Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All DNA sequences are available on Genbank under accession numbers KY564399–KY564432; OR220344-OR220389, OR531442, OR531443, OR232305-OR232317 and in the supplement.Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.Arts and Humanities Research Council (AHRC

Pig domestication and human-mediated dispersal in western eurasia revealed through ancient DNA and geometric morphometrics

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages

Data sharing reveals complexity in the westward spread of domestic animals across Neolithic Turkey

This study presents the results of a major data integration project bringing together primary archaeozoological data for over 200,000 faunal specimens excavated from seventeen sites in Turkey spanning the Epipaleolithic through Chalcolithic periods, c. 18,000-4,000 cal BC, in order to document the initial westward spread of domestic livestock across Neolithic central and western Turkey. From these shared datasets we demonstrate that the westward expansion of Neolithic subsistence technologies combined multiple routes and pulses but did not involve a set 'package' comprising all four livestock species including sheep, goat, cattle and pig. Instead, Neolithic animal economies in the study regions are shown to be more diverse than deduced previously using quantitatively more limited datasets. Moreover, during the transition to agro-pastoral economies interactions between domestic stock and local wild fauna continued. Through publication of datasets with Open Context (opencontext.org), this project emphasizes the benefits of data sharing and web-based dissemination of large primary data sets for exploring major questions in archaeology (Alternative Language Abstract S1)

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process

Fish δ13C and δ15N results from two Bronze/Iron Age sites (Tell Tweini & Sidon) along the Levantine coast

Stable isotope ratio measurements of fish remains from archaeological sites are relatively rare so here we report results of 201 fish remains from two Bronze and Iron Age sites along the Syrian (Tell Tweini) and Lebanese (Sidon) coast to document the inter- and intra-specific variation of the δ13C and δ15N isotope values. Due to poor preservation, successful isotopic results were only obtained from 42 specimens (21%). Our results were combined with previously published fish isotopic results from Sidon (n = 16) so that a total 58 specimens representing 16 different fish taxa are presented. A wide variation was observed between species that appears to be related to the ecology of the fish, in particular their salinity tolerance and feeding behaviour. The largest intra-specific variation was observed in mullets (Mugilidae) and seabreams (Sparidae) in both δ13C and δ15N values, and it appears, after comparison with published data from the Northern Aegean, some clustering occurs with location. However, the data clustering is not discrete enough to allow provenancing of fish remains from archaeological sites in this region. This large series of fish isotope values can also serve as an isotopic baseline for other studies, including the dietary reconstruction of Eastern Mediterranean human remains

Subsistence economy and land use strategies in the Burdur province (SW Anatolia) from prehistory to the Byzantine period

A reconstruction of the ancient subsistence economy and land use strategies is presented here for the province of Burdur, more specifically the area south and southeast of Lake Burdur, in southwestern Turkey. This review is based on the results from archaeozoological (including bone collagen carbon and nitrogen stable isotope analyses) and archaeobotanical analyses available from seven sites, dated to distinct time periods ranging from the Neolithic to the Middle Byzantine period. The data (both published and unpublished) are compiled with information available on settlement development and dynamics, in the study area. Results show changing agrarian and animal husbandry practices for a period of more than 8000 years, ranging between self-sustaining economies to specialised husbandry practices and an intensive agricultural exploitation of the landscape, in relation to human settlement activities