Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A 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 boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars 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 to 6,000 y 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 boars 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 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Pioneer farming in southeast Europe during the early sixth millennium BC: Climate-related adaptations in the exploitation of plants and animals.

The Old World farming system arose in the semi-arid Mediterranean environments of southwest Asia. Pioneer farmers settling the interior of the Balkans by the early sixth millennium BC were among the first to introduce southwest Asian-style cultivation and herding into areas with increasingly continental temperate conditions. Previous research has shown that the bioarchaeological assemblages from early farming sites in southeast Europe vary in their proportions of plant and animal taxa, but the relationship between taxonomic variation and climate has remained poorly understood. To uncover associations between multiple species and environmental factors simultaneously, we explored a dataset including altitude, five bioclimatic and 30 bioarchaeological variables (plant and animal taxa) for 57 of the earliest farming sites in southeast Europe using Canonical Correspondence Analysis (CCA). An extension of correspondence analysis, CCA is widely used in applied ecology to answer similar questions of species-environment relationships, but has not been previously applied in prehistoric archaeology to explore taxonomic and climatic variables in conjunction. The analyses reveal that the changes in plant and animal exploitation which occurred with the northward dispersal of farmers, crops and livestock correlate with south-north climate gradients, and emphasize the importance of adaptations in the animal domain for the initial establishment of farming beyond the Mediterranean areas.