Takashi Gakuhari

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.

The prehistoric peopling of Southeast Asia

Ancient migrations in Southeast Asia The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations. Science, this issue p. 92, p. 88; see also p. 31 Ancient genomes reveal four layers of human migration into 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 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.

First molecular data on Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae) from Sabah, Malaysian Borneo

Abstract 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 cytochrome b, 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.

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

Abstract 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.

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.

Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture

Background The Eneolithic (~ 5,500 yrBP) site of Verteba Cave in Western Ukraine contains the largest collection of human skeletal remains associated with the archaeological Cucuteni-Tripolye Culture. Their subsistence economy is based largely on agro-pastoralism and had some of the largest and most dense settlement sites during the Middle Neolithic in all of Europe. To help understand the evolutionary history of the Tripolye people, we performed mtDNA analyses on ancient human remains excavated from several chambers within the cave. Results Burials at Verteba Cave are largely commingled and secondary in nature. A total of 68 individual bone specimens were analyzed. Most of these specimens were found in association with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do not suggest continuity with local pre-Eneolithic peoples, but rather complete population replacement. We constructed maximum parsimonious networks from the data and generated population genetic statistics. Nucleotide diversity (π) is low among all sequence types and our network analysis indicates highly similar mtDNA sequence types for samples in chamber G3. Using different sample sizes due to the uncertainly in number of individuals (11, 28, or 15), we found Tajima’s D statistic to vary. When all sequence types are included (11 or 28), we do not find a trend for demographic expansion (negative but not significantly different from zero); however, when only samples from Site 7 (peak occupation) are included, we find a significantly negative value, indicative of demographic expansion. Conclusions Our results suggest individuals buried at Verteba Cave had overall low mtDNA diversity, most likely due to increased conflict among sedentary farmers and nomadic pastoralists to the East and North. Early Farmers tend to show demographic expansion. We find different signatures of demographic expansion for the Tripolye people that may be caused by existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of the Tripolye Culture are more closely related to early European farmers and lack genetic continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.