Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries).

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Asikli Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Asikli Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Asikli Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.

The 10,000-year biocultural history of fallow deer and its implications for conservation policy.

Over the last 10,000 y, humans have manipulated fallow deer populations with varying outcomes. Persian fallow deer (Dama mesopotamica) are now endangered. European fallow deer (Dama dama) are globally widespread and are simultaneously considered wild, domestic, endangered, invasive and are even the national animal of Barbuda and Antigua. Despite their close association with people, there is no consensus regarding their natural ranges or the timing and circumstances of their human-mediated translocations and extirpations. Our mitochondrial analyses of modern and archaeological specimens revealed two distinct clades of European fallow deer present in Anatolia and the Balkans. Zooarchaeological evidence suggests these regions were their sole glacial refugia. By combining biomolecular analyses with archaeological and textual evidence, we chart the declining distribution of Persian fallow deer and demonstrate that humans repeatedly translocated European fallow deer, sourced from the most geographically distant populations. Deer taken to Neolithic Chios and Rhodes derived not from nearby Anatolia, but from the Balkans. Though fallow deer were translocated throughout the Mediterranean as part of their association with the Greco-Roman goddesses Artemis and Diana, deer taken to Roman Mallorca were not locally available Dama dama, but Dama mesopotamica. Romans also initially introduced fallow deer to Northern Europe but the species became extinct and was reintroduced in the medieval period, this time from Anatolia. European colonial powers then transported deer populations across the globe. The biocultural histories of fallow deer challenge preconceptions about the divisions between wild and domestic species and provide information that should underpin modern management strategies.

Grouping groupers in the Mediterranean: Ecological baselines revealed by ancient proteins.

Marine historical ecology provides a means to establish baselines to inform current fisheries management. Groupers (Epinephelidae) are key species for fisheries in the Mediterranean, which have been heavily overfished. Species abundance and distribution prior to the 20th century in the Mediterranean remains poorly known. To reconstruct the past biogeography of Mediterranean groupers, we investigated whether Zooarchaeology by Mass Spectrometry (ZooMS) can be used for identifying intra-genus grouper bones to species level. We discovered 22 novel, species-specific ZooMS biomarkers for groupers. Applying these biomarkers to Kinet Höyük, a Mediterranean archaeological site, demonstrated 4000 years of regional Epinephelus aeneus dominance and resiliency through millennia of fishing pressures, habitat degradation and climatic changes. Combining ZooMS identifications with catch size reconstructions revealed the Epinephelus aeneus capacity for growing 30 cm larger than hitherto documented, revising the maximum Total Length from 120 to 150 cm. Our results provide ecological baselines for a key Mediterranean fishery which could be leveraged to define and assess conservation targets.

Threatened North African seagrass meadows have supported green turtle populations for millennia.

"Protect and restore ecosystems and biodiversity" is the second official aim of the current UN Ocean Decade (2021 to 2030) calling for the identification and protection of critical marine habitats. However, data to inform policy are often lacking altogether or confined to recent times, preventing the establishment of long-term baselines. The unique insights gained from combining bioarchaeology (palaeoproteomics, stable isotope analysis) with contemporary data (from satellite tracking) identified habitats which sea turtles have been using in the Eastern Mediterranean over five millennia. Specifically, our analysis of archaeological green turtle (Chelonia mydas) bones revealed that they likely foraged on the same North African seagrass meadows as their modern-day counterparts. Here, millennia-long foraging habitat fidelity has been directly demonstrated, highlighting the significance (and long-term dividends) of protecting these critical coastal habitats that are especially vulnerable to global warming. We highlight the potential for historical ecology to inform policy in safeguarding critical marine habitats.

Hunting before herding: A zooarchaeological and stable isotopic study of suids (Sus sp.) at Hardinxveld-Giessendam, the Netherlands (5450-4250 cal BC).

Suids (Sus sp.) played a crucial role in the transition to farming in northern Europe and, like in many regions, in the Netherlands pig husbandry became an important subsistence activity at Neolithic sites. Yet little is known about wild boar palaeoecology and hunting in the Late Mesolithic Netherlands with which to contextualize this transition. This paper presents the first multi-proxy analysis of archaeological suid remains in the Netherlands. It explores human-suid interactions at the Swifterbant culture sites of Hardinxveld-Giessendam Polderweg and De Bruin (5450-4250 BC) through biometric analysis, estimation of age-at-death, and stable carbon and nitrogen isotope analysis. The results reveal targeted hunting of adult wild boar in the Late Mesolithic (5450-4850 BC), with a possible shift over time towards more juveniles. The wild boar in this period are demonstrated to be of comparably large size to contemporary northern European populations and exhibiting a wide range of dietary regimes. In the final occupational period (4450-4250 BC), small suids are present, possibly domestic pigs, but there is no evidence of pig management. This study demonstrates that the nature of human-suid interactions varied over time, which may have been connected to changing environmental conditions, human mobility, and wild boar behaviour. This study also contributes the first biometric and dietary baseline for mid-Holocene wild boar in the Netherlands.

Judging a reindeer by its teeth: A user-friendly tooth wear and eruption pattern recording scheme to estimate age-at-death in reindeer (Rangifer tarandus).

Reindeer (Rangifer tarandus) have shaped the cultures and provided livelihood to peoples of the Northern Hemisphere for thousands of years. They are still the socio-economic cornerstone of many northern cultures. Insight into reindeer mortality patterns is important for understanding past human-reindeer interactions and reindeer population fluctuations in relation to climatic and environmental change. Beyond archaeology, assessing the age structures of modern reindeer populations is important for developing wildlife management strategies. This paper presents a quick, non-destructive and cheap method to estimate age in reindeer in both modern and ancient populations based on tooth wear and eruption patterns of mandibular teeth. We devised the method using a large sample of Svalbard reindeer (Rangifer tarandus platyrhynchus) of known age. We blind-tested the method and tested its applicability on another known-age Svalbard reindeer mandible assemblage. The tests demonstrate our methods' user-friendliness and reliability to generate reproducible, reusable datasets and accuracy in estimating reindeer age-at-death.

Specialized cattle farming in the Neolithic Rhine-Meuse Delta: Results from zooarchaeological and stable isotope (δ18O, δ13C, δ15N) analyses.

Schipluiden (3630-3380 cal BC), the earliest known year-round settlement in the Rhine-Meuse Delta in the Netherlands, is a key site for addressing the nature of Neolithic subsistence in the wetlands of northwestern Europe. A preliminary zooarchaeological study suggested that cattle husbandry was a major activity at Schipluiden. In contrast, stable carbon and nitrogen isotope analyses of human remains from the site indicated a marine-oriented diet, implying that the Mesolithic-Neolithic dietary transition continued well into the mid-4th Millennium BC in this region. Here, we re-investigate the role and nature of cattle husbandry at Neolithic Schipluiden using mortality profiles and stable isotope analysis (δ18O, δ13C, δ15N) of animal bone collagen and tooth enamel. The age-at-death analysis suggests that cattle were managed for both meat and milk production. The δ18O and δ13C analysis of tooth enamel provide evidence that calving spread over five-and-a-half-months, which would have led to a longer availability of milk throughout the year. Cattle were grazing in open, marshy environments near the site and winter foddering was practiced occasionally. The faunal isotopic data also reveal that the high 15N in human bone collagen is more likely to signal the consumption of products from cattle that grazed on 15N-enriched salt marsh plants around the site, rather than a marine-oriented diet. This undermines the previous interpretation of the dietary practices at Schipluiden by showing that human diet in mid-4th millennium BC Rhine-Meuse area was fully "Neolithic", based primarily on products from domesticates, especially cattle, with some input from wild terrestrial and aquatic resources available in their surroundings, contrary to what has been proposed before. Collating these results demonstrates a high level of investment in cattle husbandry, highlighting the social and economic importance of cattle at the lower Rhine-Meuse Delta during the 4th millennium BC.

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.

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.

The genetic prehistory of domesticated cattle from their origin to the spread across Europe.

BACKGROUND: Cattle domestication started in the 9(th) millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication. RESULTS: Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE. CONCLUSIONS: The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers.

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).

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.