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The makeup of the modern horse:

a history of the biological changes introduced by human management

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    Publications   

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  1. Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pardal LP, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, PratoO, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Antunes MT, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Koska Horwitz L, Ötzan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashjour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, . 2022. The genomic history and global expansion of domestic donkeys. Science 377:1172-80.

  2. Suchan T, Chauvey L, Poullet M, Tonasso-Calvière L, Schiavinato S, Clavel P, Clavel B, Lepetz S, Seguin-Orlando A, Orlando L. 2022. Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA. Mol Ecol Resour 22:2262-64.

  3. Cai D, Zhu S, Gong M, Zhanh N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang S, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Jiang Y. 2022. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. 11:e73346.

  4. Slimak L, Zanolli C, Higham T, Frouin M, Schwenninger JL, Arnold LJ, Demuro M, Douka K, Mercier N, Guérin G, Valladas H, Yvorra P, Giraud Y, Seguin-Orlando A, Orlando L, Lewis JE, Muth X, Camus H, Vandevelde S, Buckley M, Mallol C, Stringer C, Metz L. 2022. Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France. Sci Adv 8:eabj9496.

  5. Liu X, L. 2022. mapDATAge: a ShinyRpackage to chart ancient DNA data through space and time. 38:3992-4.

  6. Librado P, . 2022. Struct-f4: a Rccp package for ancestry profile and population structure inference from f4 statistics. 38:2070-1.

  7. Clavel B, Lepetz S, Chauvey L, Schiavinato S, Tonasso-Calvière L, Liu X, Fages A, Khan N, Seguin-Orlando A, Der Sarkissian C, Clavel P, Estrada O, Alioglu D, Gaunitz C, Aury JM, Barme M, Bodu P, Olive M, Bignong-Lau O, Castel JC, Boudadi-Maligne M, Boulbes N, Bourgois A, Decanter F, Foucras S, Frère S, Gardeisen A, Jouanin G, Méla C, Morand N, Nieto Espinet A, Perdereau A, Putelat O, Rivière J, Robin O, Salin M, Valenzuela-Lamas S, Vallet C, Yvinec JH, Wincker P, Orlando L. 2022. Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France. J Arc Sci Rep 41:103341.

  8. Liu X, Zhang Y, Liu W, Li Y, Pan J, Pu Y, Han J, Orlando L, Ma Y, Jiang L. 2022. A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses. Curr Biol 32:480-7.

  9. 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. 2022. Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour 22:891-907.

  10. Lepetz S, Clavel B, Alioglu D, Chauvey L, Schiavinato S, Tonasso-Calvière L, Liu X, Fages A, Khan N, Seguin-Orlando A, Der Sarkissian C, Clavel P, Estrada O, Gaunitz C, Aury JM, Barme M, Boulbes N, Bourgois A, Decanter F, Foucras S, Frère S, Gardeisen A, Jouanin G, Méla C, Morand N, Nieto Espinet A, Perdereau A, Putelat O, Rivière J, Robin O, Salin M, Valenzuela-Lamas S, Vallet C, Yvinec JH, Wincker P, . Historical management of equine resources in France from the Iron Age to the Modern Period. J Arc Sci Rep 40:103250.

  11. Clavel P, Dumoncel J, Der Sarkissian C, Seguin-Orlando A, Calvière-Tonasso L, Schiavinato S, Chauvey L, Perdereau A, Aury JM, Wincker P, Onar V, Clavel B, Lepetz S, Braga J, Orlando L. 2021. Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids. J Arc Sci 131:105383.

  12. Orlando L, Allaby R, Skoglund P, Der Sarkissian C, Stockhammer PW, Avila-Arcos MC, Fu Q, Krause J, Willerslev E, Stone AC, Warinner C. 2021. Ancient DNA analysis. Nat Rev Methods Primers 1:14.

  13. 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. 2021. The origins and spread of domestic horses from the Western Eurasian steppes. Nature 598:634-640.

  14. 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. 2021. Performance and automation of ancient DNA capture with RNA hyRAD probes. Mol Ecol Resour 22:891-907.

  15. Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. 2021. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge. Mol Ecol 30:6144-6161.

  16. Kingsley NB, Hamilton NA, Lindgren G, Orlando L, Bailey E, Brooks S, McCue M, Kalbfleisch TS, MacLeod JN, Petersen JL, Finno CJ, Bellone RR. 2021. "Adopt-a-Tissue" Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare. Front Genet 12:649959.

  17. Librado P, Orlando L. 2021. Genomics and the Evolutionary History of Equids. Annu Rev Anim Biosci 9:81-101.

  18. Wang Y, Pedersen MW, Alsos IG, De Sanctis B, Racimo F, Prohaska A, Coissac E, Owens HL, Merkel MKF, Fernandez-Guerra A, Rouillard A, Lammers Y, Alberti A, Denoeud F, Money D, Ruter AH, McColl H, Larsen NK, Cherezova AA, Edwards ME, Fedorov GB, Haile J, Orlando L, Vinner L, Korneliussen TS, Beilman DW, Bjørk AA, Cao J, Dockter C, Esdale J, Gusarova G, Kjeldsen KK, Mangerud J, Rasic JT, Skadhauge B, Svendsen JI, Tikhonov A, Wincker P, Xing Y, Zhang Y, Froese DG, Rahbek C, Nogues DB, Holden PB, Edwards NR, Durbin R, Meltzer DJ, Kjær KH, Möller P, Willerslev E. 2021. Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature 600, pages 86–92.

  19. Orlando L. 2020. The evolutionary and historical foundation of the modern horse: lessons from ancient genomics. Ann Rev Genet 54:563-81.

  20. Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, , Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. 21:677.

  21. Poullet M, Orlando L. 2020. Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes. Frontiers Ecol Evol:105.

  22. Fages A, Seguin-Orlando A, Germonpré M, .Orlando L Horse males became over-represented in archaeological assemblages during the Bronze Age. J Arc Sci Rep 31:102364

  23. Frantz L, Bradley D, Larson G, Orlando L. Animal domestication in the era of ancient genomics. Nat Rev Genet, in press [doi: 10.1038/s41576-020-0225-0]

  24. Dolle D, Fages A, Mata X, Schiavinato S, Tonasso-Calvière L, Chauvey L, Wagner S, Der Sarkissia C, Fromentier A, Seguin-Orlando A, Orlando L. CASCADE: a Custom-made Archiving System for the Conservation of Ancient DNA Experimental Data. Frontiers Ecol Evol, in press [doi: 10.3389/fevo.2020.00185]

  25. Wilkin S, Ventresca Miller A, Taylor W, Miller B, Hagan R, Bleasdale M, Scott A, Gankhuyg S, Ramsøe A, Ulziibayar S, Trachsel C, Nanni P, Grossmann J, Orlando L, Horton M, Stockhammer P, Myagmar E, Boivin N, Warinner C, Hendy J. Dairy pastoralism sustained Eastern Eurasian steppe populations for 5000 years. Nat Ecol Evol 4:346-355.

  26. Orlando L. 2020. Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics. Bioessays 42:e1900164.

  27. Orlando L, Librado P. 2019. Origin and Evolution of Deleterious Mutations in Horses. Genes (Basel) 10(9) pii: E649.

  28. Liu X, Zhang Y, Li Y, Pan J, Wang D, Chen W, Zheng Z, He X, Zhao Q, Pu Y, Guan W, Han J, Orlando L, Ma Y, Jiang L. 2019. EPAS1 gain-of-function mutation contributes to high-altitude adaptation in Tibetan horses. Mol Biol Evol 36:2591-2603.

  29. Renaud G, Schubert M, Sawyer S, Orlando L. Authentication and Assessment of Contamination in Ancient DNA. 1963:163-194.

  30. Renaud G, Hanghøj K, Korneliussen TS, Willerslev E, Orlando L. 2019. Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples. Genetics May 14. pii: genetics.302057.2019.

  31. Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Mochlov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. 2019. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series. Cell 177:1419-1435.e31.

  32. Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, De Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, , Pansu J, Pawlowski J, Tedersoo L, Thomsen PF, Willerslev E, Taberlet P. 2019. DNA metabarcoding-Need for robust experimental designs to draw sound ecological conclusions. 28:1857-1862.

  33. Hanghøj K, Renaud G, Albrechtsen A, Orlando L. 2019. DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage. Gigascience 8. pii: giz025.

  34. Renaud G, Schubert M, Sawyer S, Orlando L. Authentication and Assessment of Contamination in Ancient DNA. Methods Mol Biol 1963:163-194.

  35. Leonardi M, Boschin F, Giampoudakis K, Beyer RM, Krapp M, Bendrey R, Sommer R, Boscato P, Manica A, Nogues-Bravo D, . 2018. Late Quaternary horses in Eurasia in the face of climate and vegetation change. Sci Adv 4:eaar5589.

  36. Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, , Green RE, Miller DC, Antczak DF, MacLeod JN. 2018. Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol 1:197.

  37. Orlando L. 2018. Late Bronze Age cultural origins of dairy pastoralism in Mongolia. PNAS, pii:201817559.

  38. Taylor W, Schnaider S, Abdykanova A, Fages A, Welker F, Irmer F, Seguin-Orlando A, Khan N, Douka K, Kolobova K, , Krivoshapkin A, Boivin N. 2018. Early pastoral economies along the Ancient Silk Road: biomolecular evidence from the Alay Valley Kyrgyzstan. PLoS One 13:ee0205646.

  39. 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, Crubezy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lougas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram A, Orlando L. 2018. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 360:111-114

  40. de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V, Merz V, Biddanda A, Merz I, Loman V, Evdokimov V, Usmanova E, Hemphill B, Seguin-Orlando A, Yediay FE, Ullah I, Sjögren KG, Iversen KH, Choin J, de la Fuente C, Ilardo M, Schroeder H, Moiseyev V, Gromov A, Polyakov A, Omura S, Senyurt SY, Ahmad H, McKenzie C, Margaryan A, Hameed A, Samad A, Gul N, Khokhar MH, Goriunova OI, Bazaliiskii VI, Novembre J, Weber AW, Orlando L, Allentoft ME, Nielsen R, Kristiansen K, Sikora M, Outram AK, Durbin R, Willerslev E. 2018. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science 360 pii: eaar7711. 

  41. Nistelberger H, Pálsdóttir AH, Star B, Leifsson R, Gondeka AT, Orlandod L, Barrett JH, Hallsteinn Hallsson J, Boessenkool S. 2019. Sexing Viking Age horses from burial and non-burial sites in Iceland using ancient DNA. J Arc Sci 101:115-122

  42. Taylor W, Shnaider S, Abdykanova A, Fages A, Welker F, Irmer F, Seguin-Orlando A, Khan N, Douka K, Kolobova K, Orlando L, Krivoshapkin A, Boivin N. 2018. Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan. PLoS One 13:e0205646

  43. Orlando L. 2018. Late Bronze Age cultural origins of dairy pastoralism in Mongolia. Proc Natl Acad Sci USA 115:12083-12085

  44. Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. 2018. Improved de novo genomic assembly for the domestic donkey. Science Advances 4:eaaq0392

  45. 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. 2018.  Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nat Commun 9:2945

  46. Leonardi M, Boschin F, Giampoudakis K, Beyer RM, Krapp M, Bendrey R, Sommer R, Boscato P, Manica A, Nogues-Bravo D, Orlando L. 2018. Late Quaternary horses in Eurasia in the face of climate and vegetation change. Sci Adv 4:eaar5589

  47. Librado P, Orlando L. 2018. Detecting signatures of positive selection along defined branches of a population tree using LSD. Mol Biol Evol. 2018 Mar 29. doi: 10.1093/molbev/msy053.

  48. 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. 2018. Decline of genetic diversity in ancient domestic stallions in Europe. Sci Adv 4:eaap9691.

  49. Warinner C, Herbig A, Mann A, Fellows Yates JA, Weiß CL, Burbano HA, Orlando L, Krause J. 2017. A Robust Framework for Microbial Archaeology. Annu Rev Genomics Hum Genet 18:321-356

  50. Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L. 2017. Evaluating the impact of domestication and captivity on the horse gut microbiome. Sci Rep 7:15497.

  51. McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore A, Seguin-Orlando A, Feh C, Orlando L, Mendelson JR, Sanders J, Knight R. 2017. The Effects of Captivity on the Mammalian Gut Microbiome. Integr Comp Biol 57:690-704.

  52. Librado L, 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. 2017. Ancient genomic changes associated with domestication of the horse. Science 356:442-445.

  53. Cucchi T, Mohaseb A, Peigne S, Debue K, Orlando L, Mashkour M. Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies. R Soc Open Sci 4:160997..

  54. Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhane AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, Orlando L. 2017. Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. J Arc Sci 78:147–157.

  55. Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. 2017. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 18:565.

  56. Heintzman PD, Zazula GD, MacPhee R, Scott E, Cahill JA, McHorse BK, Kapp JD, Stiller M, Wooller MJ, Orlando L, Southon J, Froese DG, Shapiro B. 2017. A new genus of horse from Pleistocene North America. Elife 6. pii: e29944.

  57. 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. 2016. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci Rep 6:38548

  58. 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. 2016. The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 204:423-434.

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Background:

  • Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jonsson 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, Greenblat 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. 2015. Evolutionary genomics and conservation of the endangered Przewalski’s horse. Curr Biol 25:2577-83

  • Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fummagalli M, Yang MA, Gamba C, Ginolhac A, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover C, Lorente B, Nedoluzhko A, Boulougina E, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Sicheritz-Ponten T, Popov R, Alekseev AN, Rubin E, 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. PNAS 112:E6889-97

  • 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. 2014. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. PNAS 111:E5661-9

  • Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka J, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. 2014. Speciation with gene flow in equids despite extensive chromosomal plasticity. PNAS 111:18655-60

  • Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Gamba C, Willerslev E, Orlando L. 2016. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol. 2016 Jul 5. pii: syw059

  • Orlando L, Gilbert MT, Willerslev E. Reconstructing ancient genomes and epigenomes. 2015. Nat Rev Genet. 16:395-408

  • Orlando L, Cooper A. Using ancient DNA to understand evolutionary and ecological processes. 2014. Annual Reviews of Ecology, Evolution, and Systematics 45: 573-598

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Book Chapters:

  1. Fémélat A, Macé M, Orlando L. Les chevaux de Léonard de Vinci. Regards croises entre histoire de l'art, mathématiques et biologie. In: Croiser les sciences pour lire les animaux. Baratay E eds, Editions Sorbonne (ISBN-13: 979-1035105884).

  2. Clément J, Davoudi H, Fages A, Mashkour M, Mosaheb A,, Spruyt M.. Les chevaux antiques du plateau iranien: entre étude philologique, examen iconographique, recherche archéozoologique et analyse paléogénétique. Baratay E eds: Aux sources de l’histoire animale. Baratay E eds, Editions Sorbonne,

  3. Orlando L. 2019. L’ADN ancien comme nouvelle source historique. In: Aux sources de l’histoire animale. Baratay E eds, Editions Sorbonne, p 288.

  4. Orlando L. 2018. An ancient DNA perspective on horse evolution. In: Paleogenomics. Linqvist C, Rajora OP eds. Springer, pp 325-351.

  5. Hanghøj K, Orlando L. Ancient epigenetics. Springer. In: Paleogenomics. Linqvist C, Rajora OP eds. Springer, pp 75-111.

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