The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people 1 , 2 . We report genome-wide data from 166 East Asians dating to 6000 BCE – 1000 CE and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan plateau are linked by a deeply-splitting lineage likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ~3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ~84% to some groups and to the Central Plain where it contributed ~59–84% to Han Chinese. Third, people from Taiwan ~1300 BCE to 800 CE derived ~75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ~25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ~3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ~2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.

Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.

The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.

The Funadomari Jomon people were hunter-gatherers living on Rebun Island, Hokkaido, Japan c. 3500-3800 years ago. In this study, we determined the high-depth and low-depth nuclear genome sequences from a Funadomari Jomon female (F23) and male (F5), respectively. We genotyped the nuclear DNA of F23 and determined the human leukocyte antigen (HLA) class-I genotypes and the phenotypic traits. Moreover, a pathogenic mutation in the CPT1A gene was identified in both F23 and F5. The mutation provides metabolic advantages for consumption of a high-fat diet, and its allele frequency is more than 70% in Arctic populations, but is absent elsewhere. This variant may be related to the lifestyle of the Funadomari Jomon people, who fished and hunted land and marine animals. We observed high homozygosity by descent (HBD) in F23, but HBD tracts longer than 10 cM were very limited, suggesting that the population size of Northern Jomon populations were small. Our analysis suggested that population size of the Jomon people started to decrease c. 50000 years ago. The phylogenetic relationship among F23, modern/ancient Eurasians, and Native Americans showed a deep divergence of F23 in East Eurasia, probably before the split of the ancestor of Native Americans from East Eurasians, but after the split of 40000-year-old Tianyuan, indicating that the Northern Jomon people were genetically isolated from continental East Eurasians for a long period. Intriguingly, we found that modern Japanese as well as Ulchi, Korean, aboriginal Taiwanese, and Philippine populations were genetically closer to F23 than to Han Chinese. Moreover, the Y chromosome of F5 belonged to haplogroup D1b2b, which is rare in modern Japanese populations. These findings provided insights into the history and reconstructions of the ancient human population structures in East Eurasia, and the F23 genome data can be considered as the Jomon Reference Genome for future studies.

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Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.

This article uses metric and nonmetric dental data to test the "two-layer" or immigration hypothesis whereby Southeast Asia was initially occupied by an "Australo-Melanesian" population that later underwent substantial genetic admixture with East Asian immigrants associated with the spread of agriculture from the Neolithic period onwards. We examined teeth from 4,002 individuals comprising 42 prehistoric and historic samples from East Asia, Southeast Asia, Australia, and Melanesia. For the odontometric analysis, dental size proportions were compared using factor analysis and Q-mode correlation coefficients, and overall tooth size was also compared between population samples. Nonmetric population affinities were estimated by Smith's distances, using the frequencies of 16 tooth traits. The results of both the metric and nonmetric analyses demonstrate close affinities between recent Australo-Melanesian samples and samples representing early Southeast Asia, such as the Early to Middle Holocene series from Vietnam, Malaysia, and Flores. In contrast, the dental characteristics of most modern Southeast Asians exhibit a mixture of traits associated with East Asians and Australo-Melanesians, suggesting that these populations were genetically influenced by immigrants from East Asia. East Asian metric and/or nonmetric traits are also found in some prehistoric samples from Southeast Asia such as Ban Kao (Thailand), implying that immigration probably began in the early Neolithic. Much clearer influence of East Asian immigration was found in Early Metal Age Vietnamese and Sulawesi samples. Although the results of this study are consistent with the immigration hypothesis, analysis of additional Neolithic samples is needed to determine the exact timing of population dispersals into Southeast Asia.

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE – 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to ∼3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.