient DNA Data. Mol Biol Evol 2023 Mar 4;40(3).
    doi: 10.1093/molbev/msad008pubmed: 36661852google scholar: lookup
12. Sant J, Jenkins PA, Koskela J, Spanò D. EWF: simulating exact paths of the Wright-Fisher diffusion. Bioinformatics 2023 Jan 1;39(1).
    doi: 10.1093/bioinformatics/btad017pubmed: 36629450google scholar: lookup
13. 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
14. Sharif MB, Fitak RR, Wallner B, Orozco-terWengel P, Frewin S, Fremaux M, Mohandesan E. Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses. Animals (Basel) 2022 Dec 12;12(24).
    doi: 10.3390/ani12243508pubmed: 36552427google scholar: lookup
15. Wang Y, Zhao Z, Miao X, Wang Y, Qian X, Chen L, Wang C, Li S. eSMC: a statistical model to infer admixture events from individual genomics data. BMC Genomics 2022 Dec 14;23(Suppl 4):827.
    doi: 10.1186/s12864-022-09033-2pubmed: 36517735google scholar: lookup
16. Zhao X, Fu X, Yin C, Lu F. Wheat speciation and adaptation: perspectives from reticulate evolution. aBIOTECH 2021 Dec;2(4):386-402.
    doi: 10.1007/s42994-021-00047-0pubmed: 36311810google scholar: lookup
17. Leonardi M, Boschin F, Boscato P, Manica A. Following the niche: the differential impact of the last glacial maximum on four European ungulates. Commun Biol 2022 Sep 29;5(1):1038.
    doi: 10.1038/s42003-022-03993-7pubmed: 36175492google scholar: lookup
18. Srigyan M, Bolívar H, Ureña I, Santana J, Petersen A, Iriarte E, Kırdök E, Bergfeldt N, Mora A, Jakobsson M, Abdo K, Braemer F, Smith C, Ibañez JJ, Götherström A, Günther T, Valdiosera C. Bioarchaeological evidence of one of the earliest Islamic burials in the Levant. Commun Biol 2022 Jun 7;5(1):554.
    doi: 10.1038/s42003-022-03508-4pubmed: 35672445google scholar: lookup
19. 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
20. Gilroy R, Leng J, Ravi A, Adriaenssens EM, Oren A, Baker D, La Ragione RM, Proudman C, Pallen MJ. Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic diversity. PeerJ 2022;10:e13084.
    doi: 10.7717/peerj.13084pubmed: 35345588google scholar: lookup
21. Iriarte J, Ziegler MJ, Outram AK, Robinson M, Roberts P, Aceituno FJ, Morcote-Ríos G, Keesey TM. Ice Age megafauna rock art in the Colombian Amazon?. Philos Trans R Soc Lond B Biol Sci 2022 Apr 25;377(1849):20200496.
    doi: 10.1098/rstb.2020.0496pubmed: 35249392google scholar: lookup
22. Remer V, Bozlak E, Felkel S, Radovic L, Rigler D, Grilz-Seger G, Stefaniuk-Szmukier M, Bugno-Poniewierska M, Brooks S, Miller DC, Antczak DF, Sadeghi R, Cothran G, Juras R, Khanshour AM, Rieder S, Penedo MC, Waiditschka G, Kalinkova L, Kalashnikov VV, Zaitsev AM, Almarzook S, Reißmann M, Brockmann GA, Brem G, Wallner B. Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Genes (Basel) 2022 Jan 26;13(2).
    doi: 10.3390/genes13020229pubmed: 35205275google scholar: lookup
23. Gudea A, Martonos C, Cosma C, Stan F. Morphological Characteristics of a Horse Discovered in an Avar-Period Grave from Sâncraiu de Mureș (Alba County, Romania). Animals (Basel) 2022 Feb 15;12(4).
    doi: 10.3390/ani12040478pubmed: 35203187google scholar: lookup
24. Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Torres ARBYR, Navas González FJ. One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed. Vet Sci 2022 Feb 6;9(2).
    doi: 10.3390/vetsci9020068pubmed: 35202321google scholar: lookup
25. Ayad A, Almarzook S, Besseboua O, Aissanou S, Piórkowska K, Musiał AD, Stefaniuk-Szmukier M, Ropka-Molik K. Investigation of Cerebellar Abiotrophy (CA), Lavender Foal Syndrome (LFS), and Severe Combined Immunodeficiency (SCID) Variants in a Cohort of Three MENA Region Horse Breeds. Genes (Basel) 2021 Nov 26;12(12).
    doi: 10.3390/genes12121893pubmed: 34946842google scholar: lookup
26. Liu X, Zhang Y, Liu W, Li Y, Pan J, Pu Y, Han J, Orlando L, Ma Y, Jiang L. A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses. Curr Biol 2022 Jan 24;32(2):480-487.e6.
    doi: 10.1016/j.cub.2021.11.052pubmed: 34906355google scholar: lookup
27. 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
28. Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-Del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes. Nature 2021 Oct;598(7882):634-640.
    doi: 10.1038/s41586-021-04018-9pubmed: 34671162google scholar: lookup
29. Suchan T, Kusliy MA, Khan N, Chauvey L, Tonasso-Calvière L, Schiavinato S, Southon J, Keller M, Kitagawa K, Krause J, Bessudnov AN, Bessudnov AA, Graphodatsky AS, Valenzuela-Lamas S, Wilczyński J, Pospuła S, Tunia K, Nowak M, Moskal-delHoyo M, Tishkin AA, Pryor AJE, Outram AK, Orlando L. Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour 2022 Apr;22(3):891-907.
    doi: 10.1111/1755-0998.13518pubmed: 34582623google scholar: lookup
30. Hanot P, Bayarsaikhan J, Guintard C, Haruda A, Mijiddorj E, Schafberg R, Taylor W. Cranial shape diversification in horses: variation and covariation patterns under the impact of artificial selection. BMC Ecol Evol 2021 Sep 21;21(1):178.
    doi: 10.1186/s12862-021-01907-5pubmed: 34548035google scholar: lookup
31. Dussex N, Bergfeldt N, de Anca Prado V, Dehasque M, Díez-Del-Molino D, Ersmark E, Kanellidou F, Larsson P, Lemež Š, Lord E, Mármol-Sánchez E, Meleg IN, Måsviken J, Naidoo T, Studerus J, Vicente M, von Seth J, Götherström A, Dalén L, Heintzman PD. Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics. Proc Biol Sci 2021 Aug 25;288(1957):20211252.
    doi: 10.1098/rspb.2021.1252pubmed: 34428961google scholar: lookup
32. 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
33. Wang MS, Zhang JJ, Guo X, Li M, Meyer R, Ashari H, Zheng ZQ, Wang S, Peng MS, Jiang Y, Thakur M, Suwannapoom C, Esmailizadeh A, Hirimuthugoda NY, Zein MSA, Kusza S, Kharrati-Koopaee H, Zeng L, Wang YM, Yin TT, Yang MM, Li ML, Lu XM, Lasagna E, Ceccobelli S, Gunwardana HGTN, Senasig TM, Feng SH, Zhang H, Bhuiyan AKFH, Khan MS, Silva GLLP, Thuy LT, Mwai OA, Ibrahim MNM, Zhang G, Qu KX, Hanotte O, Shapiro B, Bosse M, Wu DD, Han JL, Zhang YP. Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biol 2021 Jun 16;19(1):118.
    doi: 10.1186/s12915-021-01052-xpubmed: 34130700google scholar: lookup
34. Taylor WTT, Barrón-Ortiz CI. Rethinking the evidence for early horse domestication at Botai. Sci Rep 2021 Apr 2;11(1):7440.
    doi: 10.1038/s41598-021-86832-9pubmed: 33811228google scholar: lookup
35. Kusliy MA, Vorobieva NV, Tishkin AA, Makunin AI, Druzhkova AS, Trifonov VA, Iderkhangai TO, Graphodatsky AS. Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations. Genes (Basel) 2021 Mar 12;12(3).
    doi: 10.3390/genes12030412pubmed: 33809280google scholar: lookup
36. 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
37. Trucchi E, Benazzo A, Lari M, Iob A, Vai S, Nanni L, Bellucci E, Bitocchi E, Raffini F, Xu C, Jackson SA, Lema V, Babot P, Oliszewski N, Gil A, Neme G, Michieli CT, De Lorenzi M, Calcagnile L, Caramelli D, Star B, de Boer H, Boessenkool S, Papa R, Bertorelle G. Ancient genomes reveal early Andean farmers selected common beans while preserving diversity. Nat Plants 2021 Feb;7(2):123-128.
    doi: 10.1038/s41477-021-00848-7pubmed: 33558754google scholar: lookup
38. Xu W, Lin Y, Zhao K, Li H, Tian Y, Ngatia JN, Ma Y, Sahu SK, Guo H, Guo X, Xu YC, Liu H, Kristiansen K, Lan T, Zhou X. An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data. Ecol Evol 2021 Jan;11(1):390-401.
    doi: 10.1002/ece3.7056pubmed: 33437437google scholar: lookup
39. Tuniyazi M, He J, Guo J, Li S, Zhang N, Hu X, Fu Y. Changes of microbial and metabolome of the equine hindgut during oligofructose-induced laminitis. BMC Vet Res 2021 Jan 6;17(1):11.
    doi: 10.1186/s12917-020-02686-9pubmed: 33407409google scholar: lookup
40. Guo X, He XX, Chen H, Wang ZC, Li HF, Wang JX, Wang MS, Jiang RS. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses. Zool Res 2021 Jan 18;42(1):43-50.
    doi: 10.24272/j.issn.2095-8137.2020.133pubmed: 33269825google scholar: lookup
41. Kvist L, Honka J, Niskanen M, Liedes O, Aspi J. Selection in the Finnhorse, a native all-around horse breed. J Anim Breed Genet 2021 Mar;138(2):188-203.
    doi: 10.1111/jbg.12524pubmed: 33226152google scholar: lookup
42. Vorobieva NV, Makunin AI, Druzhkova AS, Kusliy MA, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Shunkov MV, Graphodatsky AS. High genetic diversity of ancient horses from the Ukok Plateau. PLoS One 2020;15(11):e0241997.
    doi: 10.1371/journal.pone.0241997pubmed: 33180850google scholar: lookup
43. Dhorne-Pollet S, Barrey E, Pollet N. A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants. BMC Genomics 2020 Nov 11;21(1):785.
    doi: 10.1186/s12864-020-07183-9pubmed: 33176683google scholar: lookup
44. Jeong C, Wang K, Wilkin S, Taylor WTT, Miller BK, Bemmann JH, Stahl R, Chiovelli C, Knolle F, Ulziibayar S, Khatanbaatar D, Erdenebaatar D, Erdenebat U, Ochir A, Ankhsanaa G, Vanchigdash C, Ochir B, Munkhbayar C, Tumen D, Kovalev A, Kradin N, Bazarov BA, Miyagashev DA, Konovalov PB, Zhambaltarova E, Miller AV, Haak W, Schiffels S, Krause J, Boivin N, Erdene M, Hendy J, Warinner C. A Dynamic 6,000-Year Genetic History of Eurasia's Eastern Steppe. Cell 2020 Nov 12;183(4):890-904.e29.
    doi: 10.1016/j.cell.2020.10.015pubmed: 33157037google scholar: lookup
45. Bergström A, Frantz L, Schmidt R, Ersmark E, Lebrasseur O, Girdland-Flink L, Lin AT, Storå J, Sjögren KG, Anthony D, Antipina E, Amiri S, Bar-Oz G, Bazaliiskii VI, Bulatović J, Brown D, Carmagnini A, Davy T, Fedorov S, Fiore I, Fulton D, Germonpré M, Haile J, Irving-Pease EK, Jamieson A, Janssens L, Kirillova I, Horwitz LK, Kuzmanovic-Cvetković J, Kuzmin Y, Losey RJ, Dizdar DL, Mashkour M, Novak M, Onar V, Orton D, Pasarić M, Radivojević M, Rajković D, Roberts B, Ryan H, Sablin M, Shidlovskiy F, Stojanović I, Tagliacozzo A, Trantalidou K, Ullén I, Villaluenga A, Wapnish P, Dobney K, Götherström A, Linderholm A, Dalén L, Pinhasi R, Larson G, Skoglund P. Origins and genetic legacy of prehistoric dogs. Science 2020 Oct 30;370(6516):557-564.
    doi: 10.1126/science.aba9572pubmed: 33122379google scholar: lookup
46. Parker C, Rohrlach AB, Friederich S, Nagel S, Meyer M, Krause J, Bos KI, Haak W. A systematic investigation of human DNA preservation in medieval skeletons. Sci Rep 2020 Oct 26;10(1):18225.
    doi: 10.1038/s41598-020-75163-wpubmed: 33106554google scholar: lookup
47. 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
48. Valberg SJ, Finno CJ, Henry ML, Schott M, Velez-Irizarry D, Peng S, McKenzie EC, Petersen JL. Commercial genetic testing for type 2 polysaccharide storage myopathy and myofibrillar myopathy does not correspond to a histopathological diagnosis. Equine Vet J 2021 Jul;53(4):690-700.
    doi: 10.1111/evj.13345pubmed: 32896939google scholar: lookup
49. Todd ET, Thomson PC, Hamilton NA, Ang RA, Lindgren G, Viklund Å, Eriksson S, Mikko S, Strand E, Velie BD. A genome-wide scan for candidate lethal variants in Thoroughbred horses. Sci Rep 2020 Aug 4;10(1):13153.
    doi: 10.1038/s41598-020-68946-8pubmed: 32753654google scholar: lookup
50. Lado S, Elbers JP, Doskocil A, Scaglione D, Trucchi E, Banabazi MH, Almathen F, Saitou N, Ciani E, Burger PA. Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes. Commun Biol 2020 Jul 16;3(1):387.
    doi: 10.1038/s42003-020-1098-7pubmed: 32678279google scholar: lookup
51. Wang MS, Thakur M, Peng MS, Jiang Y, Frantz LAF, Li M, Zhang JJ, Wang S, Peters J, Otecko NO, Suwannapoom C, Guo X, Zheng ZQ, Esmailizadeh A, Hirimuthugoda NY, Ashari H, Suladari S, Zein MSA, Kusza S, Sohrabi S, Kharrati-Koopaee H, Shen QK, Zeng L, Yang MM, Wu YJ, Yang XY, Lu XM, Jia XZ, Nie QH, Lamont SJ, Lasagna E, Ceccobelli S, Gunwardana HGTN, Senasige TM, Feng SH, Si JF, Zhang H, Jin JQ, Li ML, Liu YH, Chen HM, Ma C, Dai SS, Bhuiyan AKFH, Khan MS, Silva GLLP, Le TT, Mwai OA, Ibrahim MNM, Supple M, Shapiro B, Hanotte O, Zhang G, Larson G, Han JL, Wu DD, Zhang YP. 863 genomes reveal the origin and domestication of chicken. Cell Res 2020 Aug;30(8):693-701.
    doi: 10.1038/s41422-020-0349-ypubmed: 32581344google scholar: lookup
52. Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M, Prabhu A, Bucca S, Bugno-Poniewierska M, Wallner B, Malek J, Miller DC, Clark AG, Antczak DF, Brooks SA. Genome Diversity and the Origin of the Arabian Horse. Sci Rep 2020 Jun 16;10(1):9702.
    doi: 10.1038/s41598-020-66232-1pubmed: 32546689google scholar: lookup
53. Hermes TR, Frachetti MD, Voyakin D, Yerlomaeva AS, Beisenov AZ, Doumani Dupuy PN, Papin DV, Motuzaite Matuzeviciute G, Bayarsaikhan J, Houle JL, Tishkin AA, Nebel A, Krause-Kyora B, Makarewicz CA. High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor. PLoS One 2020;15(5):e0233333.
    doi: 10.1371/journal.pone.0233333pubmed: 32437372google scholar: lookup
54. Dehasque M, Ávila-Arcos MC, Díez-Del-Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas AS, Marques-Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. Inference of natural selection from ancient DNA. Evol Lett 2020 Apr;4(2):94-108.
    doi: 10.1002/evl3.165pubmed: 32313686google scholar: lookup
55. Lansade L, Colson V, Parias C, Trösch M, Reigner F, Calandreau L. Female horses spontaneously identify a photograph of their keeper, last seen six months previously. Sci Rep 2020 Apr 14;10(1):6302.
    doi: 10.1038/s41598-020-62940-wpubmed: 32286345google scholar: lookup
56. Frantz LAF, Bradley DG, Larson G, Orlando L. Animal domestication in the era of ancient genomics. Nat Rev Genet 2020 Aug;21(8):449-460.
    doi: 10.1038/s41576-020-0225-0pubmed: 32265525google scholar: lookup
57. Racimo F, Sikora M, Vander Linden M, Schroeder H, Lalueza-Fox C. Beyond broad strokes: sociocultural insights from the study of ancient genomes. Nat Rev Genet 2020 Jun;21(6):355-366.
    doi: 10.1038/s41576-020-0218-zpubmed: 32127690google scholar: lookup
58. Kingsley NB, Kern C, Creppe C, Hales EN, Zhou H, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR. Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq. Genes (Basel) 2019 Dec 18;11(1).
    doi: 10.3390/genes11010003pubmed: 31861495google scholar: lookup
59. Pálsdóttir AH, Bläuer A, Rannamäe E, Boessenkool S, Hallsson JH. Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains. R Soc Open Sci 2019 Oct;6(10):191059.
    doi: 10.1098/rsos.191059pubmed: 31824712google scholar: lookup
60. McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019 Dec 2;17(1):98.
    doi: 10.1186/s12915-019-0724-7pubmed: 31791340google scholar: lookup
61. Cagliani R, Forni D, Sironi M. Mode and tempo of human hepatitis virus evolution. Comput Struct Biotechnol J 2019;17:1384-1395.
    doi: 10.1016/j.csbj.2019.09.007pubmed: 31768229google scholar: lookup
62. Almeida M, Diogo R. Human enhancement: Genetic engineering and evolution. Evol Med Public Health 2019;2019(1):183-189.
    doi: 10.1093/emph/eoz026pubmed: 31620286google scholar: lookup
63. Paris C, Servin B, Boitard S. Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model. G3 (Bethesda) 2019 Dec 3;9(12):4073-4086.
    doi: 10.1534/g3.119.400778pubmed: 31597676google scholar: lookup
64. 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
65. Orlando L, Librado P. Origin and Evolution of Deleterious Mutations in Horses. Genes (Basel) 2019 Aug 28;10(9).
    doi: 10.3390/genes10090649pubmed: 31466279google scholar: lookup
66. 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
67. Lan TM, Lin Y, Njaramba-Ngatia J, Guo XS, Li RG, Li HM, Kumar-Sahu S, Wang X, Yang XJ, Guo HB, Xu WH, Kristiansen K, Liu H, Xu YC. Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data. Genes (Basel) 2019 Jul 5;10(7).
    doi: 10.3390/genes10070509pubmed: 31284503google scholar: lookup
68. Wrighton KH. Ancient genomes shed light on dark horses. Nat Rev Genet 2019 Jul;20(7):374-375.
    doi: 10.1038/s41576-019-0136-0pubmed: 31076667google scholar: lookup
69. An T, Dugarjaviin M. Differential Expression and Analysis of TBX3 Gene in Skin Tissues of Dun Mongolian Horses with and Without Bider Markings. Animals (Basel) 2026 Jan 18;16(2).
    doi: 10.3390/ani16020297pubmed: 41594486google scholar: lookup
70. Zhu Q, Khan MZ, Jing Y, Geng M, Zhang X, Zheng Y, Cao X, Peng Y, Wang C. The Donkey Genome: From Evolutionary Insights to Sustainable Breeding Strategies. Animals (Basel) 2025 Dec 29;16(1).
    doi: 10.3390/ani16010093pubmed: 41514782google scholar: lookup
71. Crubézy É, Guarino-Vignon P, Seguin-Orlando A, Der Sarkissian C, Hanghøj K, Duchesne S, Gérard P, Thèves C, Alcouffe A, Romanova L, Nikolaeva D, Alekseeva L, Hochstrasser-Petit C, Zvénigorosky V, Keyser C, Ludes B, Petit M, Dabernat H, Géraut A, Jyrkov E, Sharaborin A, Kirianov N, Tsydenova N, Dambueva I, Bazarof B, Boland A, Deleuze JF, Bravina R, Alexeev A, Patin É, Stépanoff C, Quintana-Murci L, Orlando L. An ancient DNA perspective on the Russian conquest of Yakutia. Nature 2026 Feb;650(8101):389-398.
    doi: 10.1038/s41586-025-09856-5pubmed: 41501450google scholar: lookup
72. Sharma M, Singh A, Kumar V, Olla N, Arora R, Sharma R, Mohan NH, Ahlawat S. Advances in Equine Genomics: Decoding the Genetic Architecture of Morphology, Performance, Behavior, and Adaptation. Mol Biotechnol 2025 Dec 19;.
    doi: 10.1007/s12033-025-01544-zpubmed: 41417456google scholar: lookup
73. Scarsbrook L, Spatola GJ, Dreger DL, Feuerborn TR, Buckley RM, Carmagnini A, Fabre AC, Harris AC, Hertwig ST, Leeb T, Mousseau TA, Tabbada K, Thalmann O, Larson G, Frantz LAF, Ostrander EA. A 120-y time series of genomes reveals the consequences of closed breeding in German Shepherd Dogs. Proc Natl Acad Sci U S A 2025 Dec 2;122(48):e2421755122.
    doi: 10.1073/pnas.2421755122pubmed: 41284896google scholar: lookup
74. 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
75. Hou L, Sulayman A, Zeng Y, Zhou L, Aimaier A, Kader A, Shi L. Analysis of Genetic Diversity and Race Genetic Structure of Major Horse Breeds in Xinjiang, China. Animals (Basel) 2025 Sep 14;15(18).
    doi: 10.3390/ani15182690pubmed: 41007935google scholar: lookup
76. 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
77. Lira Garrido J, Tressières G, Chauvey L, Schiavinato S, Calvière-Tonasso L, Seguin-Orlando A, Southon J, Shapiro B, Bataille C, Birgel J, Wagner S, Khan N, Liu X, Rodanés JM, Picazo Millán JV, Giralt J, Alonso N, Aguilera I, Orsingher A, Trentacoste A, Payà X, Morán M, Iborra Eres MP, Albizuri S, Valenzuela Lamas S, Mestres Santandreu I, Duran Caixal M, Principal J, Farré Huguet J, Esteve X, Pedro Pasqual M, Sala N, Pablos A, Martín P, Vergès JM, Portero R, Arias P, Ontañón Peredo R, Detry C, Luís C, Cardoso JL, Maeir AM, Valente MJ, Grau E, Estall I Poles V, Alfonso Llorens J, Miguélez González A, Gardeisen A, Cupitò M, Tecchiati U, Bradley DG, Kolska Horwitz L, Rodríguez González E, Nieto Espinet A, Bover P, Ruiz Entrecanales R, Garcés Estallo I, Jiménez Fragoso J, Celestino S, Orlando L. The genomic history of Iberian horses since the last Ice Age. Nat Commun 2025 Aug 2;16(1):7098.
    doi: 10.1038/s41467-025-62266-zpubmed: 40753154google scholar: lookup
78. Koyama Y, Nasu M, Matsuoka Y. f(4)-statistics-based ancestry profiling and convolutional neural network phenotyping shed new light on the structure of genetic and spike shape diversity in Aegilops tauschii Coss. Proc Jpn Acad Ser B Phys Biol Sci 2025 Jun 11;101(6):357-370.
    doi: 10.2183/pjab.101.023pubmed: 40399064google scholar: lookup
79. More KD, Lebrasseur O, Garrido JL, Seguin-Orlando A, Discamps E, Estrada O, Tonasso-Calvière L, Chauvey L, Tressières G, Schiavinato S, Gibert M, Padula H, Chiavazza H, Fernández PM, Guardia NM, Borges C, Bertani S, Contreras-Mancilla J, Allccarima-Crisóstomo D, Fhon M, Barrey E, Charliquart L, Robbe E, de Noblet T, Zhumatayev R, Shakenov S, Vila E, Berthon R, Mashkour M, Khazaeli R, Nikgoftar A, Vahdati AA, Kosintsev P, Houle JL, Bayarsaikhan J, Wilczynski J, Moskal-Del Hoyo M, Nowak M, Taylor W, Bălășescu A, Dobrescu R, Benecke N, Arbuckle B, Steadman S, McMahon G, Šikanjić PR, Buric M, Vukičević TT, Alvarez N, Castel JC, Boudadi-Maligne M, Star B, Post-Melbye JR, Rødsrud CL, Stanton DWG, Charlton S, Mullin VE, Daly KG, Burgos NS, Pablos A, Dalen L, Bradley DG, Frantz L, Larson G, Orlando L. Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals. Mol Ecol Resour 2025 Oct;25(7):e14112.
    doi: 10.1111/1755-0998.14112pubmed: 40202701google scholar: lookup
80. Günther T, Chisausky J, Galindo-Pellicena ÁM, Iriarte E, Cortes Gardyn O, Eusebi PG, García-González R, Ureña I, Moreno-García M, Alday A, Rojo M, Pérez A, Tejedor Rodríguez C, García Martínez de Lagrán I, Arsuaga JL, Carretero JM, Götherström A, Smith C, Valdiosera C. The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle. Elife 2025 Mar 19;13.
    doi: 10.7554/eLife.93076pubmed: 40106345google scholar: lookup
81. Li X, Wang Z, Zhu M, Wang B, Teng S, Yan J, Wang H, Yuan P, Cao S, Qu X, Wang Z, Zhan K, Choudhury MP, Yang X, Bao Q, He S, Liu L, Zhao P, Jiang J, Xiang H, Fang L, Tang Z, Liao Y, Yi G. Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies. Adv Sci (Weinh) 2025 Apr;12(16):e2413023.
    doi: 10.1002/advs.202413023pubmed: 40009528google scholar: lookup
82. Haruda A, Evin A, Steinheimer F, Schafberg R. Evolution under intensive industrial breeding: skull size and shape comparison between historic and modern pig lineages. R Soc Open Sci 2025 Feb;12(2):241039.
    doi: 10.1098/rsos.241039pubmed: 39911888google scholar: lookup
83. Radovic L, Remer V, Rigler D, Bozlak E, Allen L, Brem G, Reissman M, Brockmann GA, Ropka-Molik K, Stefaniuk-Szmukier M, Kalinkova L, Kalashnikov VV, Zaitev AM, Raudsepp T, Castaneda C, von Butler-Wemken I, Patterson Rosa L, Brooks SA, Novoa-Bravo M, Kostaras N, Abdurasulov A, Antczak DF, Miller DC, Lopes MS, da Câmara Machado A, Lindgren G, Juras R, Cothran G, Wallner B. The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome. Proc Natl Acad Sci U S A 2024 Dec 3;121(49):e2414408121.
    doi: 10.1073/pnas.2414408121pubmed: 39556761google scholar: lookup
84. Hong JH, Fujita H, Kim J, Shin DH. Cost-effectiveness and other considerations for different research techniques applied in ancient DNA analysis. Anat Cell Biol 2025 Mar 31;58(1):8-13.
    doi: 10.5115/acb.24.125pubmed: 39500721google scholar: lookup
85. Lovász L, Sommer-Trembo C, Barth JMI, Scasta JD, Grancharova-Hill R, Lemoine RT, Kerekes V, Merckling L, Bouskila A, Svenning JC, Fages A. Rewilded horses in European nature conservation - a genetics, ethics, and welfare perspective. Biol Rev Camb Philos Soc 2025 Feb;100(1):407-427.
    doi: 10.1111/brv.13146pubmed: 39279124google scholar: lookup
86. Rambaldi Migliore N, Bigi D, Milanesi M, Zambonelli P, Negrini R, Morabito S, Verini-Supplizi A, Liotta L, Chegdani F, Agha S, Salim B, Beja-Pereira A, Torroni A, Ajmone-Marsan P, Achilli A, Colli L. Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys. PLoS One 2024;19(8):e0307511.
    doi: 10.1371/journal.pone.0307511pubmed: 39197009google scholar: lookup
87. Gmel AI, Mikko S, Ricard A, Velie BD, Gerber V, Hamilton NA, Neuditschko M. Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed. Genet Sel Evol 2024 Jul 10;56(1):53.
    doi: 10.1186/s12711-024-00922-6pubmed: 38987703google scholar: lookup
88. Fegraeus K, Rosengren MK, Naboulsi R, Orlando L, Åbrink M, Jouni A, Velie BD, Raine A, Egner B, Mattsson CM, Lång K, Zhigulev A, Björck HM, Franco-Cereceda A, Eriksson P, Andersson G, Sahlén P, Meadows JRS, Lindgren G. An endothelial regulatory module links blood pressure regulation with elite athletic performance. PLoS Genet 2024 Jun;20(6):e1011285.
    doi: 10.1371/journal.pgen.1011285pubmed: 38885195google scholar: lookup
89. Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Asensio Vilaró D, Codina F, García Dalmau C, Morer de Llorens J, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature 2024 Jul;631(8022):819-825.
    doi: 10.1038/s41586-024-07597-5pubmed: 38843826google scholar: lookup
90. Larsson MNA, Morell Miranda P, Pan L, Başak Vural K, Kaptan D, Rodrigues Soares AE, Kivikero H, Kantanen J, Somel M, Özer F, Johansson AM, Storå J, Günther T. Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region. Genome Biol Evol 2024 Jun 4;16(6).
    doi: 10.1093/gbe/evae114pubmed: 38795367google scholar: lookup
91. Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, Funder S, Gotfredsen AB, Gregersen KM, Hansen CH, Ilsøe PC, Klassen L, Kristensen IK, Ravnholt GB, Marin F, Der Sarkissian C. Advancing responsible genomic analyses of ancient mollusc shells. PLoS One 2024;19(5):e0302646.
    doi: 10.1371/journal.pone.0302646pubmed: 38709766google scholar: lookup
92. Arefnejad B, Zeinalabedini M, Talebi R, Mardi M, Ghaffari MR, Vahidi MF, Nekouei MK, Szmatoła T, Salekdeh GH. Unveiling the population genetic structure of Iranian horses breeds by whole-genome resequencing analysis. Mamm Genome 2024 Jun;35(2):201-227.
    doi: 10.1007/s00335-024-10035-6pubmed: 38520527google scholar: lookup
93. Lebrasseur O, More KD, Orlando L. Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus Evol 2024;10(1):vead087.
    doi: 10.1093/ve/vead087pubmed: 38465241google scholar: lookup
94. De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024 Jan 23;14(1):2003.
    doi: 10.1038/s41598-023-48103-7pubmed: 38263320google scholar: lookup
95. Manunza A, Ramirez-Diaz J, Cozzi P, Lazzari B, Tosser-Klopp G, Servin B, Johansson AM, Grøva L, Berg P, Våge DI, Stella A. Genetic diversity and historical demography of underutilised goat breeds in North-Western Europe. Sci Rep 2023 Nov 25;13(1):20728.
    doi: 10.1038/s41598-023-48005-8pubmed: 38007600google scholar: lookup
96. Atağ G, Vural KB, Kaptan D, Özkan M, Koptekin D, Sağlıcan E, Doğramacı S, Köz M, Yılmaz A, Söylev A, Togan İ, Somel M, Özer F. MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes. Open Res Eur 2022;2:100.
    doi: 10.12688/openreseurope.14936.3pubmed: 37829208google scholar: lookup