Genomic insights into the formation of human populations in East Asia.

The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 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 that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.

A comparative study of stress episode prevalence and duration among Jomon period foragers from Hokkaido.

This study reconstructs linear enamel hypoplasia (LEH) prevalence and stress episode duration among Jomon period foragers from Hokkaido, Japan (HKJ). Results are compared to Jomon period samples from coastal Honshu, Japan (HSJ) and Tigara Inupiat from Point Hope, Alaska (PHT) to provide a more comprehensive perspective on the manifestation of stress among circum-Pacific foragers. LEH were identified macro- and microscopically by enamel surface depressions and increased perikymata spacing within defects. Individuals with more than one anterior tooth affected by LEH were labeled as LEH positive. Stress episode durations were estimated by counting the number of perikymata within the occlusal wall of each LEH and multiplying that number by constants reflecting modal periodicities for modern human teeth. LEH prevalence and stress episode duration did not differ significantly between the two Jomon samples. Significantly greater frequencies of LEH were found in HKJ as compared to PHT foragers. However, HKJ foragers had significantly shorter stress episode durations as compared to PHT. This suggests that a greater proportion of HKJ individuals experienced stress episodes than did PHT individuals, but these stress events ended sooner. Similarity in stress experiences between the two Jomon samples and differences between the HKJ and PHT are found. These findings are important for two reasons. First, stress experiences of foraging populations differ markedly and cannot be generalized by subsistence strategy alone. Second, due to significant differences in episode duration, stress experiences cannot be understood using prevalence comparisons alone.

Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis.

To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported.

Temporal variation and interaction between nutritional and developmental instability in prehistoric Japanese populations.

We examined nutritional and developmental instability in prehistoric Japan, using data from 49 individuals across 13 archaeological sites. Hypoplasia incidence was used as a measure of nutritional stress, and fluctuating asymmetry (of upper facial breath, orbital breadth, and orbital height) as an indirect assessment of developmental instability. Abundant resources due to a stable climate during the Middle Jomon (5,000-3,000 BP) encouraged population growth, which led to regional cultural homogeneity and complexity. A population crash on Honshu in the Late/Final Jomon (roughly 4,000-2,000 BP) led to regionally divergent subsistence economies and settlement patterns. We find that the nutritional stress was consistent between periods, but developmental instability (DI) decreased in the Late/Final Jomon. While the DI values were not statistically significant, the higher values for Middle Jomon may result from sedentism, social stratification, and differential access to resources. On Hokkaido, Jomon culture persisted until the Okhotsk period (1,000-600 BP), marked by the arrival of immigrants from Sakhalin. Nutritional stress was consistent between Middle and Late/Final Jomon, but DI increased in the Late/Final. Nutritional and developmental instability decreased from Late/Final to Okhotsk, suggesting a positive immigrant effect. We expected to find an association between stress markers due to the synergistic relationship between nutrition and pathology. The data support this hypothesis, but only one finding was statistically significant. While high critical values from small sample sizes place limits on the significance of our results, we find that the impact of environmental and cultural change to prehistoric Japanese populations was minimal.

Oral and physiological paleohealth in cold adapted peoples: Northeast Asia, Hokkaido.

This paper examines variables useful in reconstructing oral (caries, antemortem tooth loss, alveolar defects) and physiological (cribra orbitalia, linear enamel hypoplasia) well-being in two bioarchaeological assemblages from Hokkaido, Japan: Okhotsk (n = 37 individuals) and Jomon (n = 60). Findings are compared and contrasted with each other, with published series from Honshu Japan, and samples from climatically near-equivalent Alaska. It was found that more meaningful comparisons of Hokkaido paleohealth could be made with Alaskan material, rather than the more southerly Jomon. Results were ambiguous with respect to physiological well-being. Low levels of LEH in the cold-adapted samples suggest operating in arctic and subarctic environments with marine-based subsistence regimes is not physiologically expensive. However, the relatively high levels of cribra orbitalia in Hokkaido, relative to Alaska, suggest the picture is not straightforward: the reasons for elevated cribra orbitalia in Hokkaido are unclear. The subarctic and arctic samples formed three broadly similar groupings in terms of oral health profiles: (1) Aleuts and Eskimo; (2) Ipiutak and Tigara; (3) Hokkaido Jomon, Okhotsk, and Kodiak Island. Differences between these groupings could be explained with a combination of sample demographics and subsistence orientations. The extremely high frequency of caries in one sample, caribou hunting Ipiutak, may have been influenced by factors such as low levels of dietary magnesium and potentially cariogenic foodstuffs, such as preparations of caribou stomach contents. It was concluded that oral health profiles are potentially sensitive to differences in subsistence strategies among cold-adapted hunter-gatherers, although they lack predictive value.

A morphometric analysis of the Late Pleistocene Human Skeleton from the Moh Khiew Cave in Thailand.

Few Late Pleistocene human remains have been found in Southeast Asia and the morphological features of the people of that age are still largely unknown due to the virtual lack of human remains in the area. Recent excavations at the Moh Khiew Cave in Thailand resulted in the discovery of a Late Pleistocene human skeleton in a relatively good state of preservation. An AMS radiocarbon date on the charcoal sample gathered from the burial gave a result of 25,800 +/- 600 BP, implying that the inhabitants of Moh Khiew Cave resided in a part of Sundaland during the last glacial age. In debates on the population history of Southeast Asia, it has been repeatedly advocated that Southeast Asia was occupied by indigenous people akin to present-day Australo-Melanesians prior to an expansion of migrants from Northeast Asia into this area. Morphometric analyses were undertaken to test the validity of this hypothesis. In the present study, cranial and dental measurements recorded from the Moh Khiew remains are compared with those of early and modern samples from Southeast Asia and Australia. These comparisons demonstrate that the Moh Khiew specimen resembles the Late Pleistocene series from Coobool Creek, Australia in both cranial and dental measurements. These results suggest that the Moh Khiew skeleton, as well as other fossil remains from the Tabon, Niah and Gua Gunung sites, represents a member of the Sundaland population during the Late Pleistocene, who may share common ancestry with the present-day Australian Aborigines and Melanesians.