Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

Abstract

Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.

Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries )

“…The phylogeographic structure that we observed in modern mitochondrial sheep haplogroups, where haplogroup B predominates in western populations and haplogroup A does so in eastern populations, is consistent with various reports [e.g., (33,(41)(42)(43)]. Such structure has been explained by means of multiple domestication origins (33,(44)(45)(46)(47), the domestication of different wild populations or species (33), introgression (41), and lineage sorting-and-gene drift (33).…”

“…In this regard, we show here that early Neolithic Aşıklı Höyük from Central Anatolia had haplogroups A, B, D, E, and unreported Z at high frequencies (0.161, 0.355, 0.306, 0.065, and 0.113, respectively) which is broadly consistent with what is reported in Neolithic sheep (see fig. S14) (41)(42)(43). These findings most definitely refute multiple domestication origins as an explanation for the modern distribution of these haplogroups.…”

Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed

“…By comparing the allele frequency in long-tailed and short-tailed sheep in multiple breeds, we observed that the above-mentioned derived allele G occurs more frequently in long-tailed sheep breeds (Supplementary Table S5 ). Further, at this position, we observed only the ancestral allele in Urial, Argali, Snow sheep, Dall sheep, Canadensis and two ancient (~8000 years) sheep genomes 31 . On the other side out of 16 investigated Asiatic mouflon 3 were heterozygous C/G and 2 homozygous G/G for the point mutation.…”

Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed

“…By comparing the allele frequency in long-tailed and short-tailed sheep in multiple breeds, we observed that the above-mentioned derived allele G occurs more frequently in long-tailed sheep breeds (Supplementary Table S4). Further, at this position, we only observed the ancestral allele in Urial, Argali, Snow sheep, Dall sheep, Canadensis and two ancient (~8,000 years) sheep genomes 63 . On the other side out of 16 investigated Asiatic mouflon 3 were heterozygous C/G and 2 homozygous G/G for the point mutation.…”