Animal domestication in the era of ancient genomics (original) (raw)

• Zeder, M. A. The domestication of animals. J. Anthropol. Res. 68, 161–190 (2012).
  Article Google Scholar
• Vigne, J.-D. The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere. C. R. Biol. 334, 171–181 (2011).
  Article PubMed Google Scholar
• Larson, G. et al. Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc. Natl Acad. Sci. USA 109, 8878–8883 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Darwin, C. The Variation of Animals and Plants Under Domestication (John Murray, 1868).
• McHugo, G. P., Dover, M. J. & MacHugh, D. E. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol. 17, 98 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Conolly, J. et al. 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).
  Article Google Scholar
• Vigne, J.-D. in The Neolithic Demographic Transition and its Consequences (eds Bocquet-Appel, J.-P. & Bar-Yosef, O.) 179–205 (Springer, 2008).
• 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).
  Article Google Scholar
• Payne, S. Kill-off patterns in sheep and goats: the mandibles from Aşvan kale. Anatol. Stud. 23, 281–303 (1973).
  Article Google Scholar
• Balasse, M. et al. 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).
  Article Google Scholar
• 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).
  Google Scholar
• Olsen, S. L. Early horse domestication: weighing the evidence. BAR. Int. Ser. 1560, 81 (2006).
  Google Scholar
• Larson, G. et al. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618–1621 (2005).
  Article CAS PubMed Google Scholar
• Luikart, G. et al. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl Acad. Sci. USA 98, 5927–5932 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Naderi, S. et al. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc. Natl Acad. Sci. USA 105, 17659–17664 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Pedrosa, S. et al. Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events. Proc. Biol. Sci. 272, 2211–2217 (2005).
  PubMed PubMed Central Google Scholar
• Vilà, C. et al. Widespread origins of domestic horse lineages. Science 291, 474–477 (2001).
  Article PubMed Google Scholar
• Eriksson, J. et al. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet. 4, e1000010 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Wright, D. Article commentary: the genetic architecture of domestication in animals. Bioinform. Biol. Insights 9S4, BBI.S28902 (2015).
  Article Google Scholar
• Shannon, L. M. et al. Genetic structure in village dogs reveals a Central Asian domestication origin. Proc. Natl Acad. Sci. USA 112, 13639–13644 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, G.-D. et al. Out of southern East Asia: the natural history of domestic dogs across the world. Cell Res. 26, 21–33 (2016).
  Article PubMed Google Scholar
• Pang, J.-F. et al. mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Mol. Biol. Evol. 26, 2849–2864 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Higuchi, R., Bowman, B., Freiberger, M., Ryder, O. A. & Wilson, A. C. DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282–284 (1984).
  Article CAS PubMed Google Scholar
• Pääbo, S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl Acad. Sci. USA 86, 1939–1943 (1989).
  Article PubMed PubMed Central Google Scholar
• Hagelberg, E. et al. Analysis of ancient bone DNA: techniques and applications. Philos. Trans. R. Soc. Lond. B Biol. Sci. 333, 399–407 (1991).
  Article CAS PubMed Google Scholar
• Römpler, H. et al. The rise and fall of the chemoattractant receptor GPR33. J. Biol. Chem. 280, 31068–31075 (2005).
  Article PubMed CAS Google Scholar
• Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M. & Pääbo, S. Ancient DNA. Nat. Rev. Genet. 2, 353–359 (2001).
  Article CAS PubMed Google Scholar
• Gilbert, M. T. P., Bandelt, H.-J., Hofreiter, M. & Barnes, I. Assessing ancient DNA studies. Trends Ecol. Evol. 20, 541–544 (2005).
  Article PubMed Google Scholar
• Goodwin, S., McPherson, J. D. & McCombie, W. R. Coming of age: ten years of next-generation sequencing technologies. Nat. Rev. Genet. 17, 333–351 (2016).
  Article CAS PubMed Google Scholar
• Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Orlando, L., Gilbert, M. T. P. & Willerslev, E. Reconstructing ancient genomes and epigenomes. Nat. Rev. Genet. 16, 395–408 (2015). This paper presents a comprehensive review of the techniques for extraction and sequencing of ancient DNA.
  Article CAS PubMed Google Scholar
• Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Albrechtsen, A., Nielsen, F. C. & Nielsen, R. Ascertainment biases in SNP chips affect measures of population divergence. Mol. Biol. Evol. 27, 2534–2547 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Boessenkool, S. et al. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol. Ecol. Resour. 17, 742–751 (2017).
  Article CAS PubMed Google Scholar
• Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).
  Article PubMed CAS Google Scholar
• Gansauge, M.-T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, e79 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).
  Article PubMed CAS Google Scholar
• 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. 370, 20130624 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Gamba, C. et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5, 5257 (2014). This paper identifies the petrous temporal bone as the best reservoir of preserved ancient DNA in human remains — a finding that extends to archaeological specimens of domesticated animals and that enables the frequent recovery of whole-genome sequences using shotgun sequencing.
  Article CAS PubMed Google Scholar
• Verdugo, M. P. et al. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science 365, 173–176 (2019). This paper presents genome data from ancient Near Eastern cattle and aurochs showing introgression of local aurochs into both early European and Levantine cattle populations. A major shift in genomes occurred ~4,000 years ago, with widespread introgression of zebu ancestry from the East, possibly linked to multi-century drought.
  Article CAS PubMed Google Scholar
• Daly, K. G. et al. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science 361, 85–88 (2018). This study is the first genome-wide investigation of ancient variation in a Fertile Crescent domesticate, the goat, and clearly shows the mosaic nature of domestication via Neolithic Iranian, Anatolian and Levantine goat populations and their asymmetrical relationships to pre-domestication wild genomes. The study also shows 8,000-year-old evidence for selection of genes linked to pigmentation and other traits.
  Article CAS PubMed Google Scholar
• Frantz, L. A. F. et al. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. Proc. Natl Acad. Sci. USA 116, 17231–17238 (2019). This paper reveals that the Near Eastern ancestry in the genomes of European domestic pigs, which is associated with the first domestic pigs that were introduced into Europe around 8,000 years ago from the Near East, almost entirely disappeared over 3,000 years ago as a result of interbreeding with local wild boars.
  Article CAS PubMed PubMed Central Google Scholar
• Colledge, S., Conolly, J., Dobney, K., Manning, K. & Shennan, S. Origins and Spread of Domestic Animals in Southwest Asia and Europe (Left Coast, 2013).
• Frantz, L. et al. The evolution of Suidae. Annu. Rev. Anim. Biosci. 4, 61–85 (2016).
  Article PubMed Google Scholar
• 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).
• 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).
  Article Google Scholar
• Perri, A. A wolf in dog’s clothing: initial dog domestication and Pleistocene wolf variation. J. Archaeol. Sci. 68, 1–4 (2016).
  Article Google Scholar
• Drake, A. G., Coquerelle, M. & Colombeau, G. 3D morphometric analysis of fossil canid skulls contradicts the suggested domestication of dogs during the late Paleolithic. Sci. Rep. 5, 8299 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Outram, A. K. et al. The earliest horse harnessing and milking. Science 323, 1332–1335 (2009).
  Article CAS PubMed Google Scholar
• Frantz, L. A. F. et al. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 352, 1228–1231 (2016). This paper presents the first analysis of an ancient dog genome. Combined with a comprehensive archaeological survey, the authors argue for a dual origin of domestic dogs.
  Article CAS PubMed Google Scholar
• Freedman, A. H. et al. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet. 10, e1004016 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Warmuth, V. et al. Reconstructing the origin and spread of horse domestication in the Eurasian steppe. Proc. Natl Acad. Sci. USA 109, 8202–8206 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• 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).
  Article PubMed Central CAS Google Scholar
• Fages, A. et al. Tracking five millennia of horse management with extensive ancient genome time series. Cell 177, 1419–1435.e31 (2019). This paper represents a milestone in ancient animal genomics, with the sequencing of over 120 ancient horse genomes. The authors draw multiple key conclusions related to the genetic make-up of modern domestic horses and the fitness cost of modern artificial selection.
  Article CAS PubMed PubMed Central Google Scholar
• Gaunitz, C. et al. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 360, 111–114 (2018). This study uses ancient horse genomes to show that the Botai horses, which are thought to be the first domestic horses, are not related to modern horses but instead form a lineage that is now almost extinct. The sole surviving representative of this lineage is the modern Przewalski’s horse, which was thought to be the last wild horse but is in fact the descendant of an ancient domesticated population.
  Article CAS PubMed Google Scholar
• Botigué, L. R. et al. Ancient European dog genomes reveal continuity since the Early Neolithic. Nat. Commun. 8, 16082 (2017). This paper describes the analysis of two newly sequenced Neolithic dog genomes from Germany, which revealed that there was no population replacement in European dogs during the Neolithic Age as predicted by Frantz et al. ( Science , 2016) , contradicting the hypothesis that dogs were domesticated more than once.
  Article PubMed PubMed Central CAS Google Scholar
• Ní Leathlobhair, M. et al. The evolutionary history of dogs in the Americas. Science 361, 81–85 (2018). This study shows that American dogs are the descendants of dogs that dispersed with humans from Siberia into the Americas. Analyses of these genomes revealed that this ancient population of dogs almost completely disappeared after the arrival of Europeans and that the last remnant of this lineage is the genome of the canine transmissible venereal tumour, a contagious cancer clone.
  Article PubMed CAS Google Scholar
• Leonard, J. A. et al. Ancient DNA evidence for Old World origin of New World dogs. Science 298, 1613–1616 (2002).
  Article CAS PubMed Google Scholar
• Frantz, L. A. F. & Larson, G. in Hybrid Communities (eds Stépanoff, C. & Vigne, J.-D.) 23–37 (Routledge, 2018).
• Larson, G. & Burger, J. A population genetics view of animal domestication. Trends Genet. 29, 197–205 (2013).
  Article CAS PubMed Google Scholar
• Park, S. D. E. et al. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol. 16, 234 (2015). This paper reports the first ancient cattle genome sequence. Analyses of this Mesolithic British auroch nuclear genome show that although there had been almost no trace found of European auroch mtDNA in modern cattle, male-mediated wild introgression had occurred within Europe.
  Article PubMed PubMed Central CAS Google Scholar
• Frantz, L. A. F. et al. Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes. Nat. Genet. 47, 1141–1148 (2015). This paper reveals that extensive gene flow between wild and domestic populations took place during the evolutionary history of pigs and hypothesizes that an ‘island of domestication’ exists in the genome of domestic animals.
  Article CAS PubMed Google Scholar
• 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. 25, 1515–1519 (2015). This paper reports the first genome-wide data retrieved from an ancient canid and shows that there was gene flow between arctic dogs and a now extinct population of Siberian wolf.
  Article CAS PubMed Google Scholar
• Marshall, F. B., Dobney, K., Denham, T. & Capriles, J. M. Evaluating the roles of directed breeding and gene flow in animal domestication. Proc. Natl Acad. Sci. USA 111, 6153–6158 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Schubert, M. et al. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc. Natl Acad. Sci. USA 111, E5661–E5669 (2014).
  CAS PubMed PubMed Central Google Scholar
• Turner, T. L., Hahn, M. W. & Nuzhdin, S. V. Genomic islands of speciation in Anopheles gambiae. PLoS Biol. 3, e285 (2005).
  Article PubMed PubMed Central CAS Google Scholar
• Briggs, W. H., McMullen, M. D., Gaut, B. S. & Doebley, J. Linkage mapping of domestication loci in a large maize–teosinte backcross resource. Genetics 177, 1915–1928 (2007).
  Article PubMed PubMed Central Google Scholar
• 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).
  Article Google Scholar
• Lord, K. A., Larson, G., Coppinger, R. P. & Karlsson, E. K. The history of farm foxes undermines the animal domestication syndrome. Trends Ecol. Evol. 35, 125–136 (2020).
  Article PubMed Google Scholar
• Librado, P. et al. Ancient genomic changes associated with domestication of the horse. Science 356, 442–445 (2017).
  Article CAS PubMed Google Scholar
• Pendleton, A. L. et al. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol. 16, 64 (2018).
  Article PubMed PubMed Central CAS Google Scholar
• Marsden, C. D. et al. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs. Proc. Natl Acad. Sci. USA 113, 152–157 (2016).
  Article CAS PubMed Google Scholar
• MacLeod, I. M., Larkin, D. M., Lewin, H. A., Hayes, B. J. & Goddard, M. E. Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors. Mol. Biol. Evol. 30, 2209–2223 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Carneiro, M. et al. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345, 1074–1079 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Allaby, R. G., Ware, R. L. & Kistler, L. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evol. Appl. 12, 29–37 (2019).
  Article PubMed Google Scholar
• Bosse, M. et al. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet. 8, e1003100 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Bollongino, R. et al. Modern taurine cattle descended from small number of near-eastern founders. Mol. Biol. Evol. 29, 2101–2104 (2012).
  Article CAS PubMed Google Scholar
• Murray, C., Huerta-Sanchez, E., Casey, F. & Bradley, D. G. Cattle demographic history modelled from autosomal sequence variation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365, 2531–2539 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Kristiansen, K. The Rise of Bronze Age Society: Travels, Transmissions and Transformations (Cambridge University Press, 2005).
• Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).
  Article CAS PubMed Google Scholar
• Damgaard, P. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018).
  Article CAS PubMed Google Scholar
• Jeong, C. et al. Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe. Proc. Natl Acad. Sci. USA 115, E11248–E11255 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Hansen, P. J. Physiological and cellular adaptations of zebu cattle to thermal stress. Anim. Reprod. Sci. 82-83, 349–360 (2004).
  Article CAS PubMed Google Scholar
• Matthews, R. Zebu: harbingers of doom in Bronze Age western Asia? Antiquity 76, 438–446 (2002).
  Article Google Scholar
• Ollivier, M. et al. Dogs accompanied humans during the Neolithic expansion into Europe. Biol. Lett. 14, 20180286 (2018).
  Article PubMed PubMed Central Google Scholar
• Ottoni, C. et al. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol. Biol. Evol. 30, 824–832 (2013).
  Article CAS PubMed Google Scholar
• Ameen, C. et al. Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic. Proc. R. Soc. B Biol. Sci. 286, 20191929 (2019).
• 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).
  Article Google Scholar
• Bosse, M. et al. Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nat. Commun. 5, 4392 (2014).
  Article CAS PubMed Google Scholar
• Bosse, M. et al. Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs. Proc. Biol. Sci. 282, 20152019 (2015).
  PubMed PubMed Central Google Scholar
• Shearin, A. L. & Ostrander, E. A. Canine morphology: hunting for genes and tracking mutations. PLoS Biol. 8, e1000310 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Boyko, A. R. The domestic dog: man’s best friend in the genomic era. Genome Biol. 12, 216 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Bosse, M. et al. Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations. Mol. Ecol. 23, 4089–4102 (2014).
  Article PubMed PubMed Central Google Scholar
• Orlando, L. & Librado, P. Origin and evolution of deleterious mutations in horses. Genes 10, E649 (2019).
  Article PubMed CAS Google Scholar
• Oltenacu, P. A. & Algers, B. Selection for increased production and the welfare of dairy cows: are new breeding goals needed? Ambio 34, 311–315 (2005).
  Article PubMed Google Scholar
• Charlier, C. et al. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock. Genome Res. 26, 1333–1341 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Derks, M. F. L. et al. Loss of function mutations in essential genes cause embryonic lethality in pigs. PLoS Genet. 15, e1008055 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Ellegren, H. The different levels of genetic diversity in sex chromosomes and autosomes. Trends Genet. 25, 278–284 (2009).
  Article CAS PubMed Google Scholar
• 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).
• Wallner, B. et al. Y chromosome uncovers the recent oriental origin of modern stallions. Curr. Biol. 27, 2029–2035.e5 (2017).
  Article CAS PubMed Google Scholar
• Girdland Flink, L. et al. Establishing the validity of domestication genes using DNA from ancient chickens. Proc. Natl Acad. Sci. USA 111, 6184–6189 (2014). This study uses ancient DNA to show that mutations that are fixed in modern populations and that were thought to be important during chicken domestication were in fact only the target of recent artificial selection.
  Article PubMed CAS PubMed Central Google Scholar
• Loog, L. et al. Inferring allele frequency trajectories from ancient DNA indicates that selection on a chicken gene coincided with changes in medieval husbandry practices. Mol. Biol. Evol. 34, 1981–1990 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Ludwig, A. et al. Coat color variation at the beginning of horse domestication. Science 324, 485 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Linderholm, A. & Larson, G. The role of humans in facilitating and sustaining coat colour variation in domestic animals. Semin. Cell Dev. Biol. 24, 587–593 (2013).
  Article PubMed Google Scholar
• Pavlidis, P., Jensen, J. D. & Stephan, W. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics 185, 907–922 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Schraiber, J. G., Evans, S. N. & Slatkin, M. Bayesian inference of natural selection from allele frequency time series. Genetics 203, 493–511 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Malaspinas, A.-S. Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. Mol. Ecol. 25, 24–41 (2016).
  Article CAS PubMed Google Scholar
• 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).
  Article Google Scholar
• 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).
  Article Google Scholar
• Ariefiandy, A. et al. Temporal and spatial dynamics of insular Rusa deer and wild pig populations in Komodo National Park. J. Mammal. 97, 1652–1662 (2016).
  Article Google Scholar
• Vigne, J.-D. et al. Pre-Neolithic wild boar management and introduction to Cyprus more than 11,400 years ago. Proc. Natl Acad. Sci. USA 106, 16135–16138 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Heinsohn, T. Animal translocation: long-term human influences on the vertebrate zoogeography of Australasia (natural dispersal versus ethnophoresy). Aust. Zool. 32, 351–376 (2003).
  Article Google Scholar
• Taberlet, P. et al. Are cattle, sheep, and goats endangered species? Mol. Ecol. 17, 275–284 (2008).
  Article CAS PubMed Google Scholar
• Taberlet, P., Coissac, E., Pansu, J. & Pompanon, F. Conservation genetics of cattle, sheep, and goats. C. R. Biol. 334, 247–254 (2011).
  Article PubMed Google Scholar
• Heckenberger, M. J., Russell, J. C., Toney, J. R. & Schmidt, M. J. The legacy of cultural landscapes in the Brazilian Amazon: implications for biodiversity. Philos. Trans. R. Soc. Lond. B Biol. Sci. 362, 197–208 (2007).
  Article PubMed PubMed Central Google Scholar
• Ellis, E. C. et al. Used planet: a global history. Proc. Natl Acad. Sci. USA 110, 7978–7985 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• 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).
  Article Google Scholar
• Plug, I. Aspects of life in the Kruger National Park during the early iron age. Goodwin Series 6, 62–68 (1989).
  Article Google Scholar
• Spyrou, M. A., Bos, K. I., Herbig, A. & Krause, J. Ancient pathogen genomics as an emerging tool for infectious disease research. Nat. Rev. Genet. 20, 323–340 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• 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).
• Boodhoo, N., Gurung, A., Sharif, S. & Behboudi, S. Marek’s disease in chickens: a review with focus on immunology. Vet. Res. 47, 119 (2016).
  Article PubMed PubMed Central CAS Google Scholar
• Witter, R. L. The changing landscape of Marek’s disease. Avian Pathol. 27, S46–S53 (1998).
  Article Google Scholar
• Bellone, R. R. et al. Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse. PLoS One 8, e78280 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• FAO. Domestic animal diversity information system. DAD-IS http://dad.fao.org/ (2017).
• Wood, A. R. et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet. 46, 1173–1186 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Makvandi-Nejad, S. et al. Four loci explain 83% of size variation in the horse. PLoS One 7, e39929 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Racimo, F., Sankararaman, S., Nielsen, R. & Huerta-Sánchez, E. Evidence for archaic adaptive introgression in humans. Nat. Rev. Genet. 16, 359–371 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Andersson, L. et al. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes Project. Genome Biol. 16, 57 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Warinner, C. et al. Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336–344 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Schubert, M. et al. Zonkey: a simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. J. Archaeol. Sci. 78, 147–157 (2017).
  Article Google Scholar
• Teasdale, M. D. et al. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing. Philos. Trans. R. Soc. Lond. B Biol. Sci. 370, 20130379 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• O’Sullivan, N. J. et al. A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing. Sci. Rep. 6, 31279 (2016).
  Article PubMed PubMed Central CAS Google Scholar
• Bro-Jørgensen, M. H. et al. Ancient DNA analysis of Scandinavian medieval drinking horns and the horn of the last aurochs bull. J. Archaeol. Sci. 99, 47–54 (2018).
  Article Google Scholar
• Zeder, M. A. in Harlan II: Biodiversity in Agriculture: Domestication, Evolution and Sustainability (eds Damania, A. & Gepts, P.) 227–229 (Univ. California, 2011).
• Hanotte, O. et al. African pastoralism: genetic imprints of origins and migrations. Science 296, 336–339 (2002).
  Article CAS PubMed Google Scholar
• Freeman, A. R., Bradley, D. G., Nagda, S., Gibson, J. P. & Hanotte, O. Combination of multiple microsatellite data sets to investigate genetic diversity and admixture of domestic cattle. Anim. Genet. 37, 1–9 (2006).
  Article CAS PubMed Google Scholar
• Rubin, C.-J. et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587–591 (2010).
  Article CAS PubMed Google Scholar
• Karlsson, A.-C. et al. The effect of a mutation in the thyroid stimulating hormone receptor (TSHR) on development, behaviour and TH levels in domesticated chickens. PLoS One 10, e0129040 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Fang, M., Larson, G., Ribeiro, H. S., Li, N. & Andersson, L. Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet. 5, e1000341 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Andersson, L. S. et al. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 488, 642–646 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Wutke, S. et al. The origin of ambling horses. Curr. Biol. 26, R697–R699 (2016).
  Article CAS PubMed Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Rajaraman, A., Tannier, E. & Chauve, C. FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinformatics 29, 2987–2994 (2013).
  Article CAS PubMed Google Scholar
• Seitz, A. & Nieselt, K. Improving ancient DNA genome assembly. PeerJ 5, e3126 (2017).
  Article PubMed PubMed Central CAS Google Scholar
• Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
  Article PubMed PubMed Central Google Scholar
• Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
  Article PubMed PubMed Central CAS Google Scholar
• Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
  Article CAS PubMed PubMed Central Google Scholar