title: Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes.
abstract: Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.
authors: Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.|Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
authors: Laurent A F
authors: LA
authors: Frantz
authors: Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA.|Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors: Joshua G
authors: JG
authors: Schraiber
authors: Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.
authors: Ole
authors: O
authors: Madsen
authors: Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.
authors: Hendrik-Jan
authors: HJ
authors: Megens
authors: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors: Alex
authors: A
authors: Cagan
authors: Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.
authors: Mirte
authors: M
authors: Bosse
authors: Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.
authors: Yogesh
authors: Y
authors: Paudel
authors: Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.
authors: Richard P M A
authors: RP
authors: Crooijmans
authors: Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
authors: Greger
authors: G
authors: Larson
authors: Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.
authors: Martien A M
authors: http://orcid.org/0000-0003-0484-4545
authors: MA
authors: Groenen
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D000835:Animals, Wild / Q000235:genetics*; D001208:Asia; D005060:Europe; D051456:Gene Flow; D016678:Genome; D013552:Swine / Q000235:genetics*