Sequenced genomes of 7,000-year-old German farmer and eight 8,000-year-old hunter-gatherers from Luxembourg and Sweden. Most present-day Europeans derive from west European hunter-gatherers contributing to all Europeans but not Near Easterners. Ancient north Eurasians related to Upper Palaeolithic Siberians contribute to both Europeans and Near Easterners. Early European farmers mainly Near Eastern origin but harbor west European hunter-gatherer ancestry. Early European farmers have 44% ancestry from basal Eurasian population that split before diversification of other non-African lineages. Three-way mixture model fits European populations. West European hunter-gatherers highly differentiated from other groups. Ancient north Eurasian ancestry present in both Europe and Near East. MA1 best surrogate for ancient north Eurasian ancestry. Differential relatedness shows distinct contributions from Stuttgart farmer, Loschbour hunter-gatherer, and others. Evidence of Siberian gene flow into far northeastern Europe. Basal Eurasians split early from non-African lineages implying deep population structure.