Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations

Infrared thermography unveiled the variation of brown adipose tissue thermogenesis among East Asian adults

The thermogenesis of brown adipose tissue (BAT) is interesting because the contribution to human adaptation to cold and obesity resistance has been suggested. 18F-fluorodeoxyglucose-positron emission tomography/computed tomography (FDG-PET/CT) is a common method for measuring BAT activity; however, it has been studied in few large cohorts due to concerns about safety and cost. Studies using alternative methods make it challenging to directly compare BAT activity among studies and interpret those results because the procedure is various. We measured the supraclavicular BAT thermogenesis of 122 healthy Japanese and Chinese adults under mild cold stress using standardized infrared thermography (IRT) and examined the effects of various factors on BAT variation. BAT thermogenesis was significantly higher in females than in males (p < 0.001) and significantly higher in Chinese than in Japanese individuals (p < 0.05). Among the 27 participants enrolled in both summer and winter experiments, BAT thermogenesis increased during winter (p < 0.05) only in Japanese participants. Additionally, individuals born at higher latitudes exhibited greater BAT thermogenesis (p < 0.05), suggesting the involvement of genetic background or cold exposure in early life stages. We obtained interesting anthropological and physiological findings with the use of non-invasive IRT.

Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago

Mainland Japanese have been recognized as having dual ancestry, originating from indigenous Jomon people and immigrants from continental East Eurasia. Although migration from the continent to the Japanese Archipelago continued from the Yayoi to the Kofun period, our understanding of these immigrants, particularly their origins, remains insufficient due to the lack of high-quality genome samples from the Yayoi period, complicating predictions about the admixture process. To address this, we sequenced the whole nuclear genome of a Yayoi individual from the Doigahama site in Yamaguchi prefecture, Japan. A comprehensive population genetic analysis of the Doigahama Yayoi individual, along with ancient and modern populations in East Asia and Northeastern Eurasia, revealed that the Doigahama Yayoi individual, similar to Kofun individuals and modern Mainland Japanese, had three distinct genetic ancestries: Jomon-related, East Asian-related, and Northeastern Siberian-related. Among non-Japanese populations, the Korean population, possessing both East Asian-related and Northeastern Siberian-related ancestries, exhibited the highest degree of genetic similarity to the Doigahama Yayoi individual. The analysis of admixture modeling for Yayoi individuals, Kofun individuals, and modern Japanese respectively supported a two-way admixture model assuming Jomon-related and Korean-related ancestries. These results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula.

(Not So) Lost in Translation: Considering the GA4GH Diversity in Datasets Policy in the Japanese Context

The genomics community has long acknowledged the lack of diversity in datasets used for research, prompting various stakeholders to confront this issue. In response, the Global Alliance for Genomics and Health (GA4GH) formulated a policy framework that recognizes the multiplicity of perspectives on diversity and proposed a systemic approach for more optimal data diversity. Given the importance of the research context, assessing this policy's applicability within countries where diversity is less discussed is important. This study investigated the feasibility of implementing the GA4GH policy in Japan, a nation with a smaller genetic diversity than many Western countries. As the proportion of East Asian genomic research is limited internationally, focusing on the Japanese genome contributes to enhancing diversity. Meanwhile, labelling findings as "Japanese" can inadvertently reinforce perceptions of homogeneity and overlook ethnic minorities. Regions and socioeconomic status are also recognized as substantial factors of diversity within academia, yet concerns persist among the public regarding the heritability of stigmatized conditions. Social inclusion of sexual minorities has begun in Japan, but research surveys generally still use binary sex and gender categories, which underscores the need for additional variables. This study found that both academia and the public need to confront the overemphasis on homogeneity within Japanese society and hesitancy in addressing genetic factors. By doing so, more inclusive and diverse datasets can advance the field both ethically and scientifically. Perhaps the most important impact of the GA4GH policy will be to draw greater attention to the complex diversity challenges ahead in Japan.

Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan

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.

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.