Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü’s cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia’s cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.

The aim of this study was to identify the prion protein (PrP) gene polymorphism in a total of 1,110 healthy sheep from 18 Turkish native sheep breeds. There were nine alleles and 22 genotypes observed based on codons 136, 154, and 171 of the PrP gene. The ARQ allele was predominant for all breeds. The most resistant allele to scrapie, ARR, was present in all breeds. The VRQ allele, associated with the highest susceptibility to scrapie, was detected at low frequencies in İvesi (0.06), Kıvırcık (0.021), Sakız (0.010), Karayaka (0.011), Çine Çaparı (0.012), and Güneykaraman (0.017). In general, the ARQ/ARQ genotype was predominant in all breeds. The most resistant genotype to scrapie, ARR/ARR, was found with the frequency lower than 0.180. The most susceptible genotype, VRQ/VRQ, was found in only Kıvırcık. The TRR and TRH alleles and the genotypes of ARR/TRR, ARR/ARK, and ARH/TRH have been found for the first time in Turkish native sheep breeds. According to these results, all breeds belong to risk group R3 followed by R2. It is propounded that the susceptibility to scrapie increased from eastern to western part of Turkey. Our findings of Turkish native sheep breeds with PrP gene polymorphisms will assist the sheep breeding program for selection of scrapie resistance genotypes to reduce the risk of scrapie.

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.

Susceptibility to 'scrapie' disease in goats is influenced by polymorphisms of the prion protein (PRNP) gene. The aim of this study was to identify PRNP gene polymorphisms in a total of 356 scrapie disease-free goats from 10 Turkish native breeds. Eighteen single-nucleotide polymorphisms were detected in the caprine PRNP open-reading frame. Ten previously described amino acid substitutions (I142M, H143R, N146S, N146D, R151H, R154H, P168Q, R211Q, Q222K and P240S) and two novel dimorphisms (G134E and Q163P) were identified. The strongest association between caprine PRNP and relative resistance to scrapie disease has been reported previously for polymorphisms at codons 146 (S/D) and 222 (K). In the present study, these three PrP variants were relatively rare with 6.3%. This is the first report on PRNP gene variation in Turkish native goat breeds and our knowledge of these polymorphisms will assist goat breeding programmes to reduce the risk of scrapie.

The aim of this study was to identify the PRNP polymorphisms outside the standard codons 136, 154 and 171 in 1110 sheep with no clinical sign of scrapie from all 18 Turkish native sheep breeds and compare our results with published data on ovine PRNP polymorphism from other regions of the world. Among the 22 amino acid polymorphisms and three silent mutations, 10 were novel for ovine PRNP: p.Gly94Gly, p.Leu128Ile, p.Met132Leu, p.Ser135Arg, p.Met137Val, p.Asn146Lys, p.Arg159Arg, p.Tyr160Asn, p.Gln163His and p.Thr193Ser. These data reveal that sheep breeds close to the historic center of small ruminant domestication have remained highly diverse in the prion gene locus, with distinctive genetic similarities to both Asian and European sheep breeds.

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22Sheep was among the first domesticated animals, but its demographic history is little 23 understood. Here we present combined analyses of mitochondrial and nuclear polymorphism 24 data from ancient central and west Anatolian sheep dating to the Late Glacial and early 25 Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the 26 early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, 27 mitochondrial haplogroup diversity increases, compatible with admixture from other 28 domestication centres and/or from wild populations. Analysing archaeogenomic data, we 29 further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day 30 European breeds, and especially those from central and north Europe. Our results indicate that 31 Asian contribution to south European breeds in the post-Neolithic era, possibly during the 32 Bronze Age, may explain this pattern.33 34 35 36 65 traits across the globe, especially within the last 5 millennia, as part of the secondary products 66 revolution 18,19 . Although the first domesticated sheep were likely used for their meat and 67 possibly their milk 20 , they started to be increasingly exploited for their wool in Bronze Age SW 68 Asia, during the 3rd millennium BCE 21 . Intriguingly, a comparison of DNA retroelements 69 across modern breeds implies an expansion of SW Asian lineages, estimated to date back to the 70 Bronze Age; according to this model, SW Asian sheep with desired traits, such as fine wool, 71 were introduced into local breeds across the globe 22 . A recent ancient DNA study reports 72 evidence consistent with novel breeds being introduced to Bronze Age Europe, coinciding with 73 archaeological evidence for the introduction of wool to this continent 21 . In later periods, export 74 and admixture of selected sheep breeds into local stocks continued 11 . Indeed, the most recent 75 common ancestor of domestic sheep breeds has been inferred to date back only 800 generations 76 ago 11 -an unexpectedly recent estimate. 77 4We currently lack a solid demographic history model to explain these observations: high 78 diversity, clear genetic structure, and recent coalescence times. What is missing is genetic data 79 on the initial steps of domestication and characterisation of the early domesticated sheep gene 80 pool. Here we present a first attempt to bridge this gap, studying ancient DNA from Neolithic 81 period sheep remains from Anatolia, one of the possible domestication centres. Analysing both 82 mitochondrial DNA (mtDNA) sequences and nuclear polymorphism data, we find support for 83 the notions that the present-day domestic sheep population has multiple origins, and also that 84 the sheep gene pool changed considerably since the Neolithic period. 85 86 Results 87 We analysed DNA from c.200 archaeological sheep bone and tooth samples from early 88 Holocene Anatolia, originating from six different sites from central and west Anatolia and 89spanning the Epipaleolithic, Neolithic, and Ch...

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.