Summary Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

Dento-alveolar pathologies: caries, ante mortem tooth loss, abscesses, calculus, alveolar resorption and tooth wear were analysed in two composite skeletal series from Croatia's eastern Adriatic coast (Dalmatia). The first consists of 103 skeletons from seven Late Antique (3rd-6th century AD) sites, the second of 151 skeletons from three Early Medieval (7th-11th centuries AD) sites. As recent bioarhaeological studies (Š laus, 2008) showed a significant increase of disease loads and trauma frequencies in Dalmatia during the Early Medieval period, the aim of this study was to investigate whether dental health was equally adversely affected by the Late Antique/Early Medieval transition. The results of our analyses show that the frequencies of carious lesions, ante mortem tooth loss, abscesses and alveolar resorption increased significantly during the Early Medieval period, as did the degree of heavy occlusal wear on posterior teeth. These data suggest a change in alimentary habits, with a significantly higher dependence on carbohydrates and a greater reliance on hard, fibrous foods requiring vigorous mastication in the Early Medieval diet. The combination of higher calculus and lower caries rates in the Late Antique series similarly suggests more protein in the Late Antique diet and is, therefore, also consistent with the hypothesised change in alimentary habits. In general (the two exceptions are male caries and female alveolar resorption frequencies) lesion frequencies increased uniformly in both sexes suggesting that the deterioration of dental health during the Early Medieval period equally affected males and females. Cumulatively, the collected data suggest that the political, social, economic and religious changes that characterised the Late Antique/Early Medieval transition in Dalmatia resulted in a clear discontinuity, not only from the cultural, but also from the biological point of view with an evident deterioration of oral health during the Early Medieval period.

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We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.