Ancient pigs reveal a near complete genomic turnover following their introduction to Europe
Frantz, L. A. F., Haile, J., Lin, A. T., Scheu, A., Geӧrg, C., Benecke, N., Alexander, M., Linderholm, A., Mullin, V. E., Daly, K. G., Battista, V. M., Price, M., Gron, K. J., Panoraia, A., Arbogast, R.-M., Arbuckle, B., Bălăşescu, A., Barnett, R., Bartosiewicz, L., Baryshnikov, G. , Bonsall, C., Borić, D., Boroneanţ, A., Bulatović, J., Çakirlar, C., Carretero, J.-M., Chapman, J., Church, M., Crooijmans, R., Cupere, B. D., Detry, C., Dimitrijevic, V., Dumitraşcu, V., Plessis, L., Edwards, C. J., Erek, M. C., Erim-Ӧzdoğan, A., Ervynck, A., Fulgione, D., Gligor, M., Gӧtherstrӧm Anders, A., Gourichon, L., Groenen, M. A. M., Helmer, D., Hongo, H., Horwitz, L. K., Irving-Pease, E. K., Ophélie, L., Lesur, J., Malone, C., Manaseryan, N., Marciniak, A., Martlew, H., Mashkour, M., Matthews, R.
It is advisable to refer to the publisher's version if you intend to cite from this work. See Guidance on citing. To link to this item DOI: 10.1073/pnas.1901169116 Abstract/SummaryArchaeological evidence indicates that pig domestication had begun by ~10,500 years before present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that they arrived in Europe alongside farmers ~8,500 BP. Few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boar. This turnover could be accounted for by substantial gene flow from local European wild boar, though it is also possible that European wild boar were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100-6,000 BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boar resulted in a near complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that, while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 years focused on the genomic fraction derived from the European wild boar, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 years of the domestication process.
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