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.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
Nature Communications Open Access 18 July 2023
BMC Genomics Open Access 08 June 2023
BMC Genomics Open Access 14 December 2022
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Rent or buy this article
Prices vary by article type
Prices may be subject to local taxes which are calculated during checkout
Zeder, M. A. The domestication of animals. J. Anthropol. Res. 68, 161–190 (2012).
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).
Larson, G. et al. Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc. Natl Acad. Sci. USA 109, 8878–8883 (2012).
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).
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).
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).
Payne, S. Kill-off patterns in sheep and goats: the mandibles from Aşvan kale. Anatol. Stud. 23, 281–303 (1973).
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).
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).
Olsen, S. L. Early horse domestication: weighing the evidence. BAR. Int. Ser. 1560, 81 (2006).
Larson, G. et al. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618–1621 (2005).
Luikart, G. et al. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl Acad. Sci. USA 98, 5927–5932 (2001).
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).
Pedrosa, S. et al. Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events. Proc. Biol. Sci. 272, 2211–2217 (2005).
Vilà, C. et al. Widespread origins of domestic horse lineages. Science 291, 474–477 (2001).
Eriksson, J. et al. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet. 4, e1000010 (2008).
Wright, D. Article commentary: the genetic architecture of domestication in animals. Bioinform. Biol. Insights 9S4, BBI.S28902 (2015).
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).
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).
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).
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).
Pääbo, S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl Acad. Sci. USA 86, 1939–1943 (1989).
Hagelberg, E. et al. Analysis of ancient bone DNA: techniques and applications. Philos. Trans. R. Soc. Lond. B Biol. Sci. 333, 399–407 (1991).
Römpler, H. et al. The rise and fall of the chemoattractant receptor GPR33. J. Biol. Chem. 280, 31068–31075 (2005).
Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M. & Pääbo, S. Ancient DNA. Nat. Rev. Genet. 2, 353–359 (2001).
Gilbert, M. T. P., Bandelt, H.-J., Hofreiter, M. & Barnes, I. Assessing ancient DNA studies. Trends Ecol. Evol. 20, 541–544 (2005).
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).
Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).
Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).
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.
Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).
Albrechtsen, A., Nielsen, F. C. & Nielsen, R. Ascertainment biases in SNP chips affect measures of population divergence. Mol. Biol. Evol. 27, 2534–2547 (2010).
Boessenkool, S. et al. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol. Ecol. Resour. 17, 742–751 (2017).
Gansauge, M.-T. & Meyer, M. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat. Protoc. 8, 737–748 (2013).
Gansauge, M.-T. et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res. 45, e79 (2017).
Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).
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).
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.
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.
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.
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.
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).
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).
Perri, A. A wolf in dog’s clothing: initial dog domestication and Pleistocene wolf variation. J. Archaeol. Sci. 68, 1–4 (2016).
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).
Outram, A. K. et al. The earliest horse harnessing and milking. Science 323, 1332–1335 (2009).
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.
Freedman, A. H. et al. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet. 10, e1004016 (2014).
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).
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).
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.
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.
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.
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.
Leonard, J. A. et al. Ancient DNA evidence for Old World origin of New World dogs. Science 298, 1613–1616 (2002).
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).
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.
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.
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.
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).
Schubert, M. et al. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc. Natl Acad. Sci. USA 111, E5661–E5669 (2014).
Turner, T. L., Hahn, M. W. & Nuzhdin, S. V. Genomic islands of speciation in Anopheles gambiae. PLoS Biol. 3, e285 (2005).
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).
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).
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).
Librado, P. et al. Ancient genomic changes associated with domestication of the horse. Science 356, 442–445 (2017).
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).
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).
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).
Carneiro, M. et al. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345, 1074–1079 (2014).
Allaby, R. G., Ware, R. L. & Kistler, L. A re-evaluation of the domestication bottleneck from archaeogenomic evidence. Evol. Appl. 12, 29–37 (2019).
Bosse, M. et al. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet. 8, e1003100 (2012).
Bollongino, R. et al. Modern taurine cattle descended from small number of near-eastern founders. Mol. Biol. Evol. 29, 2101–2104 (2012).
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).
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).
Damgaard, P. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018).
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).
Hansen, P. J. Physiological and cellular adaptations of zebu cattle to thermal stress. Anim. Reprod. Sci. 82-83, 349–360 (2004).
Matthews, R. Zebu: harbingers of doom in Bronze Age western Asia? Antiquity 76, 438–446 (2002).
Ollivier, M. et al. Dogs accompanied humans during the Neolithic expansion into Europe. Biol. Lett. 14, 20180286 (2018).
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).
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).
Bosse, M. et al. Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nat. Commun. 5, 4392 (2014).
Bosse, M. et al. Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs. Proc. Biol. Sci. 282, 20152019 (2015).
Shearin, A. L. & Ostrander, E. A. Canine morphology: hunting for genes and tracking mutations. PLoS Biol. 8, e1000310 (2010).
Boyko, A. R. The domestic dog: man’s best friend in the genomic era. Genome Biol. 12, 216 (2011).
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).
Orlando, L. & Librado, P. Origin and evolution of deleterious mutations in horses. Genes 10, E649 (2019).
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).
Charlier, C. et al. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock. Genome Res. 26, 1333–1341 (2016).
Derks, M. F. L. et al. Loss of function mutations in essential genes cause embryonic lethality in pigs. PLoS Genet. 15, e1008055 (2019).
Ellegren, H. The different levels of genetic diversity in sex chromosomes and autosomes. Trends Genet. 25, 278–284 (2009).
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).
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.
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).
Ludwig, A. et al. Coat color variation at the beginning of horse domestication. Science 324, 485 (2009).
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).
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).
Schraiber, J. G., Evans, S. N. & Slatkin, M. Bayesian inference of natural selection from allele frequency time series. Genetics 203, 493–511 (2016).
Malaspinas, A.-S. Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective. Mol. Ecol. 25, 24–41 (2016).
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).
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).
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).
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).
Heinsohn, T. Animal translocation: long-term human influences on the vertebrate zoogeography of Australasia (natural dispersal versus ethnophoresy). Aust. Zool. 32, 351–376 (2003).
Taberlet, P. et al. Are cattle, sheep, and goats endangered species? Mol. Ecol. 17, 275–284 (2008).
Taberlet, P., Coissac, E., Pansu, J. & Pompanon, F. Conservation genetics of cattle, sheep, and goats. C. R. Biol. 334, 247–254 (2011).
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).
Ellis, E. C. et al. Used planet: a global history. Proc. Natl Acad. Sci. USA 110, 7978–7985 (2013).
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).
Plug, I. Aspects of life in the Kruger National Park during the early iron age. Goodwin Series 6, 62–68 (1989).
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).
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).
Witter, R. L. The changing landscape of Marek’s disease. Avian Pathol. 27, S46–S53 (1998).
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).
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).
Makvandi-Nejad, S. et al. Four loci explain 83% of size variation in the horse. PLoS One 7, e39929 (2012).
Racimo, F., Sankararaman, S., Nielsen, R. & Huerta-Sánchez, E. Evidence for archaic adaptive introgression in humans. Nat. Rev. Genet. 16, 359–371 (2015).
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).
Warinner, C. et al. Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336–344 (2014).
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).
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).
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).
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).
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).
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).
Rubin, C.-J. et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587–591 (2010).
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).
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).
Andersson, L. S. et al. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 488, 642–646 (2012).
Wutke, S. et al. The origin of ambling horses. Curr. Biol. 26, R697–R699 (2016).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012).
Rajaraman, A., Tannier, E. & Chauve, C. FPSAC: fast phylogenetic scaffolding of ancient contigs. Bioinformatics 29, 2987–2994 (2013).
Seitz, A. & Nieselt, K. Improving ancient DNA genome assembly. PeerJ 5, e3126 (2017).
Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).
Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).
Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).
Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).
L.A.F.F. and G.L. were supported by a European Research Council (ERC) grant (ERC-2013–396 StG-337574-UNDEAD) and/or Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S00078X/1, NE/S007067/1 and NE/S007067/1). L.A.F.F. was also supported by a Wellcome Trust grant (210119/Z/18/Z). L.O. was supported by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 681605). D.G.B. was supported by ERC Investigator grant 295729-CodeX.
The authors declare no competing interests.
Peer review information
Nature Reviews Genetics thanks S. Olsen, P. Ajmone-Marsan and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
An archaeological period that began ~12,000 years ago in the Near East (later in other parts of the world), following the appearance of farming communities and the domestication of plants and animals. This period marks the latest stage of the ‘Stone Age’ and ends with the development of metallurgy (Bronze Age).
- Bronze Age
An archaeological period that began over 5,000 years ago in Southern Europe and part of the Near East. This period is associated with the use of bronze and, in some regions, the advent of more urban societies.
- Next-generation sequencing
(NGS). Also known as ultra-high-throughput sequencing. Sequencing technologies that allow researchers to sequence entire genomes (DNA) or transcriptomes (RNA) substantially faster and cheaper than the older technologies.
- Endogenous DNA
DNA extracted from the tissue (such as bone or skin) of an organism that is no longer alive, whereas exogenous DNA originates from outside (such as from soil bacteria). The proportion of endogenous DNA molecules can vary considerably depending on the origin and the age of a sample.
- Capture techniques
Also known as target enrichment, these techniques help focus sequencing efforts to a subset of the DNA templates present in DNA libraries, through hybridization to target-specific probes.
- Neural crest cell
A temporary cell that differentiates into multiple cell types involved in the formation of the nervous component of bones and cartilages. Research suggests that the behaviour of neural crest cells may have been modified by domestication, leading to the development of multiple traits that are common across many domesticated animal species (also known as ‘domestication syndrome’), including depigmentation, smaller brain, floppy ear and shorter muzzle.
- Runs of homozygosity
(ROH). Regions of the genome that are depleted of heterozygosity, which can arise when a diploid individual inherits two identical stretches of DNA at a specific position of the genome, due to the mating of two closely related parents (such as cousins). The length and the number of ROH across the genome can provide powerful information to infer levels of inbreeding.
- Artificial selection
The process by which humans breed animals to enhance specific characteristics (traits).
- Yamnaya culture
An early Bronze Age culture from the northern shore of the Black Sea (Pontic steppe).
- Sintashta culture
A Bronze Age culture of the northern Eurasian steppe, which is considered to be an offshoot of the Yamnaya culture.
- 4.2k event
A severe aridification event beginning ~4,200 years ago, which has been hypothesized to have caused the collapse of multiple civilizations across Eurasia.
Registries that contain the list of animals that belong to the same breed and for which the parents are known.
- Breeder’s equation
A mathematical formula that allows breeders to predict the response to selection of a specific heritable trait.
- Purifying selection
Also known as negative selection. Removal of deleterious variants in a population by natural selection.
- Deleterious variants
Alleles that have a detrimental effect on the phenotype of an individual.
- Mutational load
The mutational burden in a population or an individual resulting from deleterious variants.
- Relaxed selection
The weakening or removal of a selective pressure, such as when domesticated animals are less subject to selective pressure from predators.
- Justinianic plague
A historical pandemic of Yersinia pestis (541–542 ad) that affected Mediterranean port cities, including Constantinople, and that resulted in the death of 25–50 million people.
- Black Death
A historical pandemic of Yersinia pestis (1346–1353 ad) that resulted in the death of 75–200 million people across Eurasia and that is thought to have had a profound effect on European history.
About this article
Cite this article
Frantz, L.A.F., Bradley, D.G., Larson, G. et al. Animal domestication in the era of ancient genomics. Nat Rev Genet 21, 449–460 (2020). https://doi.org/10.1038/s41576-020-0225-0