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.

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.

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

Armenia has been little-studied genetically, even though it is situated in an important area with respect to theories of ancient Middle Eastern population expansion and the spread of Indo-European languages. We screened 734 Armenian males for 11 biallelic and 6 microsatellite Y chromosome markers, segregated them according to paternal grandparental region of birth within or close to Armenia, and compared them with data from other population samples. We found significant regional stratification, on a level greater than that found in some comparisons between different ethno-national identities. A diasporan Armenian sub-sample (collected in London) was not sufficient to describe this stratified haplotype distribution adequately, warning against the use of such samples as surrogates for the non-diasporan population in future studies. The haplotype distribution and pattern of genetic distances suggest a high degree of genetic isolation in the mountainous southern and eastern regions, while in the northern, central and western regions there has been greater admixture with populations from neighbouring Middle Eastern countries. Georgia, to the north of Armenia, also appears genetically more distinct, suggesting that in the past Trans-Caucasia may have acted as a genetic barrier. A Bayesian full-likelihood analysis of the Armenian sample yields a mean estimate for the start of population growth of 4.8 thousand years ago (95% credible interval: 2.0-11.1), consistent with the onset of Neolithic farming. The more isolated southern and eastern regions have high frequencies of a microsatellite defined cluster within haplogroup 1 that is centred on a modal haplotype one step removed from the Atlantic Modal Haplotype, the centre of a cluster found at high frequencies in England, Friesland and Atlantic populations, and which may represent a remnant paternal signal of a Paleolithic migration event.

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.