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.
A major challenge in zooarchaeology is to morphologically distinguish closely related species’ remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and ...comparative alignment to the candidate species’ reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at
https://github.com/goztag/MTaxi
.
In this study, 182 male animals from 12 native sheep breeds, as well as Karacabey Merino and Karagül breeds of Anatolia, wild sheep Anatolian Mouflon (Ovis gmelinii anatolica) were used as the study ...material. Based on SRY and SRYM18 regions on the Y-chromosome, haplotypes of the populations were analyzed using DNA sequence analyses. The SRY region, A-oY1 allele was observed in all of the individuals studied. On the other hand, four different alleles corresponding to four Y-chromosome haplotypes were detected at the SRYM18 microsatellite region. Among native Anatolian breeds (n=143), H6 haplotype (80.41%), H4 haplotype (9.09%), H8 haplotype (8.40%) and H12 haplotype (2.1%) were identified. H6 haplotype was observed in all 16 individuals of Ovis gmelinii anatolica. Pairwise FST values based on haplotype frequencies were calculated for domestic sheep, and the highest FST value was observed between Karagül and Kıvırcık along with Karagül and Ovis gmelinii anatolica with pairwise FST value of 0.43202 (P<0.01). Y chromosome polymorphism of sheep from Turkey were examined comparatively with the accumulated data in the literature. Out of seven haplotypes (H4, H5, H6, H7, H8, H12, H19) observed in Europe and Asia, 4 haplotypes (H4, H6, H8 and H12) were observed in Anatolia. H12 was a private haplotype of Sakız, H6 seems to be the predominant haplotype of domestic sheep (79.51%) as well as being the only haplotype observed in Ovis gmelini anatolica. H4 haplotype seemed to be associated with fat tailed sheep migrating to Turkey, entering from south east of Turkey, which may be related with the arrival of nomadic Turks.
Objective: The genetic diversity parameters for gazelle populations sampled in Turkey were estimated to assess the effects of captive breeding on the populations' gene pools and effective population ...sizes. Materials and Methods: Four individuals from a recently discovered Gazella gazella population in Hatay and two captive gazelle populations were sampled (the Kizilkuyu State Farm (n=48) and the Erikce State Farm (n=25)) and analyzed using nuclear DNA, mtDNA and Y-chromosome markers. Results: The mtDNA cyt-b partial sequence analysis assigned the Erikce and Kizilkuyu samples to Gazella marica. The structure analysis differentiated significantly between them, and revealed samples originating from wild population. Both, the Y-chromosome INRA126 locus sequences of Gazella gazella and Gazella marica males and the mtDNA partial cyt-b region RFLP analysis from all the samples distinguished the two gazelle species from each other. Based on microsatellites, the estimated effective population sizes were 9.7, 8.9 and 6.4 for the Kizilkuyu, Erikce and Hatay populations, respectively. When the Kizilkuyu and Erikce populations (where severe inbreeding depressions seems to be occurring already) were pooled, the estimated Ne was 24.5. All these estimates were too small for the sustainability of either individual or pooled populations in the wild or even in captivity. Conclusion: The markers used in the study provided information on two of the gazelle species (Gazella marica, and Gazella gazella): their species identity, degree of divergences, effective population sizes and the presence of admixture within the populations. These results turned out to be invaluable in terms of their contribution to future studies for the conservation of these species. Keywords: Conservation Genetics, Biodiversity, Phylogeny, Microsatellites, mtDNA, Y-Chromosome, RFLP Analysis
In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern ...wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum Höyük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E. To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations. Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).
Information on large mammals in Turkey is limited, and widely applicable, reliable field methods need to be used to gather appropriate data for conservation and management. To evaluate local ...information on mammal species we conducted interview and ground surveys, followed by a camera trap survey, during January–May 2006 in Yenice Forest, a globally important and intact region for mammals in Turkey. Interviews with local people provided information on the occurrence of wolf Canis lupus, brown bear Ursus arctos, wild cat Felis silvestris, red fox Vulpes vulpes, Eurasian badger Meles meles, pine marten Martes martes, roe deer Capreolus capreolus, wild boar Sus scrofa and Eurasian lynx Lynx lynx. The ground and camera trap surveys confirmed the presence of all these species except lynx. In addition, the camera trap survey documented the presence of jackal Canis aureus and brown hare Lepus europaeus, signs of which were not found in the ground survey and whose presence was not known by local people. Local information on wildlife is important but management and conservation initiatives should not solely depend on such information and, as our study indicates, interview surveys cannot replace field research. The Turkish Ministry of Environment and Forestry needs to consider the establishment of a protected area large enough to secure the future of the large mammals of Yenice Forest.
The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited ...insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3–5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.
•Genetic kinship estimated from co-buried individuals’ genomes in Neolithic Anatolia•Close relatives are common among co-burials in Aşıklı and Boncuklu•Many unrelated infants found buried in the same building in Çatalhöyük and Barcın•Neolithic societies in Southwest Asia may have held diverse concepts of kinship
Yaka et al. use ancient genomes from Neolithic Anatolia and present evidence for diverse concepts of social kinship in Neolithic societies. In some communities, like Çatalhöyük, many genetically unrelated infants were buried together inside the same buildings, whereas in other sites, people buried together were frequently close biological kin.
The 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 1–3. 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.
•Pre-pottery farmers had low genetic diversity, akin to Mesolithic hunter-gatherers•Genetic diversity levels are higher in the subsequent Pottery Neolithic•Central Anatolian farmers belonged to the same gene pool as early European farmers•Copper Age genetic affinities suggest a second wave of Anatolian gene flow
Kılınç et al. study ancient genomes from the earliest farmers of central Anatolia, one of the first areas where farming appears outside the Fertile Crescent. Genetic diversity increases as the Neolithic develops, indicating rising mobility. Similarities between Anatolian and European farmers suggest two gene flow events from Anatolia into Europe.
The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into ...the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter–gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.
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