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.

Correction: Of herds and societies-Seasonal aspects of Vinca culture herding and land use practices revealed using sequential stable isotope analysis of animal teeth.

[This corrects the article DOI: 10.1371/journal.pone.0258230.].

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.

Ancient chicken remains reveal the origins of virulence in Marek's disease virus.

The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.

Of herds and societies-Seasonal aspects of Vinca culture herding and land use practices revealed using sequential stable isotope analysis of animal teeth.

Late Neolithic Vinca communities, spread over much of central and northern Balkans during the late sixth to mid-fifth millennium BC and characterised by unusually large and densely population centres, would have required highly organised food production systems. Zooarchaeological analysis indicates that domesticate livestock were herded, but little is known about the seasonal husbandry practices that helped ensure a steady supply of animal products to Vinca farming communities. Here, we present new stable carbon (δ13C) and oxygen (δ18O) isotopic measurements of incremental bioapatite samples from the teeth of domesticated livestock and wild herbivore teeth from two late Neolithic Vinca culture sites: Vinca-Belo brdo and Stubline (Serbia). Our results show a low variation overall within sheep and goats in terms of pasture type that may have been composed of seasonal halophyte plant communities, which have higher δ13C values due to the saline rich growing environments. Cattle feeding strategies were more variable and provided with supplementary forage, such as cut branches or leafy hay, during winter. The sharp distinction in the management of cattle and sheep/goat may be associated with the development of herding strategies that sought to balance livestock feeding behaviours with available forage or, more provocatively, the emergence of household-based control over cattle-an animal that held a central economic and symbolic role in Vinca societies.

Origins and genetic legacy of prehistoric dogs.

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent.

Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift indicates rapid and widespread introgression of zebu, Bos indicus, from the Indus Valley. This process was likely stimulated at the onset of the current geological age, ~4.2 thousand years ago, by a widespread multicentury drought. In contrast to genome-wide admixture, mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival. This human-mediated migration of zebu-derived genetics has continued through millennia, altering tropical herding on each continent.

Spavin in red deer: A case study from the Early Neolithic Blagotin, Serbia.

Pathological modifications are rarely observed in the remains of wild animals from archaeological sites. We present one such specific, pathological change - a case of spavin in a red deer specimen from the Early Neolithic site of Blagotin, in central Serbia. The left tarsal joint presented proliferative new bone formation, which was analyzed macroscopically, then subjected to X-ray and computed tomography (CT) imaging. We assume that the initial degenerative changes in this red deer tarsal joint were probably caused by ageing, although the environment may have likely contributed to the progression of the disorder. Spavin usually results in stiffness of the joints and in lameness, perhaps contributing in the animal's capture by Neolithic hunters. This case is important in that it demonstrates that spavin is not necessarily a consequence of riding or traction work.

Paleopathological changes in an early iron age horse skeleton from the Central Balkans (Serbia).

During a rescue archeological excavation in 2012 at the site of Ranutovac-Meaniste near Vranje, southern Serbia, remains of an Early Iron Age (Hallstatt B-C) settlement were revealed. In one of the settlement pits a complete horse skeleton was discovered. The skeleton belongs to a mare, aged 4-5 years at death. In this paper, paleopathological changes in the horse skeleton are described and analyzed using macroscopic, radiographic and scanning electron microscopy techniques to interpret the possible use of the animal. Potential bitting damage is observed in the lower second premolars (P2) and mandibular diastema. Several pathologies are recorded in thoracic (T10-17) and lumbar vertebrae (L1). Paleopathological changes in forelimbs are restricted to the lower leg bones. Bone changes in the hind-limbs, beside the metatarsals and the first phalanges, are also observed in the right femur, right calcaneum and both tibiae. These paleopathological changes were caused by chronic inflammation of ligaments as a consequence of the intensive exploitation of the animal, most likely riding. This paper is one of the first publications of animal paleopathology in Serbia and the first identified example of coxofemoral osteochondrosis in horse in the paleopathological literature.