We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

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.

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

The Lower to Middle Paleolithic transition (~400,000 to 200,000 years ago) is marked by technical, behavioral, and anatomical changes among hominin populations throughout Africa and Eurasia. The replacement of bifacial stone tools, such as handaxes, by tools made on flakes detached from Levallois cores documents the most important conceptual shift in stone tool production strategies since the advent of bifacial technology more than one million years earlier and has been argued to result from the expansion of archaic Homo sapiens out of Africa. Our data from Nor Geghi 1, Armenia, record the earliest synchronic use of bifacial and Levallois technology outside Africa and are consistent with the hypothesis that this transition occurred independently within geographically dispersed, technologically precocious hominin populations with a shared technological ancestry.

85between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. 86 We show that the earliest populations of the Near East derived around half their 87 ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture 88 and that separated from other non-African lineages prior to their separation from each 89 other. The first farmers of the southern Levant (Israel and Jordan) and Zagros 90 Mountains (Iran) were strongly genetically differentiated, and each descended from 91 local hunter-gatherers. By the time of the Bronze Age, these two populations and 92 Anatolian-related farmers had mixed with each other and with the hunter-gatherers of 93 Europe to drastically reduce genetic differentiation. The impact of the Near Eastern 94 farmers extended beyond the Near East: farmers related to those of Anatolia spread 95 westward into Europe; farmers related to those of the Levant spread southward into 96 East Africa; farmers related to those from Iran spread northward into the Eurasian 97 steppe; and people related to both the early farmers of Iran and to the pastoralists of 98 the Eurasian steppe spread eastward into South Asia. 99 Between 10,000-9,000 BCE, humans began practicing agriculture in the Near East 1 . In the 100 ensuing five millennia, plants and animals domesticated in the Near East spread throughout 101 West Eurasia (a vast region that also includes Europe) and beyond. The relative homogeneity 102 of present-day West Eurasians in a world context 2 suggests the possibility of extensive 103 migration and admixture that homogenized geographically and genetically disparate sources 104 of ancestry. The spread of the world's first farmers from the Near East would have been a 105mechanism for such homogenization. To date, however, due to the poor preservation of DNA 106 in warm climates, it has been impossible to study the population structure and history of the 107 first farmers and to trace their contribution to later populations. 108In order to overcome the obstacle of poor DNA preservation, we took advantage of two 109 methodological developments. First, we sampled from the inner ear region of the petrous 110 bone 3,4 that can yield up to ~100 times more endogenous DNA than other skeletal elements 4 . 111Second, we used in-solution hybridization 5 to enrich extracted DNA for about 1.2 million 112 single nucleotide polymorphism (SNP) targets 6,7 , making efficient sequencing practical by 113 filtering out microbial and non-informative human DNA. We merged all sequences extracted 114 from each individual, and randomly sampled a single sequence to represent each SNP, 115 restricting to individuals with at least 9,000 SNPs covered at least once. We obtained 116 genome-wide data passing quality control for 45 individuals on whom we had a median 117 4 coverage of 172,819 SNPs (Methods). We assembled radiocarbon dates for 26 individuals