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 Tianluoshan—a 7,000-y-old rice cultivation village in the lower Yangtze River valley, China—using 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.
Archaeological evidence indicates that dogs appeared in Japan at least 9300 years ago, during the Jomon period. The Jomon period dogs (Jomon dogs) retained the morphological characteristics of ...ancient domestic dogs throughout the Jomon period, possibly due to their geographical isolation from continental dogs. Therefore, we expect them to retain the genetic characteristics of ancient domestic dogs. To explore this possibility, we determined the mitochondrial genomes of five Jomon dogs, including one of the oldest dogs in Japan (7400–7200 cal BP), and seven late-8th-century Japanese dogs (Suwada dogs). We analyzed these sequences with 719 mitochondrial genomes of ancient and modern canids. The dog mitochondrial DNA (mtDNA) sequences have been grouped into six clades (haplogroups A–F), and clade A comprises six sub-clades (sub-haplogroups A1–A6). Classification of the Jomon dogs’ mtDNA haplotypes revealed that these dogs belong to a nested A2/A3 sub-haplogroup not shared by other modern or ancient samples. The mtDNA sequences of Jomon dogs form a monophyletic clade which is sister to the A3 sub-clade in the phylogenetic trees. Network analysis showed that the Jomon dogs’ mtDNA sub-clade diverged close to the base of the A2 and A3 haplotype network, which was centered by an ancient dog from South China. The Jomon dog mtDNAs diverged from A3 (~11500 years ago) soon after the A2 and A3 divergence (~12800 years ago), indicating early divergence of the Jomon dogs’ sub-clade. These results suggest that the Jomon dogs were possibly introduced into the Japanese archipelago 11500–9300 years ago. The mtDNAs of late-8th-century dogs were more diverse and were different haplogroups than that of Jomon dogs, suggesting that other haplogroups likely replaced the haplogroup of Jomon dogs through the introduction of dogs that accompanied the migration of people into Japan in later periods.
A draft whole genome sequence of a Jomon woman from the Ikawazu shell-mound site has been reported recently. The adult woman, IK002, was excavated with a child, IK001. Because of the burial situation ...with the child located above the adult, the two individuals were thought to be a mother–child relationship. In this study, we conducted a target capture sequencing, and obtained 258-fold coverage of the complete mitochondrial (mt) genome sequence of IK001. Comparing the mtDNA nucleotide sequences of IK001 and IK002, we found these were unambiguously different from each other. Thus, the mitogenome sequence analysis clarified that both have a non-mother–child relationship. This result sheds new light on the relationship between burial and kinship in Jomon archaeology.
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.
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.
The life history of a female individual skeleton (ST61) from the Edo period (AD 1603–1868) 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 C4 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.
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient ...hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
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•Genomic imputation accurately brings ancient Asian genomes to higher coverages•Selection scans of imputed genomes reveal adaptive evolution in the ancient Jomon•Well-known adaptive variants in Asia (EDAR/ADH1B/ALDH2) emerged post-agriculture
Genomics; Anthropology
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.
Abstract 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 is 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.
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.
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