a Principal component analysis (PCA) of ancient and present-day individuals from worldwide populations after the out-of-Africa expansion. Gray labels represent population codes showing coordinates for individuals. Colored circles indicate ancient individuals. b ADMIXTURE ancestry components (K = 15) for ancient and selected contemporary individuals. The color of light blue represents the component of IK002, which is shared with the present-day Japanese and Ulchi. c Maximum-likelihood phylogenetic tree (TreeMix) with bootstrap support of 100% unless indicated otherwise. The tree shows phylogenetic relationship among present-day Southeast/East Asians, Northeast Siberians, Native Americans, and ancient East Eurasians. Mbuti are the present-day Africans; Ust’Ishim is an Upper-Paleolithic individual (45 kya) from Western Siberia83; Mal′ta (MA-1)25 and Sunghir is Upper-Paleolithic individuals (24 kya and 34 kya)29, and Loschbour is a Mesolithic individual from West Eurasia88; La368 is a pre-Neolithic Hòabìnhian hunter-gatherer (8.0 kya) in Laos and Önge is the present-day hunter-gatherers in the Andaman island, both of who are from Southeast Asia17; Tiányuán is an Upper-Paleolithic individual (40 kya) in Beijing, China35; Kusunda are the present-day minority people in Nepal; Chokhopani is an Iron-age individual (3.0–2.4 kya) and Sherpa are the present-day minority people, both of who are in Tibet6; Han, Ami and main-island Japanese are the present-day East Asians31; Devils Gate Cave is a Neolithic individual (8.0 kya) in the Primorye region of Northeast Siberia, and Shamanka and Lokomotive are Early-Neolithic individuals (8.0 kya) from Central Siberia, respectively47; USR1 and Clovis are late-Paleolithic individuals (11.5 kya and 12.6 kya) in Alaska and Montana, respectively49,89. Colored arrows represent the migration pathways and signals of admixture among all datasets. The migration weight represents the fraction of ancestry derived from the migration edge.
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