SummaryThe archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [1, 2, 3]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [4]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.

Two anchovy forms identified from their external morphology and designated as 'Silver' and 'Blue' anchovies were captured in Mersin Bay (Eastern Mediterranean Sea). Silver anchovy seemed to inhabit shallower waters (9-77 m) than Blue anchovy (majority at depths of 69-111 m). Significant differences in body shape, which was analyzed through geometric morphometrics, and in otolith shape, examined using Fourier analysis, separated the two forms. Length polymorphisms at two intron and 9 microsatellite loci showed strong genetic differences between the two forms. Mersin-Bay Blue anchovy were genetically related to Engraulis encrasicolus from the Western Mediterranean Sea. Mersin-Bay Silver anchovy possessed an original genetic composition that distinguished them from both E. encrasicolus and E. albidus at the two intron loci, while presenting affinities to E. albidus based on microsatellite markers. Mersin-Bay Silver anchovy were assigned to the latter species, of which they are considered as a geographically isolated population. This is the first record of E. albidus in the Levantine basin and confirmation of its presence in the Eastern Mediterranean Sea. These results have implications for the management of anchovy populations and their habitats.

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.

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...

Despite the region's complex sociopolitical history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.