Keywords: domestication, evolution, gene flow, Neolithic

A Neolithic Mitochondrial Turnover.

Our mtDNA analysis revealed 2 broad groups: 1 from Western and Eastern Europe, including mt-Italian, mt-A, mt-C, and mt-Y2 haplogroups (Fig. 1A andSI Appendix, Figs. S7 and S8), and 1 from the Near East, including haplogroups mt-Y1 and mt-ArmT (Fig. 1A andSI Appendix, Figs. S7 and S8). These results substantiate previous findings that mt-Y1 and mt-ArmT are indigenous to the Near East, although mt-Y2, previously thought to be found exclusively in the Near East (21), also appears to be present in wild boars from the Balkans and northeast Italy (19,27) (SI Appendix). In addition, the mt-Y1 signature, originally restricted to the Near East (Fig. 1A), was not only identified in early Neolithic contexts in the Near East and Europe but was also found in pigs that (based on context and traditional biometrical analysis) were assigned a domestic status (21,28) (SI Appendix).

Altogether, this confirms that Near Eastern farmers brought domestic pigs possessing an mt-Y1 signature into Europe during the Neolithic expansion (21,28). Our analysis of mtDNA data from 2,099 samples (557 newly generated data), including 1,318 ancient samples (262 of wild boars, 592 of domestic pigs, and 464 of unknown status) and 781 modern samples (467 of wild boars and 314 of domestic pigs), demonstrates that the first appearance of the mt-Y1 haplotype in our continental European dataset was ∼8,000 y ago in Neolithic Bulgarian pigs (Kovačevo: Kov18, Kov21), and its terminal appearance in a Neolithic context was ∼5,100 y ago in a Polish sample (AA134, Żegotki 2).

The few pigs possessing an mt-Y1 signature from post-Neolithic contexts were found mostly on islands beyond mainland Europe in southwestern Greece (4,350 to 3,250 y BP: MM495, MM486, MM303), in Crete (3,100 y BP), in Sardinia (∼3,750 y BP) (29), near Naples (∼800 y BP: VM_CM01, VM_CM02, VM_CM03), and in Corsica (modern noncommercial pigs) (21), as well as in Tuscany (∼800 y BP: VM_TM01) (Fig. 1 andSI Appendix). The persistence of the mt-Y1 signature within pigs on islands mimics the patterns seen in isolated island populations of both sheep and humans. For instance, sheep in Orkney and St. Kilda (30), and human populations in Sardinia (31), were not subjected to significant introgression from later migratory waves and, instead, possess a larger proportion of Anatolian/Near Eastern ancestry relative to their mainland counterparts.

Gene Flow and a Corresponding Near-Complete Nuclear Turnover.

While these data confirm the existence of a complete turnover of mtDNA, this marker does not provide sufficient power to assess whether the turnover was the result of introgression with local female wild boars or the result of an indigenous domestication process (28). To address this issue, we sequenced 2 high-coverage, 7 medium-coverage, and 54 low-coverage ancient genomes spanning over 9,000 y. A neighbor-joining phylogenetic reconstruction of modern and ancient wild boars nuclear data reflects the distinct geographic partitioning of mtDNA data in western Eurasia (32). More specifically, distinct ancestries are present within ancient European and Near Eastern wild boars remains that predate domestication (Fig. 2A andSI Appendix, Fig. S10). An ADMIXTURE analysis of 38 wild boars nuclear genomes, including an ancient wild boars from Aşıklı Höyük (∼10,000 y BP, Turkey) reveals that modern wild individuals from Greece possess 33 to 38% Near Eastern nuclear ancestry, while those from Italy possess only 6 to 10% (Fig. 2A). The decreasing proportion of Near Eastern ancestry among wild boars from Greece to Italy most likely reflects admixture between wild populations from Anatolia into Greece and then into Italy (SI Appendix, Fig. S12). It is also possible, however, that a portion of the Anatolian ancestry found in Italian wild boars is the result of admixture from domestic pigs derived from the Near East into wild populations, instances of which have previously been shown to have occurred in northern Germany (33).

Additional ADMIXTURE analyses, including 111 genomes, clearly demonstrate that most modern domestic pigs (77 of 85) do not possess significant levels of Near Eastern ancestry (SI Appendix, Figs. S15 and S16). In fact, when modern European domestic pigs are treated as a single population, our haplotype-based analyses [GLOBETROTTER (34)] indicate that their overall Near Eastern ancestry is only ∼4% (SI Appendix), and most of this Near Eastern signal is derived from a few modern breeds from Italy, Hungary, and Spain that possessed 1.7 to 6.4% Near Eastern nuclear ancestry (Fig. 2B). Interestingly, the majority of these breeds occur in regions of Europe where modern wild boar possess, on average, higher levels of Near Eastern ancestry (6 to 33%;Fig. 2A andB), and, as opposed to many other European populations, these breeds were not mixed with Chinese pigs during breed improvement programs during the 19th century (35,36) (SI Appendix, Figs. S15 and S16). It is therefore likely that the limited Near Eastern ancestral component detected in these samples was acquired through gene flow with local wild boars (in Italy or the Balkans), and maintained as a result of a lack of admixture with introduced Chinese pigs.

We further assessed the degree of Near Eastern ancestry in archaeological pigs. Our ADMIXTURE analysis indicates that Bronze Age domestic pigs from western Iran (∼4,300 y BP: AA363) and Armenia (∼3,500 y BP: AA119) did not possess any European ancestry, and were exclusively derived from ancient Near Eastern wild boar (SI Appendix, Figs. S15 and S16). In Europe, 4 ancient high/medium-coverage domestic pigs did possess Near Eastern nuclear ancestry (Fig. 2B). Specifically, 2 early Neolithic samples from Herxheim, Germany (∼7,100 y BP: KD033, KD037) possessed ∼54% and ∼9% Near Eastern ancestry, respectively; a domestic pig from la Baume d’Oulen, France (∼7,100 y BP: AA288) possessed 15%; a Late Neolithic sample from Durrington Walls in Britain (∼4,500 y BP: VEM185) possessed ∼10%; and a 1,000-y-old Viking Age sample from the Faroe Islands (AA451) possessed only 5%. Of these, only the Herxheim sample (KD033), with ∼54% Near Eastern ancestry, possessed the Near Eastern mt-Y1 haplotype (Dataset S1), and also had substantially more Near Eastern ancestry than any of the ancient or modern European wild boar (Fig. 2B). This is supported by outgroup f3-statistics analysis, which indicates that KD033 shares more drift with Near Eastern wild boar than any other ancient or modern pig genome (SI Appendix, Fig. S17), as well as significant D-statistics of the form D (outgroup, Near Eastern wild boar; European wild boar: KD033) (Z << 3;SI Appendix, Fig. S18). These results indicate that European wild boars were being incorporated into domestic populations relatively soon after the latter were introduced from the Near East.

To obtain a more precise temporal and geographic resolution of the disappearance of Near Eastern genomic signatures in Europe, we performed additional analyses of 54 low-coverage ancient genomes (<1-fold) that possessed sufficient data (>5,000 SNPs covered from a panel of ∼12 million SNPs;SI Appendix) to be confidently projected onto a principal component analysis (PCA) alongside both modern and (high- and medium-coverage) ancient genomes. We analyzed these data together with those of Asian wild and domestic pigs. In this analysis, principal component 1 (PC1) separated European and Asian pigs, while PC2 separated Near Eastern and European pigs (SI Appendix, Fig. S14). After removing Asian pigs, PC1 separated modern European domestic pigs from all other samples, while PC2 separated European from Near Eastern pigs (Fig. 2C). The separation between European domestic pigs and all other samples on PC1 is most likely the result of admixture between Asian and European breeds following breed improvement programs in the 19th century (35,36) (SI Appendix, Figs. S15 and S16).

The PCA revealed 2 groups of ancient European pigs (including 25 previously identified as domestic using a combination of morphometric and contextual data and 10 with unknown status) (Fig. 2C). The first group consisted of 8 domestic pigs that are closer to Near Eastern wild boars and ancient Near Eastern domestic pigs (Fig. 2C). In all, this group comprised Neolithic pigs from contexts dating from 7,650 to 6,100 y BP, including the following: Madzhari, Northern Macedonia (∼7,650 y BP: BLT022, BLT023); Herxheim, Germany (7,100 y BP: KD033, KD032); Măgura, Romania (7,100 y BP: BLT010); Pločnik, Serbia (∼6,650 y BP: AA212); Vinča Belo Brdo, Serbia (∼6,500 y BP: BLT014); and Căscioarele, Romania (∼6,000 y BP: AA072). Interestingly, 7 of these samples also possessed the Near Eastern mt-Y1 haplogroup (AA212 is unknown) (Dataset S1). We also identified 3 samples from Buran-Kaya, Crimea (∼7,000 y BP: AA380, AA480, AA483) that also cluster close to Near Eastern wild boars, although they each possess the mt-Y2 haplotype and so are thought to be local wild boars (Dataset S1).

The second group of ancient European samples was closer to wild and modern domestic pigs from Europe and included samples that are mostly younger in age than the first group. This second group consisted of 18 domestic samples from overall more recent archaeological sites dating from 7,100 to 900 y BP, including the following: Herxheim, Germany (7,100 y BP: KD037); Oulens, France (∼7,100 y BP: AA288); Bozdia, Poland (∼6,700 y BP: AA346; ∼900 y BP: AA343, AA341); Durrington Walls, England (∼4,500 y BP: VEM183, VEM184, VEM185); Utrecht, The Netherlands (∼2,300 y BP: KD025; ∼700 y BP: KD024); Basel, Switzerland (∼2,000 y BP: AA266); Coppergate, England (∼1,800 y BP: AA301); Undir Junkariusfløtti, Faroe Islands (∼1,000 y BP: AA451, AA411, AA414, AA418, AA440); and Ciechrz, Poland (∼900 y BP: AA139). This group also comprised 7 ancient samples that could not be identified as either wild or domestic, including the following: la Grotte du Taï, France (∼7,100 y BP: AA294); Santa Maria in Selva, Italy (Late Neolithic: AA629); and El Portalón, Spain (∼5,400 y BP: AA513; ∼4,500 y BP: AA507; ∼3,600 y BP: AA512, AA511;∼900 y BP: AA513). Lastly, 2 ancient wild boars, 1 from Birsmatten-Basisgrotte, Switzerland (∼7,700 y BP: AA241) and 1 from Siniarzewo, Poland (∼2,900 y BP: LG507) were also found to fall closer to modern European wild boars. All of these samples possessed a European mtDNA signature (Dataset S1).

Collectively, these results reveal a fluctuating temporal pattern of Near Eastern genomic ancestry in western Eurasian domestic pigs, and the general trend shows that the samples closer in time and space to the source of the first Near Eastern pigs possessed a greater proportion of Near Eastern ancestry. In mainland Europe, domestic pigs from Neolithic sites situated around the Styrmon (e.g., Northern Macedonia), Danube (e.g., Romania), and Rhin (e.g., Germany) river systems in Germany, Romania, Macedonia, and Serbia possessed substantially more Near Eastern ancestry than is present in European wild boar (Fig. 2B andC). The timing of the first (∼8,000 y BP) and last (∼5,100 y BP) appearances of Near Eastern mtDNA signatures in continental Europe [apart from 4 Italian suids from AD 1800 (37)] is coincident with our nuclear data, indicating that <3,000 y after domestic pigs were introduced, their Near Eastern ancestry (at both mitochondrial and nuclear levels) had all but vanished. The hybrid nature of the high-coverage genome from the Neolithic Herxheim pig in Germany (7,100 y BP: KD033;Fig. 2B) indicates that this disappearance was most likely gradual, and was the result of gene flow from European wild boar into the introduced Near Eastern domestic pig populations.

The Extent of Near Eastern Ancestry in Modern Domestic Pigs.

To assess the threshold above which we could confidently identify Near Eastern ancestry in our ancient data, we simulated genomes with predefined Near Eastern ancestry proportions and analyzed the data using ADMIXTURE (38). We then used a binomial distribution to compute the probability of successfully detecting Near Eastern ancestry in 8 of 85 genomes (reflecting our modern data) (Fig. 2B andSI Appendix, Fig. S19). For admixture values ≥5%, the probability of observing only 8 genomes with Near Eastern ancestry is <1% (SI Appendix, Fig. S19A). This indicates that ADMIXTURE should detect significantly more pigs with Near Eastern ancestry if the genome of every modern domestic pig possessed a Near Eastern component ≥5%. Additionally, our simulations indicate that the GLOBETROTTER (34) analysis can accurately detect 4% Near Eastern ancestry (SI Appendix, Fig. S19B), which is less than what is present in modern Italian and Balkan wild boar. If a degree of Near Eastern ancestry was essential for the maintenance of the domestic phenotype in Europe, we would therefore predict that the underlying causative variants are present in no more than ∼4% of the genome.

To further explore this possibility, we investigated whether regions of modern domestic pig genomes reported to be subjected to positive selection (26) were more closely related to either Near Eastern or European wild boar. To do so, we first phased modern and high-coverage ancient genome data using shapeit (39). For each positively selected region, we computed the nucleotide distance between every pair of domestic and wild haplotypes. For each domestic pig haplotype, we computed the normalized difference between the nucleotide distance of the closest European haplotype and the closest Near Eastern wild boar haplotype. We then plotted the mean and SD of this statistic for each sweep region (SI Appendix). Our results show that a large majority of domestic pig haplotypes within these sweep regions share a closer genetic affinity to European wild boars than to Near Eastern wild boar (271 of 298;SI Appendix, Fig. S20). In fact, we did not identify a single region that was closer to Near Eastern wild boars (SI Appendix, Fig. S20). This suggests that the majority of human-mediated selection that took place after the arrival of pigs in Europe most likely did not target haplotypes of Near Eastern origin. We could not, however, distinguish between European and Near Eastern ancestry in ∼10 sweep regions. Given the bias toward modern European wild boar haplotypes in our dataset, it is possible that our analysis did not possess sufficient power to identify Near Eastern ancestry in those ∼10 regions. Doing so will require additional sequencing of modern and ancient Near Eastern pigs.

The Evolution and Dispersal of Black Coat Color.

To further assess the potential relevance of Near Eastern ancestry to the genetic and phenotypic makeup of early and modern domestic pigs, we investigated the Melanocortin 1 Receptor (MC1R) gene. This gene has been shown to harbor functional mutations (linked to the loss of camouflage coat color) that are highly correlated with domestic status (SI Appendix). Our analyses of previously published and novel modern and ancientMC1R sequence data (269 domestic pigs and 46 wild boar) demonstrate that a specific nonsynonymously derived mutation [D124N (40)], which is associated with black (or black and white spotted) coat color in western Eurasian domestic pigs, is almost absent in both modern and ancient wild boars from the Near East and Europe (1 of 92;SI Appendix, Fig. S8). The only wild boar that possessed 1 copy of the derived allele originated from a population in The Netherlands that is known to have recently interbred with domestic pigs (41). By characterizing this SNP in ancient domestic pigs (using NGS and PCR assays;Dataset S1), we identified 64 of 76 animals with at least 1 copy of the derived allele (the remaining 12 were homozygous for the wild type). Altogether, this suggests that while the ancestral allele at this locus cannot be used to unequivocally distinguish wild and domestic pigs, the derived allele is highly indicative of domestic status.

The earliest pigs that possessed the derived allele were found at Neolithic Ulucak Höyük in western Anatolia (∼8,650 y BP: AL1102; ∼8,250 y BP: Ulu48). The earliest European pigs that possess the derived allele are from Neolithic sites in Bulgaria (∼7,500 y BP: Cav6, Kov19), Romania (∼7,200 y BP: Uiv10), and Germany (∼7,100 y BP: KD033, KD037). Further phylogenetic analysis of the ∼100-kb region surrounding theMC1R gene indicated that 169 of 174 phased sequences, obtained from high-coverage modern and ancient domestic pigs that possessed the D124N allele, clustered in a monophyletic clade (SI Appendix, Fig. S9).

This result suggests that the D124N mutation found in Near Eastern and European pigs arose just once and was maintained, despite substantial gene flow with European wild boars. Interestingly, the nearest clade to this monophyletic cluster consisted of 2 haplotypes found in modern wild boar with European ancestry (The Netherlands) and Near Eastern ancestry (from Samos off the Anatolian west coast;SI Appendix, Fig. S9). This finding indicates that we do not possess the resolution to infer whether the D124N mutation (now fixed in many domestic breeds) first arose in the Near East or in Europe. Although we cannot definitively identify the geographic origin of the D124N mutation using phylogenetic analysis, the fact that it occurred in Anatolia before the arrival of domestic pigs into Europe, and that it likely arose only once, strongly suggests that this trait originated in Anatolia and was present in the first pigs that were transported into Europe.

• 1.Zeder M. A., “Out of the fertile crescent: The dispersal of domestic livestock through Europe and Africa” in Human Dispersal and Species Movement: From Prehistory to the Present, Boivin N., Crassard R., Petraglia M., Eds. (Cambridge University Press, 2017), pp. 261–303. [Google Scholar]
• 2.Hofmanová Z., et al. , Early farmers from across Europe directly descended from Neolithic Aegeans. Proc. Natl. Acad. Sci. U.S.A.113, 6886–6891 (2016). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 3.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). [Google Scholar]
• 4.Peters J., von den Driesch A., Helmer D., “The Upper Euphrates-Tigris Basin: Cradle of agro-pastoralism?” in The First Steps of Animal Domestication: New Archaeozoological Approaches. Proceedings of the Ninth International Council of Archeozoology, Vigne J.D., Peters J., Helmer D., Eds. (Oxbow Books, Oxford, 2005), pp. 96–123. [Google Scholar]
• 5.Daly K. G., et al. , Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science361, 85–88 (2018). [DOI] [PubMed] [Google Scholar]
• 6.Colledge S., Conolly J., Dobney K., Manning K., Shennan S., Origins and Spread of Domestic Animals in Southwest Asia and Europe (Left Coast Press, 2013). [Google Scholar]
• 7.Frantz L., et al. , The evolution ofSuidae. Annu. Rev. Anim. Biosci.4, 61–85 (2016). [DOI] [PubMed] [Google Scholar]
• 8.Rowley-Conwy P., Albarella U., Dobney K., Distinguishing wild boar from domestic pigs in prehistory: A review of approaches and recent results. J. World Prehist.25, 1–44 (2012). [Google Scholar]
• 9.Lemoine X., Zeder M. A., Bishop K. J., Rufolo S. J., A new system for computing dentition-based age profiles in Sus scrofa. J. Archaeol. Sci.47, 179–193 (2014). [Google Scholar]
• 10.Zeder M. A., Core questions in domestication research. Proc. Natl. Acad. Sci. U.S.A.112, 3191–3198 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 11.Evin A., et al. , The long and winding road: Identifying pig domestication through molar size and shape. J. Archaeol. Sci.40, 735–743 (2013). [Google Scholar]
• 12.Cucchi T., Hulme-Beaman A., Yuan J., Dobney K., Early Neolithic pig domestication at Jiahu, Henan Province, China: Clues from molar shape analyses using geometric morphometric approaches. J. Archaeol. Sci.38, 11–22 (2011). [Google Scholar]
• 13.Balasse M., et al. , “Wild game or farm animal? Tracking human-pig relationships in ancient times through stable isotope analysis” in Hybrid Communities Biosocial Approaches to Domestication and Other Trans-species Relationships, Stépanoff C., Vigne J.-D., Eds. (Routledge Studies in Anthropology, Routledge, Abingdon, Oxon, UK, ed. 1, 2018), pp. 81–96. [Google Scholar]
• 14.Dinu A., Boroneant A., Balasescu A., Soficaru A., Miritoiu D., Mesolithic and Neolithic pigs of the northern Balkans: Astragali vs. teeth as markers of domestication. Mesolithic Miscellany19, 7–12 (2008). [Google Scholar]
• 15.Legge A., Practice with science: Molar tooth eruption ages in domestic, feral and wild pigs (Sus scrofa). Int. J. Osteoarchaeol. (2013)https://onlinelibrary.wiley.com/page/journal/10991212/homepage/News.html. Accessed 25 July 2019. [Google Scholar]
• 16.Legge A. J., “Bone measurements and body weights from some Australian feral pigs” in Economic Zooarchaeology: Studies in Hunting, Herding and Early Agriculture, Rowley-Conwy P., Sergeantson D., Halstead P., Eds. (Oxbow Books, Oxford, ed. 1, 2017). [Google Scholar]
• 17.Payne S., Bull G., Components of variation in measurements of pig bones and teeth, and the use of measurements to distinguish wild from domestic pig remains. Archaeozoologia2, 27–65 (1988). [Google Scholar]
• 18.Lega C., Raia P., Rook L., Fulgione D., Size matters: A comparative analysis of pig domestication. Holocene26, 327–332 (2016). [Google Scholar]
• 19.Evin A., et al. , Unravelling the complexity of domestication: A case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania. Philos. Trans. R. Soc. Lond. B Biol. Sci.370, 20130616 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 20.Evin A., et al. , Phenotype and animal domestication: A study of dental variation between domestic, wild, captive, hybrid and insular Sus scrofa. BMC Evol. Biol.15, 6 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 21.Larson G., et al. , Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc. Natl. Acad. Sci. U.S.A.104, 15276–15281 (2007). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 22.Manunza A., et al. , A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar. PLoS One8, e55891 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 23.Gron K. J., Sørensen L., Cultural and economic negotiation: A new perspective on the Neolithic transition of Southern Scandinavia. Antiquity92, 958–974 (2018). [Google Scholar]
• 24.Sillitoe P., “Pigs in the New Guinea Highlands: An ethnographic example” in Pigs and Humans: 10,000 Years of Interaction, Albarella U., Dobney K., Ervynck A., Eds. (Oxford University Press, Oxford, UK, 2007), vol. 10, pp. 330–356. [Google Scholar]
• 25.Studer J., Pillonel D., “Traditional pig butchery by the Yali people of West Papua (Irian Jaya): An ethnographic and archaeozoological example” in Pigs and Humans: 10,000 Years of Interaction, Albarella U., Dobney K., Ervynck A., Eds. (Oxford University Press, Oxford, UK, 2007), pp. 308–329. [Google Scholar]
• 26.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). [DOI] [PubMed] [Google Scholar]
• 27.Vai S., et al. , The Biarzo case in northern Italy: Is the temporal dynamic of swine mitochondrial DNA lineages in Europe related to domestication?Sci. Rep.5, 16514 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 28.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). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 29.Lega C., et al. , Like a pig out of water: Seaborne spread of domestic pigs in Southern Italy and Sardinia during the Bronze and iron ages. Heredity118, 154–159 (2017). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 30.Chessa B., et al. , Revealing the history of sheep domestication using retrovirus integrations. Science324, 532–536 (2009). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 31.Haak W., et al. , Massive migration from the steppe was a source for Indo-European languages in Europe. Nature522, 207–211 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 32.Larson G., et al. , Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science307, 1618–1621 (2005). [DOI] [PubMed] [Google Scholar]
• 33.Krause-Kyora B., et al. , Use of domesticated pigs by Mesolithic hunter-gatherers in northwestern Europe. Nat. Commun.4, 2348 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 34.Hellenthal G., et al. , A genetic atlas of human admixture history. Science343, 747–751 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 35.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). [Google Scholar]
• 36.Bosse M., et al. , Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression. Nat. Commun.5, 4392 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 37.Maselli V., et al. , Southern Italian wild boar population, hotspot of genetic diversity. Hystrix It. J. Mammal, 10.4404/hystrix-27.2-1148927 (2016). [DOI]
• 38.Alexander D. H., Novembre J., Lange K., Fast model-based estimation of ancestry in unrelated individuals. Genome Res.19, 1655–1664 (2009). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 39.Delaneau O., Marchini J., Zagury J.-F., A linear complexity phasing method for thousands of genomes. Nat. Methods9, 179–181 (2011). [DOI] [PubMed] [Google Scholar]
• 40.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). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 41.Goedbloed D. J., et al. , Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations. Mol. Ecol.22, 856–866 (2013). [DOI] [PubMed] [Google Scholar]
• 42.Albarella U., Manconi F., Trentacoste A., “A week on the plateau: Pig husbandry, mobility and resource exploitation in central Sardinia” in Ethnozooarchaeology. The Present and Past of Human-Animal Relationships, Albarella U., Trentacoste A., Eds. (Oxbow Books, Oxford, 2011), pp. 143–159. [Google Scholar]
• 43.Hadjikoumis A., “The origins and evolution of pig domestication in prehistoric Spain” PhD thesis, University of Sheffield, Sheffield, UK (2010).http://etheses.whiterose.ac.uk/23773/. Accessed 16 May 2019.
• 44.Halstead P., Isaakidou V., “A Pig Fed by Hand is Worth Two in the Bush” in Ethnozooarchaeology: The Present and Past of Human-Animal Relationships, Albarella U., Trentacoste A., Eds. (Oxbow Books, Oxford, 2011), pp. 160–174. [Google Scholar]
• 45.MacKinnon M., High on the hog: Linking zooarchaeological, literary, and artistic data for pig breeds in Roman Italy. Am. J. Archaeol.105, 649–673 (2001). [Google Scholar]
• 46.Currat M., Ruedi M., Petit R. J., Excoffier L., The hidden side of invasions: Massive introgression by local genes. Evolution62, 1908–1920 (2008). [DOI] [PubMed] [Google Scholar]
• 47.Larson G., Burger J., A population genetics view of animal domestication. Trends Genet.29, 197–205 (2013). [DOI] [PubMed] [Google Scholar]
• 48.Frantz L. A. F., Larson G., “A genetic perspective on the domestication continuum” in Hybrid Communities, Stépanoff C., Vigne J.-D., Eds. (Routledge Studies in Anthropology, Routledge, Abingdon, Oxon, UK, ed. 1, 2018), vol. 46, pp 23–37. [Google Scholar]
• 49.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). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 50.Warmuth V., et al. , Reconstructing the origin and spread of horse domestication in the Eurasian steppe. Proc. Natl. Acad. Sci. U.S.A.109, 8202–8206 (2012). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 51.Ní Leathlobhair M., et al. , The evolutionary history of dogs in the Americas. Science361, 81–85 (2018). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 52.Eriksson J., et al. , Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet.4, e1000010 (2008). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 53.Myles S., et al. , Genetic structure and domestication history of the grape. Proc. Natl. Acad. Sci. U.S.A.108, 3530–3535 (2011). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 54.Cornille A., et al. , New insight into the history of domesticated apple: Secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet.8, e1002703 (2012). [DOI] [PMC free article] [PubMed] [Google Scholar]
• 55.Kistler L., et al. , Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science362, 1309–1313 (2018). [DOI] [PubMed] [Google Scholar]
• 56.da Fonseca R. R., et al. , The origin and evolution of maize in the Southwestern United States. Nat. Plants1, 14003 (2015). [DOI] [PubMed] [Google Scholar]

Supplementary Materials