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.

Late Pleistocene beach deposits in 22 selected sites around Cyprus demonstrate the vertical changes in the Earth's crust in that island over the last 125 ka. The beach/shallow-marine deposits were observed on the abraded coastal cliffs at 3-22 m above the present sea-level. They overlie Pliocene marls, and some of them contain the Senegalese marine gastropods Persististrombus latus, Bursa granularis and Conus ermineus that no longer live in the Mediterranean. These are index fossils for the Marine Isotope Stage (MIS) 5e in the Mediterranean and, as such, suggest an uplift of up to 15.5 m over about the last 125 ka: that is a maximal rate of 0.12 mm a 21 . These findings are in accordance with Holocene beachrocks, abrasion platforms, wave notches and Roman/ Byzantine fish tanks that retained their elevations, and thus enable the reconstruction of the coast encountered by the early colonizers. While the maximal uplift since the early Holocene has been minor and did not exceed 1.2-1.5 m, the sea-level changes have reached 40-50 m. The transition between the impermeable Pliocene marls and the porous Late Pleistocene deposits above them is the origin of freshwater springs and associated vegetation. The early colonizers seemed to recognize the potential of that essential permanent source of water and excavated wells, the earliest wells known so far. The locations of the Early Neolithic settlements (Mylouthkia and Akanthou) adjacent to visible water springs along the coastal cliffs may not be incidental. Not surprisingly, recent wells dug in the coastal Pleistocene deposits rely on the very same hydrological setting.Supplementary material: Appendices 1 -4, which include tables and diagrams showing the vertical changes (m) and rates of vertical changes (mm ka 21 ), assuming that MIS5e isotope stage deposits are 122 ka old and are at elevation of 7.2 m asl, or 116 ka at 6.5 m, are available at

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...

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