Analyze Diet
Nature reviews. Genetics2020; 21(8); 449-460; doi: 10.1038/s41576-020-0225-0

Animal domestication in the era of ancient genomics.

Abstract: The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
Publication Date: 2020-04-07 PubMed ID: 32265525PubMed Central: 3384140DOI: 10.1038/s41576-020-0225-0Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
  • Historical Article
  • Journal Article
  • Research Support
  • Non-U.S. Gov't
  • Review

Summary

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

This research article explores the domestication of animals and their adaption to human environments over time, particularly focusing on the use of innovative genomic methods to sequence whole ancient genomes and thus reconstruct the process of how these animals became domesticated.

Understanding Animal Domestication

  • The research begins with the recognition of animal domestication as a pivotal movement in human history, marking the shift from a hunter-gatherer lifestyle to fixed agricultural practices. This shift significantly impacted the size and stability of human populations, giving rise to more complex societies.
  • The impact on animals is noted as well, as the researchers point to substantial changes in the phenotype and genotype of various animal species due to their adaptation to human lifestyles. Species mentioned include dogs, pigs, sheep, goats, cattle, and horses.

Role of Genomics in Studying Animal Domestication

  • The paper takes a departure from traditional viewpoints to shed light on the novel methodology used to study animal domestication. It particularly focuses on the innovations in the field of genomics, specifically ancient DNA extraction methods and next-generation sequencing.
  • These innovative methodological approaches have enabled complete sequencing of whole ancient genomes, a breakthrough that was not previously possible. This sequencing allows for a deeper understanding of the domestication process through the reconstruction of genetic histories.

The Influence of Ancient Genomics

  • The researchers provide updates on key concepts in animal domestication, incorporating recent findings from the study of ancient genomics. They emphasize the significance of these contributions in updating our knowledge about animal domestication, reflecting the scientific advances in the field.
  • The paper also reiterates the potential implications of understanding animal domestication in light of genomic findings. It concludes by reinforcing the value of genetic research in shedding new light on how domestic relationships between humans and animals were formed and evolved over time.

Cite This Article

APA
Frantz LAF, Bradley DG, Larson G, Orlando L. (2020). Animal domestication in the era of ancient genomics. Nat Rev Genet, 21(8), 449-460. https://doi.org/10.1038/s41576-020-0225-0

Publication

ISSN: 1471-0064
NlmUniqueID: 100962779
Country: England
Language: English
Volume: 21
Issue: 8
Pages: 449-460

Researcher Affiliations

Frantz, Laurent A F
  • School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. laurent.frantz@qmul.ac.uk.
Bradley, Daniel G
  • Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
Larson, Greger
  • The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.
Orlando, Ludovic
  • Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France. ludovic.orlando@univ-tlse3.fr.
  • Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark. ludovic.orlando@univ-tlse3.fr.

MeSH Terms

  • Animal Husbandry
  • Animals
  • Animals, Wild
  • DNA, Ancient
  • DNA, Mitochondrial
  • Domestication
  • Founder Effect
  • Genomics / history
  • Genomics / methods
  • History, Ancient
  • Models, Theoretical
  • Selection, Genetic
  • Spatio-Temporal Analysis

Grant Funding

  • 210119/Z/18/Z / Wellcome Trust

References

This article includes 151 references
  1. Zeder M. A.. The domestication of animals. J. Anthropol. Res. 68, 161–190 (2012).
  2. Vigne JD. The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere.. C R Biol 2011 Mar;334(3):171-81.
    pubmed: 21377611doi: 10.1016/j.crvi.2010.12.009google scholar: lookup
  3. Larson G, Karlsson EK, Perri A, Webster MT, Ho SY, Peters J, Stahl PW, Piper PJ, Lingaas F, Fredholm M, Comstock KE, Modiano JF, Schelling C, Agoulnik AI, Leegwater PA, Dobney K, Vigne JD, Vilà C, Andersson L, Lindblad-Toh K. Rethinking dog domestication by integrating genetics, archeology, and biogeography.. Proc Natl Acad Sci U S A 2012 Jun 5;109(23):8878-83.
    pubmed: 22615366doi: 10.1073/pnas.1203005109pmc: 3384140google scholar: lookup
  4. Darwin C.. The Variation of Animals and Plants Under Domestication. John Murray, 1868.
  5. 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.
    pubmed: 31791340pmc: 6889691doi: 10.1186/s12915-019-0724-7google scholar: lookup
  6. Conolly J.. Meta-analysis of zooarchaeological data from SW Asia and SE Europe provides insight into the origins and spread of animal husbandry. J. Archaeol. Sci. 38, 538–545 (2011).
    doi: 10.1016/j.jas.2010.10.008google scholar: lookup
  7. Vigne, J.-D. in The Neolithic Demographic Transition and its Consequences (eds Bocquet-Appel, J.-P. & Bar-Yosef, O.) 179–205 (Springer, 2008).
  8. Ervynck A., Dobney K., Hongo H., Meadow R.. Born free? New evidence for the status of ‘Sus scrofa’ at Neolithic Çayönü Tepesi (Southeastern Anatolia, Turkey). Paléorient 27, 47–73 (2001).
    doi: 10.3406/paleo.2001.4731google scholar: lookup
  9. Payne S.. Kill-off patterns in sheep and goats: the mandibles from Aşvan kale. Anatol. Stud. 23, 281–303 (1973).
    doi: 10.2307/3642547google scholar: lookup
  10. Balasse M.. Wild, domestic and feral? Investigating the status of suids in the Romanian Gumelniţa (5th mil. cal BC) with biogeochemistry and geometric morphometrics. J. Anthropol. Archaeol. 42, 27–36 (2016).
    doi: 10.1016/j.jaa.2016.02.002google scholar: lookup
  11. Pitulko V. V., Kasparov A. K.. Archaeological dogs from the Early Holocene Zhokhov site in the Eastern Siberian Arctic. J. Archaeol. Sci. Rep. 13, 491–515 (2017).
  12. Olsen S. L.. Early horse domestication: weighing the evidence. BAR. Int. Ser. 1560, 81 (2006).
  13. Larson G, Dobney K, Albarella U, Fang M, Matisoo-Smith E, Robins J, Lowden S, Finlayson H, Brand T, Willerslev E, Rowley-Conwy P, Andersson L, Cooper A. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication.. Science 2005 Mar 11;307(5715):1618-21.
    pubmed: 15761152doi: 10.1126/science.1106927google scholar: lookup
  14. Luikart G, Gielly L, Excoffier L, Vigne JD, Bouvet J, Taberlet P. Multiple maternal origins and weak phylogeographic structure in domestic goats.. Proc Natl Acad Sci U S A 2001 May 8;98(10):5927-32.
    pubmed: 11344314doi: 10.1073/pnas.091591198pmc: 33315google scholar: lookup
  15. Naderi S, Rezaei HR, Pompanon F, Blum MG, Negrini R, Naghash HR, Balkiz O, Mashkour M, Gaggiotti OE, Ajmone-Marsan P, Kence A, Vigne JD, Taberlet P. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals.. Proc Natl Acad Sci U S A 2008 Nov 18;105(46):17659-64.
    pubmed: 19004765doi: 10.1073/pnas.0804782105pmc: 2584717google scholar: lookup
  16. Pedrosa S, Uzun M, Arranz JJ, Gutiérrez-Gil B, San Primitivo F, Bayón Y. Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events.. Proc Biol Sci 2005 Oct 22;272(1577):2211-7.
    pubmed: 16191632pmc: 1559946doi: 10.1098/rspb.2005.3204google scholar: lookup
  17. Vilà C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H. Widespread origins of domestic horse lineages.. Science 2001 Jan 19;291(5503):474-7.
    pubmed: 11161199doi: 10.1126/science.291.5503.474google scholar: lookup
  18. Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, Strömstedt L, Wright D, Jungerius A, Vereijken A, Randi E, Jensen P, Andersson L. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken.. PLoS Genet 2008 Feb 29;4(2):e1000010.
    pubmed: 18454198pmc: 2265484doi: 10.1371/journal.pgen.1000010google scholar: lookup
  19. Wright D.. Article commentary: the genetic architecture of domestication in animals. Bioinform. Biol. Insights 9S4, BBI.S28902 (2015).
    doi: 10.4137/BBI.S28902google scholar: lookup
  20. Shannon LM, Boyko RH, Castelhano M, Corey E, Hayward JJ, McLean C, White ME, Abi Said M, Anita BA, Bondjengo NI, Calero J, Galov A, Hedimbi M, Imam B, Khalap R, Lally D, Masta A, Oliveira KC, Pérez L, Randall J, Tam NM, Trujillo-Cornejo FJ, Valeriano C, Sutter NB, Todhunter RJ, Bustamante CD, Boyko AR. Genetic structure in village dogs reveals a Central Asian domestication origin.. Proc Natl Acad Sci U S A 2015 Nov 3;112(44):13639-44.
    pubmed: 26483491doi: 10.1073/pnas.1516215112pmc: 4640804google scholar: lookup
  21. Wang GD, Zhai W, Yang HC, Wang L, Zhong L, Liu YH, Fan RX, Yin TT, Zhu CL, Poyarkov AD, Irwin DM, Hytönen MK, Lohi H, Wu CI, Savolainen P, Zhang YP. Out of southern East Asia: the natural history of domestic dogs across the world.. Cell Res 2016 Jan;26(1):21-33.
    pubmed: 26667385doi: 10.1038/cr.2015.147google scholar: lookup
  22. Pang JF, Kluetsch C, Zou XJ, Zhang AB, Luo LY, Angleby H, Ardalan A, Ekström C, Sköllermo A, Lundeberg J, Matsumura S, Leitner T, Zhang YP, Savolainen P. mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves.. Mol Biol Evol 2009 Dec;26(12):2849-64.
    pubmed: 19723671pmc: 2775109doi: 10.1093/molbev/msp195google scholar: lookup
  23. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. DNA sequences from the quagga, an extinct member of the horse family.. Nature 1984 Nov 15-21;312(5991):282-4.
    pubmed: 6504142doi: 10.1038/312282a0google scholar: lookup
  24. Pääbo S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.. Proc Natl Acad Sci U S A 1989 Mar;86(6):1939-43.
    pubmed: 2928314doi: 10.1073/pnas.86.6.1939pmc: 286820google scholar: lookup
  25. Hagelberg E, Bell LS, Allen T, Boyde A, Jones SJ, Clegg JB. Analysis of ancient bone DNA: techniques and applications.. Philos Trans R Soc Lond B Biol Sci 1991 Sep 30;333(1268):399-407.
    pubmed: 1684050doi: 10.1098/rstb.1991.0090google scholar: lookup
  26. Römpler H, Schulz A, Pitra C, Coop G, Przeworski M, Pääbo S, Schöneberg T. The rise and fall of the chemoattractant receptor GPR33.. J Biol Chem 2005 Sep 2;280(35):31068-75.
    pubmed: 15987686doi: 10.1074/jbc.M503586200google scholar: lookup
  27. Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S. Ancient DNA.. Nat Rev Genet 2001 May;2(5):353-9.
    pubmed: 11331901doi: 10.1038/35072071google scholar: lookup
  28. Gilbert MT, Bandelt HJ, Hofreiter M, Barnes I. Assessing ancient DNA studies.. Trends Ecol Evol 2005 Oct;20(10):541-4.
    pubmed: 16701432doi: 10.1016/j.tree.2005.07.005google scholar: lookup
  29. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies.. Nat Rev Genet 2016 May 17;17(6):333-51.
    pubmed: 27184599doi: 10.1038/nrg.2016.49google scholar: lookup
  30. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo.. Nature 2010 Feb 11;463(7282):757-62.
    pubmed: 20148029pmc: 3951495doi: 10.1038/nature08835google scholar: lookup
  31. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome.. Science 2010 May 7;328(5979):710-722.
    pubmed: 20448178pmc: 5100745doi: 10.1126/science.1188021google scholar: lookup
  32. Orlando L, Gilbert MT, Willerslev E. Reconstructing ancient genomes and epigenomes.. Nat Rev Genet 2015 Jul;16(7):395-408.
    pubmed: 26055157doi: 10.1038/nrg3935google scholar: lookup
  33. 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.
    pubmed: 25731166pmc: 5048219doi: 10.1038/nature14317google scholar: lookup
  34. Albrechtsen A, Nielsen FC, Nielsen R. Ascertainment biases in SNP chips affect measures of population divergence.. Mol Biol Evol 2010 Nov;27(11):2534-47.
    pubmed: 20558595pmc: 3107607doi: 10.1093/molbev/msq148google scholar: lookup
  35. Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek AT, Orlando L, Barrett JH, Star B. Combining bleach and mild predigestion improves ancient DNA recovery from bones.. Mol Ecol Resour 2017 Jul;17(4):742-751.
    pubmed: 27790833doi: 10.1111/1755-0998.12623google scholar: lookup
  36. Gansauge MT, Meyer M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA.. Nat Protoc 2013 Apr;8(4):737-48.
    pubmed: 23493070doi: 10.1038/nprot.2013.038google scholar: lookup
  37. Gansauge MT, Gerber T, Glocke I, Korlevic P, Lippik L, Nagel S, Riehl LM, Schmidt A, Meyer M. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase.. Nucleic Acids Res 2017 Jun 2;45(10):e79.
    pubmed: 28119419pmc: 5449542doi: 10.1093/nar/gkw835google scholar: lookup
  38. 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.
    pubmed: 20028723doi: 10.1093/nar/gkp1163google scholar: lookup
  39. 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.
    pubmed: 25487342pmc: 4275898doi: 10.1098/rstb.2013.0624google scholar: lookup
  40. Gamba C, Jones ER, Teasdale MD, McLaughlin RL, Gonzalez-Fortes G, Mattiangeli V, Domboróczki L, Kővári I, Pap I, Anders A, Whittle A, Dani J, Raczky P, Higham TF, Hofreiter M, Bradley DG, Pinhasi R. Genome flux and stasis in a five millennium transect of European prehistory.. Nat Commun 2014 Oct 21;5:5257.
    pubmed: 25334030doi: 10.1038/ncomms6257google scholar: lookup
  41. Verdugo MP, Mullin VE, Scheu A, Mattiangeli V, Daly KG, Maisano Delser P, Hare AJ, Burger J, Collins MJ, Kehati R, Hesse P, Fulton D, Sauer EW, Mohaseb FA, Davoudi H, Khazaeli R, Lhuillier J, Rapin C, Ebrahimi S, Khasanov M, Vahidi SMF, MacHugh DE, Ertuğrul O, Koukouli-Chrysanthaki C, Sampson A, Kazantzis G, Kontopoulos I, Bulatovic J, Stojanović I, Mikdad A, Benecke N, Linstädter J, Sablin M, Bendrey R, Gourichon L, Arbuckle BS, Mashkour M, Orton D, Horwitz LK, Teasdale MD, Bradley DG. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent.. Science 2019 Jul 12;365(6449):173-176.
    pubmed: 31296769doi: 10.1126/science.aav1002google scholar: lookup
  42. Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çakırlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.. Science 2018 Jul 6;361(6397):85-88.
    pubmed: 29976826doi: 10.1126/science.aas9411google scholar: lookup
  43. Frantz LAF, Haile J, Lin AT, Scheu A, Geörg C, Benecke N, Alexander M, Linderholm A, Mullin VE, Daly KG, Battista VM, Price M, Gron KJ, Alexandri P, Arbogast RM, Arbuckle B, Bӑlӑşescu A, Barnett R, Bartosiewicz L, Baryshnikov G, Bonsall C, Borić D, Boroneanţ A, Bulatović J, Çakirlar C, Carretero JM, Chapman J, Church M, Crooijmans R, De Cupere B, Detry C, Dimitrijevic V, Dumitraşcu V, du Plessis L, Edwards CJ, Erek CM, Erim-Özdoğan A, Ervynck A, Fulgione D, Gligor M, Götherström A, Gourichon L, Groenen MAM, Helmer D, Hongo H, Horwitz LK, Irving-Pease EK, Lebrasseur O, Lesur J, Malone C, Manaseryan N, Marciniak A, Martlew H, Mashkour M, Matthews R, Matuzeviciute GM, Maziar S, Meijaard E, McGovern T, Megens HJ, Miller R, Mohaseb AF, Orschiedt J, Orton D, Papathanasiou A, Pearson MP, Pinhasi R, Radmanović D, Ricaut FX, Richards M, Sabin R, Sarti L, Schier W, Sheikhi S, Stephan E, Stewart JR, Stoddart S, Tagliacozzo A, Tasić N, Trantalidou K, Tresset A, Valdiosera C, van den Hurk Y, Van Poucke S, Vigne JD, Yanevich A, Zeeb-Lanz A, Triantafyllidis A, Gilbert MTP, Schibler J, Rowley-Conwy P, Zeder M, Peters J, Cucchi T, Bradley DG, Dobney K, Burger J, Evin A, Girdland-Flink L, Larson G. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.. Proc Natl Acad Sci U S A 2019 Aug 27;116(35):17231-17238.
    pubmed: 31405970doi: 10.1073/pnas.1901169116pmc: 6717267google scholar: lookup
  44. Colledge S., Conolly J., Dobney K., Manning K., Shennan S.. Origins and Spread of Domestic Animals in Southwest Asia and Europe. Left Coast, 2013.
  45. Frantz L, Meijaard E, Gongora J, Haile J, Groenen MA, Larson G. The Evolution of Suidae.. Annu Rev Anim Biosci 2016;4:61-85.
  46. Helmer, D., Gourichon, L., Monchot, H., Peters, J. & Segui, M. S. in The First Steps of Animal Domestication (eds D. Vigne, J., Peters, J. & Helmer, D.). 86–95 (Oxbow Books, 2005).
  47. Hongo H., Pearson J., Öksüz B., Ilgezdi G.. The process of ungulate domestication at Cayönü, Southeastern Turkey: a multidisciplinary approach focusing on Bos sp. and Cervus elaphus. Anthropozoologica 44, 63–78 (2009).
    doi: 10.5252/az2009n1a3google scholar: lookup
  48. Perri A.. A wolf in dog’s clothing: initial dog domestication and Pleistocene wolf variation. J. Archaeol. Sci. 68, 1–4 (2016).
    doi: 10.1016/j.jas.2016.02.003google scholar: lookup
  49. Drake AG, Coquerelle M, Colombeau G. 3D morphometric analysis of fossil canid skulls contradicts the suggested domestication of dogs during the late Paleolithic.. Sci Rep 2015 Feb 5;5:8299.
    pubmed: 25654325pmc: 5389137doi: 10.1038/srep08299google scholar: lookup
  50. 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
  51. Frantz LA, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, Larson G. Genomic and archaeological evidence suggest a dual origin of domestic dogs.. Science 2016 Jun 3;352(6290):1228-31.
    pubmed: 27257259doi: 10.1126/science.aaf3161google scholar: lookup
  52. Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J. Genome sequencing highlights the dynamic early history of dogs.. PLoS Genet 2014 Jan;10(1):e1004016.
    pubmed: 24453982pmc: 3894170doi: 10.1371/journal.pgen.1004016google scholar: lookup
  53. Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, Hanks BK, Li S, Lomitashvili D, Ochir-Goryaeva M, Sizonov GV, Soyonov V, Manica A. Reconstructing the origin and spread of horse domestication in the Eurasian steppe.. Proc Natl Acad Sci U S A 2012 May 22;109(21):8202-6.
    pubmed: 22566639doi: 10.1073/pnas.1111122109pmc: 3361400google scholar: lookup
  54. The Bovine Genome Sequencing and Analysis Consortium et al.. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522–528 (2009).
    pmc: 2943200doi: 10.1126/science.1169588google scholar: lookup
  55. 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, Monchalov 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. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.. Cell 2019 May 30;177(6):1419-1435.e31.
    pubmed: 31056281pmc: 6547883doi: 10.1016/j.cell.2019.03.049google scholar: lookup
  56. 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
  57. Botigué LR, Song S, Scheu A, Gopalan S, Pendleton AL, Oetjens M, Taravella AM, Seregély T, Zeeb-Lanz A, Arbogast RM, Bobo D, Daly K, Unterländer M, Burger J, Kidd JM, Veeramah KR. Ancient European dog genomes reveal continuity since the Early Neolithic.. Nat Commun 2017 Jul 18;8:16082.
    pubmed: 28719574pmc: 5520058doi: 10.1038/ncomms16082google scholar: lookup
  58. Ní Leathlobhair M, Perri AR, Irving-Pease EK, Witt KE, Linderholm A, Haile J, Lebrasseur O, Ameen C, Blick J, Boyko AR, Brace S, Cortes YN, Crockford SJ, Devault A, Dimopoulos EA, Eldridge M, Enk J, Gopalakrishnan S, Gori K, Grimes V, Guiry E, Hansen AJ, Hulme-Beaman A, Johnson J, Kitchen A, Kasparov AK, Kwon YM, Nikolskiy PA, Lope CP, Manin A, Martin T, Meyer M, Myers KN, Omura M, Rouillard JM, Pavlova EY, Sciulli P, Sinding MS, Strakova A, Ivanova VV, Widga C, Willerslev E, Pitulko VV, Barnes I, Gilbert MTP, Dobney KM, Malhi RS, Murchison EP, Larson G, Frantz LAF. The evolutionary history of dogs in the Americas.. Science 2018 Jul 6;361(6397):81-85.
    pubmed: 29976825doi: 10.1126/science.aao4776google scholar: lookup
  59. Leonard JA, Wayne RK, Wheeler J, Valadez R, Guillén S, Vilà C. Ancient DNA evidence for Old World origin of New World dogs.. Science 2002 Nov 22;298(5598):1613-6.
    pubmed: 12446908doi: 10.1126/science.1076980google scholar: lookup
  60. Frantz, L. A. F. & Larson, G. in Hybrid Communities (eds Stépanoff, C. & Vigne, J.-D.) 23–37 (Routledge, 2018).
  61. Larson G, Burger J. A population genetics view of animal domestication.. Trends Genet 2013 Apr;29(4):197-205.
    pubmed: 23415592doi: 10.1016/j.tig.2013.01.003google scholar: lookup
  62. Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.. Genome Biol 2015 Oct 26;16:234.
    pubmed: 26498365pmc: 4620651doi: 10.1186/s13059-015-0790-2google scholar: lookup
  63. Frantz LA, Schraiber JG, Madsen O, Megens HJ, Cagan A, Bosse M, Paudel Y, Crooijmans RP, Larson G, Groenen MA. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.. Nat Genet 2015 Oct;47(10):1141-8.
    pubmed: 26323058doi: 10.1038/ng.3394google scholar: lookup
  64. Skoglund P, Ersmark E, Palkopoulou E, Dalén L. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds.. Curr Biol 2015 Jun 1;25(11):1515-9.
    pubmed: 26004765doi: 10.1016/j.cub.2015.04.019google scholar: lookup
  65. Marshall FB, Dobney K, Denham T, Capriles JM. Evaluating the roles of directed breeding and gene flow in animal domestication.. Proc Natl Acad Sci U S A 2014 Apr 29;111(17):6153-8.
    pubmed: 24753599doi: 10.1073/pnas.1312984110pmc: 4035985google scholar: lookup
  66. 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.
    pubmed: 25512547pmc: 4284583doi: 10.1073/pnas.1416991111google scholar: lookup
  67. Turner TL, Hahn MW, Nuzhdin SV. Genomic islands of speciation in Anopheles gambiae.. PLoS Biol 2005 Sep;3(9):e285.
    pubmed: 16076241pmc: 1182689doi: 10.1371/journal.pbio.0030285google scholar: lookup
  68. Briggs WH, McMullen MD, Gaut BS, Doebley J. Linkage mapping of domestication loci in a large maize teosinte backcross resource.. Genetics 2007 Nov;177(3):1915-28.
    pubmed: 17947434pmc: 2147989doi: 10.1534/genetics.107.076497google scholar: lookup
  69. Trut L.. Early canid domestication: the Farm-Fox Experiment Foxes bred for tamability in a 40-year experiment exhibit remarkable transformations that suggest an interplay between behavioral genetics and development. Am. Sci. 87, 160–169 (1999).
    doi: 10.1511/1999.2.160google scholar: lookup
  70. Lord KA, Larson G, Coppinger RP, Karlsson EK. The History of Farm Foxes Undermines the Animal Domestication Syndrome.. Trends Ecol Evol 2020 Feb;35(2):125-136.
    pubmed: 31810775doi: 10.1016/j.tree.2019.10.011google scholar: lookup
  71. 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
  72. Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication.. BMC Biol 2018 Jun 28;16(1):64.
    pubmed: 29950181pmc: 6022502doi: 10.1186/s12915-018-0535-2google scholar: lookup
  73. Marsden CD, Ortega-Del Vecchyo D, O'Brien DP, Taylor JF, Ramirez O, Vilà C, Marques-Bonet T, Schnabel RD, Wayne RK, Lohmueller KE. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.. Proc Natl Acad Sci U S A 2016 Jan 5;113(1):152-7.
    pubmed: 26699508doi: 10.1073/pnas.1512501113google scholar: lookup
  74. MacLeod IM, Larkin DM, Lewin HA, Hayes BJ, Goddard ME. Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors.. Mol Biol Evol 2013 Sep;30(9):2209-23.
    pubmed: 23842528pmc: 3748359doi: 10.1093/molbev/mst125google scholar: lookup
  75. Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.. Science 2014 Aug 29;345(6200):1074-1079.
    pubmed: 25170157pmc: 5421586doi: 10.1126/science.1253714google scholar: lookup
  76. Allaby RG, Ware RL, Kistler L. A re-evaluation of the domestication bottleneck from archaeogenomic evidence.. Evol Appl 2019 Jan;12(1):29-37.
    pubmed: 30622633doi: 10.1111/eva.12680google scholar: lookup
  77. Bosse M, Megens HJ, Madsen O, Paudel Y, Frantz LA, Schook LB, Crooijmans RP, Groenen MA. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape.. PLoS Genet 2012;8(11):e1003100.
    pubmed: 23209444pmc: 3510040doi: 10.1371/journal.pgen.1003100google scholar: lookup
  78. Bollongino R, Burger J, Powell A, Mashkour M, Vigne JD, Thomas MG. Modern taurine cattle descended from small number of near-eastern founders.. Mol Biol Evol 2012 Sep;29(9):2101-4.
    pubmed: 22422765doi: 10.1093/molbev/mss092google scholar: lookup
  79. Murray C, Huerta-Sanchez E, Casey F, Bradley DG. Cattle demographic history modelled from autosomal sequence variation.. Philos Trans R Soc Lond B Biol Sci 2010 Aug 27;365(1552):2531-9.
    pubmed: 20643743pmc: 2935105doi: 10.1098/rstb.2010.0103google scholar: lookup
  80. Kristiansen K.. The Rise of Bronze Age Society: Travels, Transmissions and Transformations. Cambridge University Press, 2005.
  81. 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
  82. Damgaard PB, Marchi N, Rasmussen S, Peyrot M, Renaud G, Korneliussen T, Moreno-Mayar JV, Pedersen MW, Goldberg A, Usmanova E, Baimukhanov N, Loman V, Hedeager L, Pedersen AG, Nielsen K, Afanasiev G, Akmatov K, Aldashev A, Alpaslan A, Baimbetov G, Bazaliiskii VI, Beisenov A, Boldbaatar B, Boldgiv B, Dorzhu C, Ellingvag S, Erdenebaatar D, Dajani R, Dmitriev E, Evdokimov V, Frei KM, Gromov A, Goryachev A, Hakonarson H, Hegay T, Khachatryan Z, Khaskhanov R, Kitov E, Kolbina A, Kubatbek T, Kukushkin A, Kukushkin I, Lau N, Margaryan A, Merkyte I, Mertz IV, Mertz VK, Mijiddorj E, Moiyesev V, Mukhtarova G, Nurmukhanbetov B, Orozbekova Z, Panyushkina I, Pieta K, Smrčka V, Shevnina I, Logvin A, Sjögren KG, Štolcová T, Taravella AM, Tashbaeva K, Tkachev A, Tulegenov T, Voyakin D, Yepiskoposyan L, Undrakhbold S, Varfolomeev V, Weber A, Wilson Sayres MA, Kradin N, Allentoft ME, Orlando L, Nielsen R, Sikora M, Heyer E, Kristiansen K, Willerslev E. 137 ancient human genomes from across the Eurasian steppes.. Nature 2018 May;557(7705):369-374.
    pubmed: 29743675doi: 10.1038/s41586-018-0094-2google scholar: lookup
  83. Jeong C, Wilkin S, Amgalantugs T, Bouwman AS, Taylor WTT, Hagan RW, Bromage S, Tsolmon S, Trachsel C, Grossmann J, Littleton J, Makarewicz CA, Krigbaum J, Burri M, Scott A, Davaasambuu G, Wright J, Irmer F, Myagmar E, Boivin N, Robbeets M, Rühli FJ, Krause J, Frohlich B, Hendy J, Warinner C. Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe.. Proc Natl Acad Sci U S A 2018 Nov 27;115(48):E11248-E11255.
    pubmed: 30397125doi: 10.1073/pnas.1813608115pmc: 6275519google scholar: lookup
  84. Hansen PJ. Physiological and cellular adaptations of zebu cattle to thermal stress.. Anim Reprod Sci 2004 Jul;82-83:349-60.
  85. Matthews R.. Zebu: harbingers of doom in Bronze Age western Asia?. Antiquity 76, 438–446 (2002).
    doi: 10.1017/S0003598X00090542google scholar: lookup
  86. Ollivier M, Tresset A, Frantz LAF, Bréhard S, Bălăşescu A, Mashkour M, Boroneanţ A, Pionnier-Capitan M, Lebrasseur O, Arbogast RM, Bartosiewicz L, Debue K, Rabinovich R, Sablin MV, Larson G, Hänni C, Hitte C, Vigne JD. Dogs accompanied humans during the Neolithic expansion into Europe.. Biol Lett 2018 Oct 17;14(10).
    pubmed: 30333260pmc: 6227856doi: 10.1098/rsbl.2018.0286google scholar: lookup
  87. Ottoni C, Flink LG, Evin A, Geörg C, De Cupere B, Van Neer W, Bartosiewicz L, Linderholm A, Barnett R, Peters J, Decorte R, Waelkens M, Vanderheyden N, Ricaut FX, Cakirlar C, Cevik O, Hoelzel AR, Mashkour M, Karimlu AF, Seno SS, Daujat J, Brock F, Pinhasi R, Hongo H, Perez-Enciso M, Rasmussen M, Frantz L, Megens HJ, Crooijmans R, Groenen M, Arbuckle B, Benecke N, Vidarsdottir US, Burger J, Cucchi T, Dobney K, Larson G. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.. Mol Biol Evol 2013 Apr;30(4):824-32.
    pubmed: 23180578doi: 10.1093/molbev/mss261google scholar: lookup
  88. Ameen C.. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic. Proc. R. Soc. B Biol. Sci. 286, 20191929 (2019).
  89. White S.. From globalized pig breeds to capitalist pigs: a study in animal cultures and evolutionary history. Environ. Hist. Durh. N. C. 16, 94–120 (2011).
    doi: 10.1093/envhis/emq143google scholar: lookup
  90. Bosse M, Megens HJ, Frantz LA, Madsen O, Larson G, Paudel Y, Duijvesteijn N, Harlizius B, Hagemeijer Y, Crooijmans RP, Groenen MA. Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression.. Nat Commun 2014 Jul 15;5:4392.
    pubmed: 25025832doi: 10.1038/ncomms5392google scholar: lookup
  91. Bosse M, Lopes MS, Madsen O, Megens HJ, Crooijmans RP, Frantz LA, Harlizius B, Bastiaansen JW, Groenen MA. Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs.. Proc Biol Sci 2015 Dec 22;282(1821):20152019.
    pubmed: 26702043pmc: 4707752doi: 10.1098/rspb.2015.2019google scholar: lookup
  92. Shearin AL, Ostrander EA. Canine morphology: hunting for genes and tracking mutations.. PLoS Biol 2010 Mar 2;8(3):e1000310.
    pubmed: 20209140pmc: 2830451doi: 10.1371/journal.pbio.1000310google scholar: lookup
  93. Boyko AR. The domestic dog: man's best friend in the genomic era.. Genome Biol 2011;12(2):216.
    pubmed: 21338479pmc: 3188790doi: 10.1186/gb-2011-12-2-216google scholar: lookup
  94. Bosse M, Megens HJ, Madsen O, Frantz LA, Paudel Y, Crooijmans RP, Groenen MA. Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations.. Mol Ecol 2014 Aug;23(16):4089-102.
    pubmed: 24863459pmc: 4225523doi: 10.1111/mec.12807google scholar: lookup
  95. Orlando L, Librado P. Origin and Evolution of Deleterious Mutations in Horses.. Genes (Basel) 2019 Aug 28;10(9).
    pubmed: 31466279doi: 10.3390/genes10090649google scholar: lookup
  96. Oltenacu PA, Algers B. Selection for increased production and the welfare of dairy cows: are new breeding goals needed?. Ambio 2005 Jun;34(4-5):311-5.
    pubmed: 16092261doi: 10.1579/0044-7447-34.4.311google scholar: lookup
  97. Charlier C, Li W, Harland C, Littlejohn M, Coppieters W, Creagh F, Davis S, Druet T, Faux P, Guillaume F, Karim L, Keehan M, Kadri NK, Tamma N, Spelman R, Georges M. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock.. Genome Res 2016 Oct;26(10):1333-1341.
    pubmed: 27646536pmc: 5052051doi: 10.1101/gr.207076.116google scholar: lookup
  98. Derks MFL, Gjuvsland AB, Bosse M, Lopes MS, van Son M, Harlizius B, Tan BF, Hamland H, Grindflek E, Groenen MAM, Megens HJ. Loss of function mutations in essential genes cause embryonic lethality in pigs.. PLoS Genet 2019 Mar;15(3):e1008055.
    pubmed: 30875370pmc: 6436757doi: 10.1371/journal.pgen.1008055google scholar: lookup
  99. Ellegren H. The different levels of genetic diversity in sex chromosomes and autosomes.. Trends Genet 2009 Jun;25(6):278-84.
    pubmed: 19481288doi: 10.1016/j.tig.2009.04.005google scholar: lookup
  100. Peters, J., Arbuckle, B. S. & Pöllath, N. in The Neolithic in Turkey Vol. 6 (eds Özdogan, M., Baflgelen, N. & Kuniholm, P.). 1–65 (Archaeology and Art, 2012).
  101. 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
  102. Girdland Flink L, Allen R, Barnett R, Malmström H, Peters J, Eriksson J, Andersson L, Dobney K, Larson G. Establishing the validity of domestication genes using DNA from ancient chickens.. Proc Natl Acad Sci U S A 2014 Apr 29;111(17):6184-9.
    pubmed: 24753608doi: 10.1073/pnas.1308939110pmc: 4035994google scholar: lookup
  103. Loog L, Thomas MG, Barnett R, Allen R, Sykes N, Paxinos PD, Lebrasseur O, Dobney K, Peters J, Manica A, Larson G, Eriksson A. Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.. Mol Biol Evol 2017 Aug 1;34(8):1981-1990.
    pubmed: 28444234pmc: 5850110doi: 10.1093/molbev/msx142google scholar: lookup
  104. Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castaños P, Cieslak M, Lippold S, Llorente L, Malaspinas AS, Slatkin M, Hofreiter M. Coat color variation at the beginning of horse domestication.. Science 2009 Apr 24;324(5926):485.
    pubmed: 19390039pmc: 5102060doi: 10.1126/science.1172750google scholar: lookup
  105. Linderholm A, Larson G. The role of humans in facilitating and sustaining coat colour variation in domestic animals.. Semin Cell Dev Biol 2013 Jun-Jul;24(6-7):587-93.
    pubmed: 23567209doi: 10.1016/j.semcdb.2013.03.015google scholar: lookup
  106. Pavlidis P, Jensen JD, Stephan W. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations.. Genetics 2010 Jul;185(3):907-22.
    pubmed: 20407129pmc: 2907208doi: 10.1534/genetics.110.116459google scholar: lookup
  107. Schraiber JG, Evans SN, Slatkin M. Bayesian Inference of Natural Selection from Allele Frequency Time Series.. Genetics 2016 May;203(1):493-511.
    pubmed: 27010022pmc: 4858794doi: 10.1534/genetics.116.187278google scholar: lookup
  108. Malaspinas AS. Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective.. Mol Ecol 2016 Jan;25(1):24-41.
    pubmed: 26613371doi: 10.1111/mec.13492google scholar: lookup
  109. Barrios-Garcia M. N., Ballari S. A.. Impact of wild boar (Sus scrofa) in its introduced and native range: a review. Biol. Invasions 14, 2283–2300 (2012).
    doi: 10.1007/s10530-012-0229-6google scholar: lookup
  110. Boyd J. M., Doney J. M., Gunn R. G., Jewell P. A.. The Soay sheep of the island of Hirta, St. Kilda. A study of a feral population. Proc. Zool. Soc. London 142, 129–164 (1964).
  111. Ariefiandy A.. Temporal and spatial dynamics of insular Rusa deer and wild pig populations in Komodo National Park. J. Mammal. 97, 1652–1662 (2016).
    doi: 10.1093/jmammal/gyw131google scholar: lookup
  112. Vigne JD, Zazzo A, Saliège JF, Poplin F, Guilaine J, Simmons A. Pre-Neolithic wild boar management and introduction to Cyprus more than 11,400 years ago.. Proc Natl Acad Sci U S A 2009 Sep 22;106(38):16135-8.
    pubmed: 19706455doi: 10.1073/pnas.0905015106pmc: 2752532google scholar: lookup
  113. Heinsohn T.. Animal translocation: long-term human influences on the vertebrate zoogeography of Australasia (natural dispersal versus ethnophoresy). Aust. Zool. 32, 351–376 (2003).
    doi: 10.7882/AZ.2002.014google scholar: lookup
  114. Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P. Are cattle, sheep, and goats endangered species?. Mol Ecol 2008 Jan;17(1):275-84.
  115. Taberlet P, Coissac E, Pansu J, Pompanon F. Conservation genetics of cattle, sheep, and goats.. C R Biol 2011 Mar;334(3):247-54.
    pubmed: 21377620doi: 10.1016/j.crvi.2010.12.007google scholar: lookup
  116. Heckenberger MJ, Russell JC, Toney JR, Schmidt MJ. The legacy of cultural landscapes in the Brazilian Amazon: implications for biodiversity.. Philos Trans R Soc Lond B Biol Sci 2007 Feb 28;362(1478):197-208.
    pubmed: 17255029pmc: 2311456doi: 10.1098/rstb.2006.1979google scholar: lookup
  117. Ellis EC, Kaplan JO, Fuller DQ, Vavrus S, Klein Goldewijk K, Verburg PH. Used planet: a global history.. Proc Natl Acad Sci U S A 2013 May 14;110(20):7978-85.
    pubmed: 23630271doi: 10.1073/pnas.1217241110pmc: 3657770google scholar: lookup
  118. Piperno D. R., McMichael C., Bush M. B.. Amazonia and the Anthropocene: what was the spatial extent and intensity of human landscape modification in the Amazon basin at the end of prehistory?. Holocene 25, 1588–1597 (2015).
    doi: 10.1177/0959683615588374google scholar: lookup
  119. Plug I.. Aspects of life in the Kruger National Park during the early iron age. Goodwin Series 6, 62–68 (1989).
    doi: 10.2307/3858133google scholar: lookup
  120. Spyrou MA, Bos KI, Herbig A, Krause J. Ancient pathogen genomics as an emerging tool for infectious disease research.. Nat Rev Genet 2019 Jun;20(6):323-340.
    pubmed: 30953039pmc: 7097038doi: 10.1038/s41576-019-0119-1google scholar: lookup
  121. Roman-Binois A.. L’archéologie des épizooties: mise en évidence et diagnostic des crises de mortalité chez les animaux d’élevage, du Néolithique à Pasteur. Université Panthéon-Sorbonne-Paris I, 2017.
  122. Boodhoo N, Gurung A, Sharif S, Behboudi S. Marek's disease in chickens: a review with focus on immunology.. Vet Res 2016 Nov 28;47(1):119.
    pubmed: 27894330pmc: 5127044doi: 10.1186/s13567-016-0404-3google scholar: lookup
  123. Witter R. L.. The changing landscape of Marek’s disease. Avian Pathol. 27, S46–S53 (1998).
    doi: 10.1080/03079459808419292google scholar: lookup
  124. Bellone RR, Holl H, Setaluri V, Devi S, Maddodi N, Archer S, Sandmeyer L, Ludwig A, Foerster D, Pruvost M, Reissmann M, Bortfeldt R, Adelson DL, Lim SL, Nelson J, Haase B, Engensteiner M, Leeb T, Forsyth G, Mienaltowski MJ, Mahadevan P, Hofreiter M, Paijmans JL, Gonzalez-Fortes G, Grahn B, Brooks SA. Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse.. PLoS One 2013;8(10):e78280.
    pubmed: 24167615pmc: 3805535doi: 10.1371/journal.pone.0078280google scholar: lookup
  125. FAO. Domestic animal diversity information system. DAD-IS http://dad.fao.org/ (2017).
  126. Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z, Amin N, Buchkovich ML, Croteau-Chonka DC, Day FR, Duan Y, Fall T, Fehrmann R, Ferreira T, Jackson AU, Karjalainen J, Lo KS, Locke AE, Mägi R, Mihailov E, Porcu E, Randall JC, Scherag A, Vinkhuyzen AA, Westra HJ, Winkler TW, Workalemahu T, Zhao JH, Absher D, Albrecht E, Anderson D, Baron J, Beekman M, Demirkan A, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Fraser RM, Goel A, Gong J, Justice AE, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Lui JC, Mangino M, Mateo Leach I, Medina-Gomez C, Nalls MA, Nyholt DR, Palmer CD, Pasko D, Pechlivanis S, Prokopenko I, Ried JS, Ripke S, Shungin D, Stancáková A, Strawbridge RJ, Sung YJ, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Afzal U, Arnlöv J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Blüher M, Bolton JL, Böttcher Y, Boyd HA, Bruinenberg M, Buckley BM, Buyske S, Caspersen IH, Chines PS, Clarke R, Claudi-Boehm S, Cooper M, Daw EW, De Jong PA, Deelen J, Delgado G, Denny JC, Dhonukshe-Rutten R, Dimitriou M, Doney AS, Dörr M, Eklund N, Eury E, Folkersen L, Garcia ME, Geller F, Giedraitis V, Go AS, Grallert H, Grammer TB, Gräßler J, Grönberg H, de Groot LC, Groves CJ, Haessler J, Hall P, Haller T, Hallmans G, Hannemann A, Hartman CA, Hassinen M, Hayward C, Heard-Costa NL, Helmer Q, Hemani G, Henders AK, Hillege HL, Hlatky MA, Hoffmann W, Hoffmann P, Holmen O, Houwing-Duistermaat JJ, Illig T, Isaacs A, James AL, Jeff J, Johansen B, Johansson Å, Jolley J, Juliusdottir T, Junttila J, Kho AN, Kinnunen L, Klopp N, Kocher T, Kratzer W, Lichtner P, Lind L, Lindström J, Lobbens S, Lorentzon M, Lu Y, Lyssenko V, Magnusson PK, Mahajan A, Maillard M, McArdle WL, McKenzie CA, McLachlan S, McLaren PJ, Menni C, Merger S, Milani L, Moayyeri A, Monda KL, Morken MA, Müller G, Müller-Nurasyid M, Musk AW, Narisu N, Nauck M, Nolte IM, Nöthen MM, Oozageer L, Pilz S, Rayner NW, Renstrom F, Robertson NR, Rose LM, Roussel R, Sanna S, Scharnagl H, Scholtens S, Schumacher FR, Schunkert H, Scott RA, Sehmi J, Seufferlein T, Shi J, Silventoinen K, Smit JH, Smith AV, Smolonska J, Stanton AV, Stirrups K, Stott DJ, Stringham HM, Sundström J, Swertz MA, Syvänen AC, Tayo BO, Thorleifsson G, Tyrer JP, van Dijk S, van Schoor NM, van der Velde N, van Heemst D, van Oort FV, Vermeulen SH, Verweij N, Vonk JM, Waite LL, Waldenberger M, Wennauer R, Wilkens LR, Willenborg C, Wilsgaard T, Wojczynski MK, Wong A, Wright AF, Zhang Q, Arveiler D, Bakker SJ, Beilby J, Bergman RN, Bergmann S, Biffar R, Blangero J, Boomsma DI, Bornstein SR, Bovet P, Brambilla P, Brown MJ, Campbell H, Caulfield MJ, Chakravarti A, Collins R, Collins FS, Crawford DC, Cupples LA, Danesh J, de Faire U, den Ruijter HM, Erbel R, Erdmann J, Eriksson JG, Farrall M, Ferrannini E, Ferrières J, Ford I, Forouhi NG, Forrester T, Gansevoort RT, Gejman PV, Gieger C, Golay A, Gottesman O, Gudnason V, Gyllensten U, Haas DW, Hall AS, Harris TB, Hattersley AT, Heath AC, Hengstenberg C, Hicks AA, Hindorff LA, Hingorani AD, Hofman A, Hovingh GK, Humphries SE, Hunt SC, Hypponen E, Jacobs KB, Jarvelin MR, Jousilahti P, Jula AM, Kaprio J, Kastelein JJ, Kayser M, Kee F, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kooner JS, Kooperberg C, Koskinen S, Kovacs P, Kraja AT, Kumari M, Kuusisto J, Lakka TA, Langenberg C, Le Marchand L, Lehtimäki T, Lupoli S, Madden PA, Männistö S, Manunta P, Marette A, Matise TC, McKnight B, Meitinger T, Moll FL, Montgomery GW, Morris AD, Morris AP, Murray JC, Nelis M, Ohlsson C, Oldehinkel AJ, Ong KK, Ouwehand WH, Pasterkamp G, Peters A, Pramstaller PP, Price JF, Qi L, Raitakari OT, Rankinen T, Rao DC, Rice TK, Ritchie M, Rudan I, Salomaa V, Samani NJ, Saramies J, Sarzynski MA, Schwarz PE, Sebert S, Sever P, Shuldiner AR, Sinisalo J, Steinthorsdottir V, Stolk RP, Tardif JC, Tönjes A, Tremblay A, Tremoli E, Virtamo J, Vohl MC, Amouyel P, Asselbergs FW, Assimes TL, Bochud M, Boehm BO, Boerwinkle E, Bottinger EP, Bouchard C, Cauchi S, Chambers JC, Chanock SJ, Cooper RS, de Bakker PI, Dedoussis G, Ferrucci L, Franks PW, Froguel P, Groop LC, Haiman CA, Hamsten A, Hayes MG, Hui J, Hunter DJ, Hveem K, Jukema JW, Kaplan RC, Kivimaki M, Kuh D, Laakso M, Liu Y, Martin NG, März W, Melbye M, Moebus S, Munroe PB, Njølstad I, Oostra BA, Palmer CN, Pedersen NL, Perola M, Pérusse L, Peters U, Powell JE, Power C, Quertermous T, Rauramaa R, Reinmaa E, Ridker PM, Rivadeneira F, Rotter JI, Saaristo TE, Saleheen D, Schlessinger D, Slagboom PE, Snieder H, Spector TD, Strauch K, Stumvoll M, Tuomilehto J, Uusitupa M, van der Harst P, Völzke H, Walker M, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Zanen P, Deloukas P, Heid IM, Lindgren CM, Mohlke KL, Speliotes EK, Thorsteinsdottir U, Barroso I, Fox CS, North KE, Strachan DP, Beckmann JS, Berndt SI, Boehnke M, Borecki IB, McCarthy MI, Metspalu A, Stefansson K, Uitterlinden AG, van Duijn CM, Franke L, Willer CJ, Price AL, Lettre G, Loos RJ, Weedon MN, Ingelsson E, O'Connell JR, Abecasis GR, Chasman DI, Goddard ME, Visscher PM, Hirschhorn JN, Frayling TM. Defining the role of common variation in the genomic and biological architecture of adult human height.. Nat Genet 2014 Nov;46(11):1173-86.
    pubmed: 25282103pmc: 4250049doi: 10.1038/ng.3097google scholar: lookup
  127. Makvandi-Nejad S, Hoffman GE, Allen JJ, Chu E, Gu E, Chandler AM, Loredo AI, Bellone RR, Mezey JG, Brooks SA, Sutter NB. Four loci explain 83% of size variation in the horse.. PLoS One 2012;7(7):e39929.
    pubmed: 22808074pmc: 3394777doi: 10.1371/journal.pone.0039929google scholar: lookup
  128. Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E. Evidence for archaic adaptive introgression in humans.. Nat Rev Genet 2015 Jun;16(6):359-71.
    pubmed: 25963373pmc: 4478293doi: 10.1038/nrg3936google scholar: lookup
  129. Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.. Genome Biol 2015 Mar 25;16(1):57.
    pubmed: 25854118pmc: 4373242doi: 10.1186/s13059-015-0622-4google scholar: lookup
  130. Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM Jr, Collins MJ, Gilbert MT, Rühli F, Cappellini E. Pathogens and host immunity in the ancient human oral cavity.. Nat Genet 2014 Apr;46(4):336-44.
    pubmed: 24562188pmc: 3969750doi: 10.1038/ng.2906google scholar: lookup
  131. Schubert M.. Zonkey: a simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. J. Archaeol. Sci. 78, 147–157 (2017).
    doi: 10.1016/j.jas.2016.12.005google scholar: lookup
  132. Teasdale MD, van Doorn NL, Fiddyment S, Webb CC, O'Connor T, Hofreiter M, Collins MJ, Bradley DG. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130379.
    pubmed: 25487331pmc: 4275887doi: 10.1098/rstb.2013.0379google scholar: lookup
  133. O'Sullivan NJ, Teasdale MD, Mattiangeli V, Maixner F, Pinhasi R, Bradley DG, Zink A. A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing.. Sci Rep 2016 Aug 18;6:31279.
    pubmed: 27537861pmc: 4989873doi: 10.1038/srep31279google scholar: lookup
  134. Bro-Jørgensen M. H.. Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull. J. Archaeol. Sci. 99, 47–54 (2018).
    doi: 10.1016/j.jas.2018.09.001google scholar: lookup
  135. Zeder, M. A. in Harlan II: Biodiversity in Agriculture: Domestication, Evolution and Sustainability (eds Damania, A. & Gepts, P.) 227–229 (Univ. California, 2011).
  136. Hanotte O, Bradley DG, Ochieng JW, Verjee Y, Hill EW, Rege JE. African pastoralism: genetic imprints of origins and migrations.. Science 2002 Apr 12;296(5566):336-9.
    pubmed: 11951043doi: 10.1126/science.1069878google scholar: lookup
  137. Freeman AR, Bradley DG, Nagda S, Gibson JP, Hanotte O. Combination of multiple microsatellite data sets to investigate genetic diversity and admixture of domestic cattle.. Anim Genet 2006 Feb;37(1):1-9.
  138. Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S, Hallböök F, Besnier F, Carlborg O, Bed'hom B, Tixier-Boichard M, Jensen P, Siegel P, Lindblad-Toh K, Andersson L. Whole-genome resequencing reveals loci under selection during chicken domestication.. Nature 2010 Mar 25;464(7288):587-91.
    pubmed: 20220755doi: 10.1038/nature08832google scholar: lookup
  139. Karlsson AC, Svemer F, Eriksson J, Darras VM, Andersson L, Jensen P. The Effect of a Mutation in the Thyroid Stimulating Hormone Receptor (TSHR) on Development, Behaviour and TH Levels in Domesticated Chickens.. PLoS One 2015;10(6):e0129040.
    pubmed: 26053744pmc: 4460094doi: 10.1371/journal.pone.0129040google scholar: lookup
  140. Fang M, Larson G, Ribeiro HS, Li N, Andersson L. Contrasting mode of evolution at a coat color locus in wild and domestic pigs.. PLoS Genet 2009 Jan;5(1):e1000341.
    pubmed: 19148282pmc: 2613536doi: 10.1371/journal.pgen.1000341google scholar: lookup
  141. Andersson LS, Larhammar M, Memic F, Wootz H, Schwochow D, Rubin CJ, Patra K, Arnason T, Wellbring L, Hjälm G, Imsland F, Petersen JL, McCue ME, Mickelson JR, Cothran G, Ahituv N, Roepstorff L, Mikko S, Vallstedt A, Lindgren G, Andersson L, Kullander K. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice.. Nature 2012 Aug 30;488(7413):642-6.
    pubmed: 22932389pmc: 3523687doi: 10.1038/nature11399google scholar: lookup
  142. Wutke S, Andersson L, Benecke N, Sandoval-Castellanos E, Gonzalez J, Hallsson JH, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M, Muñoz-Rodríguez MB, Ruttkay M, Trinks A, Hofreiter M, Ludwig A. The origin of ambling horses.. Curr Biol 2016 Aug 8;26(15):R697-R699.
    pubmed: 27505236doi: 10.1016/j.cub.2016.07.001google scholar: lookup
  143. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.. Bioinformatics 2009 Jul 15;25(14):1754-60.
    pubmed: 19451168pmc: 2705234doi: 10.1093/bioinformatics/btp324google scholar: lookup
  144. Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L. Improving ancient DNA read mapping against modern reference genomes.. BMC Genomics 2012 May 10;13:178.
    pubmed: 22574660pmc: 3468387doi: 10.1186/1471-2164-13-178google scholar: lookup
  145. Rajaraman A, Tannier E, Chauve C. FPSAC: fast phylogenetic scaffolding of ancient contigs.. Bioinformatics 2013 Dec 1;29(23):2987-94.
    pubmed: 24068034doi: 10.1093/bioinformatics/btt527google scholar: lookup
  146. Seitz A, Nieselt K. Improving ancient DNA genome assembly.. PeerJ 2017;5:e3126.
    pubmed: 28392981pmc: 5384568doi: 10.7717/peerj.3126google scholar: lookup
  147. 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.
    pubmed: 22960212pmc: 3522152doi: 10.1534/genetics.112.145037google scholar: lookup
  148. Patterson N, Price AL, Reich D. Population structure and eigenanalysis.. PLoS Genet 2006 Dec;2(12):e190.
    pubmed: 17194218pmc: 1713260doi: 10.1371/journal.pgen.0020190google scholar: lookup
  149. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals.. Genome Res 2009 Sep;19(9):1655-64.
    pubmed: 19648217pmc: 2752134doi: 10.1101/gr.094052.109google scholar: lookup
  150. 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.
    pubmed: 21325092pmc: 3144383doi: 10.1093/molbev/msr048google scholar: lookup
  151. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data.. PLoS Genet 2012;8(11):e1002967.
    pubmed: 23166502pmc: 3499260doi: 10.1371/journal.pgen.1002967google scholar: lookup

Citations

This article has been cited 97 times.