Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing.

We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis of JEWEL revealed genetic characteristics of the Japanese population that were not discernible using microarray data. First, rare variant-based analysis revealed an unprecedented fine-scale genetic structure. Together with population genetics analysis, the present-day Japanese can be decomposed into three ancestral components. Second, we identified unreported loss-of-function (LoF) variants and observed that for specific genes, LoF variants appeared to be restricted to a more limited set of transcripts than would be expected by chance, with PTPRD as a notable example. Third, we identified 44 archaic segments linked to complex traits, including a Denisovan-derived segment at NKX6-1 associated with type 2 diabetes. Most of these segments are specific to East Asians. Fourth, we identified candidate genetic loci under recent natural selection. Overall, our work provided insights into genetic characteristics of the Japanese population.

Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands.

A tripartite structure for the genetic origin of Japanese populations states that present-day populations are descended from three main ancestors: (1) the indigenous Jomon hunter-gatherers; (2) a Northeast Asian component that arrived during the agrarian Yayoi period; and (3) a major influx of East Asian ancestry in the imperial Kofun period. However, the genetic heterogeneity observed in different regions of the Japanese archipelago highlights the need to assess the applicability and suitability of this model. Here, we analyse historic genomes from the southern Ryukyu Islands, which have unique cultural and historical backgrounds compared with other parts of Japan. Our analysis supports the tripartite structure as the best fit in this region, with significantly higher estimated proportions of Jomon ancestry than mainland Japanese. Unlike the main islands, where each continental ancestor was directly brought by immigrants from the continent, those who already possessed the tripartite ancestor migrated to the southern Ryukyu Islands and admixed with the prehistoric people around the eleventh century AD, coinciding with the emergence of the Gusuku period. These results reaffirm the tripartite model in the southernmost extremes of the Japanese archipelago and show variability in how the structure emerged in diverse geographic regions.

Multiple lines of evidence of early goose domestication in a 7,000-y-old rice cultivation village in the lower Yangtze River, China.

Poultry are farmed globally, with chicken (Gallus gallus domesticus) being the leading domesticated species. Although domestic chicken bones have been reported from some Early Holocene sites, their origin is controversial and there is no reliable domestic chicken bone older than the Middle Holocene. Here, we studied goose bones from Tianluoshan­a 7,000-y-old rice cultivation village in the lower Yangtze River valley, China­using histological, geochemical, biochemical, and morphological approaches. Histological analysis revealed that one of the bones was derived from a locally bred chick, although no wild goose species breed in southern China. The analysis of oxygen-stable isotope composition supported this observation and further revealed that some of the mature bones were also derived from locally bred individuals. The nitrogen-stable isotope composition showed that locally bred mature birds fed on foods different from those eaten by migrant individuals. Morphological analysis revealed that the locally bred mature birds were homogenous in size, whereas radiocarbon dating clearly demonstrated that the samples from locally bred individuals were ∼7,000 y old. The histological, geochemical, biochemical, morphological, and contextual evidence suggest that geese at Tianluoshan village were at an early stage of domestication. The goose population appears to have been maintained for several generations without the introduction of individuals from other populations and may have been fed cultivated paddy rice. These findings indicate that goose domestication dates back 7,000 y, making geese the oldest domesticated poultry species in history.

Ancient genomics reveals tripartite origins of Japanese populations.

Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations.

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.

Interpretation of bulk nitrogen and carbon isotopes in archaeological foodcrusts on potsherds.

RATIONALE: Foodcrust, the charred deposit adhering to the surface of containers, is a possible source of information on the function of ancient vessels and the subsistence of prehistoric humans. While the carbon isotope ratios in those materials are useful in detecting the usage of C4 plants, the reliability of nitrogen isotopic signatures has not been fully investigated. METHODS: The validity of bulk nitrogen isotope ratios has previously been investigated in coastal or riverine environments, where multiple resources from terrestrial and aquatic ecosystems were available, but not in terrestrial settings which provide a simpler mixing of terrestrial animals and plants. Hence, we conducted an exhaustive study on charred deposits on potsherds at two inland archaeological sites belonging to prehistoric Jomon hunter-gathers in central Japan, focusing on δ15 N values and atomic N/C ratios determined using an isotope ratio mass spectrometer and an elemental analyzer, respectively. RESULTS: For both sites, the δ15 N values showed significant correlations with the N/C ratios among samples from the inner surface, suggesting that these have recorded animal contribution. Furthermore, previous studies of Neolithic pottery from North Europe and Far East Russia bearing strong marine signatures had shown reasonably higher δ15 N values and N/C ratios in comparison with our data from terrestrial settings. On the other hand, some charred materials probably originating from plant starch showed lower values with both parameters. Samples from the outer surface produced less meaningful isotopic and elemental ratios altered by a thermal effect and/or contamination from soot. CONCLUSIONS: When the samples of foodcrusts were selected carefully from the inner surface, bulk nitrogen isotopes and N/C ratios reflect the composition of what was cooked or processed in containers. This will provide useful information for understanding the human adaptation from the Late Pleistocene to the Holocene in conjunction with residual lipid analyses.

A paleopathological approach to early human adaptation for wet-rice agriculture: The first case of Neolithic spinal tuberculosis at the Yangtze River Delta of China.

The earliest evidence of human tuberculosis can be traced to at least the early dynastic periods, when full-scaled wet-rice agriculture began or entered its early developmental stages, in circum-China countries (Japan, Korea, and Thailand). Early studies indicated that the initial spread of tuberculosis coincided with the development of wet-rice agriculture. It has been proposed that the adaptation to agriculture changed human social/living environments, coincidentally favoring survival and spread of pathogenic Mycobacterial strains that cause tuberculosis. Here we present a possible case of spinal tuberculosis evident in the remains of a young female (M191) found among 184 skeletal individuals who were Neolithic wet-rice agriculturalists from the Yangtze River Delta of China, associated with Songze culture (3900-3200 B.C.). This early evidence of tuberculosis in East Asia serves as an example of early human morbidity following the adoption of the wet-rice agriculture.

The prehistoric peopling of Southeast Asia.

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 Jomon), 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.

A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes.

To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome regions with substantial length.

Homogeneous diet of contemporary Japanese inferred from stable isotope ratios of hair.

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.

Trial application of oxygen and carbon isotope analysis in tooth enamel for identification of past-war victims for discriminating between Japanese and US soldiers.

Stable isotope analysis has undergone rapid development in recent years and yielded significant results in the field of forensic sciences. In particular, carbon and oxygen isotopic ratios in tooth enamel obtained from human remains can provide useful information for the crosschecking of morphological and DNA analyses and facilitate rapid on-site prescreening for the identification of remains. This study analyzes carbon and oxygen isotopic ratios in the tooth enamel of Japanese people born between 1878 and 1930, in order to obtain data for methodological differentiation of Japanese and American remains from the Second World War. The carbon and oxygen isotopic ratios in the tooth enamel of the examined Japanese individuals are compared to previously reported data for American individuals (born post WWII), and statistical analysis is conducted using a discrimination method based on a logistic regression analysis. The discrimination between the Japanese and US populations, including Alaska and Hawaii, is found to be highly accurate. Thus, the present method has potential as a discrimination technique for both populations for use in the examination of mixed remains comprising Japanese and American fallen soldiers.

Complete mitochondrial genomes of the tooth of a poached Bornean banteng (Bos javanicus lowi; Cetartiodactyla, Bovidae).

Here we report the complete mitochondrial genome of the Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae), which was determined using next-generation sequencing. The mitochondrial genome is 16,344 bp in length containing 13 protein-coding genes, 21 tRNAs and 2 rRNAs. It shows the typical pattern of bovine mitochondrial arrangement. Phylogenetic tree analysis of complete mtDNA sequences showed that Bornean banteng is more closely related to gaur than to other banteng subspecies. Divergence dating indicated that Bornean banteng and gaur diverged from their common ancestor approximately 5.03 million years ago. These results suggest that Bornean banteng might be a distinct species in need of conservation.