Ancient DNA makes it possible to directly witness natural selection by analyzing samples from populations before, during and after adaptation events. Here we report the first scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture whose genetic material we extracted from the DNA-rich petrous bone and who we show were members of the population that was the source of Europe’s first farmers. We also report a complete transect of the steppe region in Samara between 5500 and 1200 BCE that allows us to recognize admixture from at least two external sources into steppe populations during this period. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

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.

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE – brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europe’s population.

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We assembled genome-wide data from nineteen ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. We show that Minoans and Mycenaeans were genetically similar, having at least three quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean 1 , 2 , and most of the remainder from ancient populations like those of the Caucasus 3 and Iran 4 , 5 . However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter-gatherers of eastern Europe and Siberia 6 – 8 , introduced via a proximal source related to either the inhabitants of either the Eurasian steppe 1 , 6 , 9 or Armenia 4 , 9 . Modern Greeks resemble the Mycenaeans, but with some additional dilution of the early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

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