The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

Ancient genomes uncover multiple migratory pulses to Japan with the spread of wet rice farming and the rise of the state.

The globalization of food production and distribution has homogenized human dietary patterns irrespective of geography, but it is uncertain how far this homogenization has progressed. This study investigated the carbon and nitrogen isotope ratios in the scalp hair of 1305 contemporary Japanese and found values of −19.4 ± 0.6‰ and 9.4 ± 0.6‰ (mean ± SD), respectively. Within Japan, the inter-regional differences for both isotope ratios was less than 1‰, which indicates low dietary heterogeneity among prefectural divisions. The carbon and nitrogen isotope ratios of the hair showed a significant correlation with the results of questionnaires on self-reported dietary habits. The carbon isotope ratios from Japan were lower than those in samples from the USA but higher than those in samples from Europe. These differences stem from the varying dietary proportions of food products originally derived from C3 and C4 plants. The dietary variation of Japan is as small as those of Europe and USA and smaller than those of some Asian countries. These results indicate that dietary homogeneity has progressed in Japan, which may indicate the influence from the spread of the Western-style diet and food globalization, although dietary heterogeneity among countries is still preserved.

Nine human remains were recovered from Shiraho-Saonetabaru Cave on Ishigaki Island, Okinawa Prefecture, Japan, between 2007 and 2009. Six of the nine samples produced well-preserved biogenic collagen, which was submitted to radiocarbon dating by accelerator mass spectrometry. Three human samples (Nos. 2, 4, and 8) from the fossil chamber were dated to between 16 and 20 ka BP, and can clearly be assigned to the Late Pleistocene. One animal bone from the same chamber which was treated and measured for radiocarbon independently was also of great antiquity (c. 12 ka BP). These dates are the first concrete evidence of human occupation on the Ryukyu Islands during the Pleistocene, based on the direct radiocarbon dates of human remains. It is expected that more human remains and archaeological objects of the Pleistocene will be recovered from Shiraho-Saonetabaru Cave and the surrounding region by future intensive collaborations between anthropologists, archaeologists, and speleologists.

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Phylogenetic relationships among three subspecies of banteng, Burma banteng Bos javanicus birmanicus in mainland Southeast Asia, Javan banteng Bos javanicus javanicus in Java, and Bornean banteng Bos javanicus lowi in Borneo, and the presence/absence of interbreeding between wild Bornean banteng and domestic cattle in Sabah, Malaysia, were investigated by partial sequences of cytochrome b and D-loop of mitochondrial DNA. The results show that genetic distance of the Bornean banteng are relatively close to the gaur Bos gaurus/gayal Bos frontalis (the cytochrome b, 0.004-0.025; the D-loop, 0.012-0.021) followed by Burma banteng (the cytochrome b, 0.027-0.035; the D-loop, 0.040-0.045), and kouprey Bos sauveli (the cytochrome b, 0.031-0.035; the D-loop, 0.037-0.042). There are much greater distances between Bornean banteng and domestic cattle, Bos taurus and Bos indicus (the cytochromeb, 0.059-0.076; the D-loop, 0.081-0.090). These results suggest that the Bornean banteng diverged genetically from other banteng subspecies and that the wild Bornean banteng from this study are pure strain and have high conservation value.

The life history of a female individual skeleton (ST61) from the Edo period (AD 1603(AD -1868 was investigated by using multi-tissue and multi-isotope analyses. Her gravestone and historical documents revealed that ST61 was a grandmother of a chief retainer of the Akashi clan who died in 1732 aged 77 years. Radiocarbon and sulfur stable isotope analyses indicated that the contribution of marine foods to the ST61 diet was relatively low (17.2% protein) despite the relatively higher nitrogen isotope ratio of the rib bone collagen. Carbon and nitrogen stable isotope analysis of the serial section of tooth dentin along the growth lines indicated that breast milk was not the major protein source of ST61 after roughly 1-1.5 years of age, although this weaning pattern was not evident from the oxygen stable isotope ratios of her tooth enamel serial sections. The carbon stable isotopes in tooth dentin collagen and tooth enamel apatite suggested that her diet from 0.5 to 5 years of age possibly contained a small proportion of C 4 plants. Stable isotope ratios of the rib bone and the tooth dentin collagen differed, consistent with historical documents describing a residential change at the age of 27. The calibrated radiocarbon ages of the associated rice hull were at least 80-120 years older than the year of death of ST61. Sulfur stable isotope ratio of the rice hull suggested that fish fertilizers might have been used for paddy rice at that time. Multi-tissue and multi-isotope analyses can provide information of several kinds from different time windows even from an individual skeleton.