The evolving Japanese: the dual structure hypothesis at 30

A biogeographical ancestry inference pipeline using PCA-XGBoost model and its application in Asian populations

Biogeographical ancestry (BGA) inference plays a crucial role in genetics, anthropology, forensic science, and medical research. Current methods like principal component analysis (PCA) and ADMIXTURE, based on single nucleotide polymorphisms, are commonly used. Here, we introduce a bio-geographical ancestry inference pipeline that integrates prior population structure and clustering. Our pipeline first analyzes genetic structure on cleaned data to obtain optimal parameters and classification model labels. An XGBoost (eXtreme Gradient Boosting) classification model is constructed using principal components from PCA, and model predictions are evaluated with LR (likelihood ratio). The pipeline was applied to a dataset of Asian populations, with a first prediction accuracy of 96.27 % achieved. The LR-based evaluation accuracy reached 98.96 %, showing an improvement of 2.69 % with the introduction of LR assessment. This highlights the robust predictive capability of our pipeline and the improved accuracy in evaluation with LR. This successful application will benefit genetic research, human history studies, and criminal investigations. Additionally, the pipeline's versatility allows application to new datasets.

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.

A 3000-year-old founder variant in the DRC1 gene causes primary ciliary dyskinesia in Japan and Korea

Primary ciliary dyskinesia (PCD) is a genetic disorder characterized by ciliary structural abnormalities and dysfunction, leading to chronic rhinosinusitis, otitis media with effusion, bronchiectasis, and infertility. Approximately half of Japanese PCD cases are attributed to variants in the dynein regulatory complex subunit 1 (DRC1) gene, predominantly featuring homogeneous deletions of exons 1-4 spanning 27,748 base pairs on chromosome 2. Here, we report 10 new PCD cases (9 families) in addition to 29 previously reported cases (24 families) caused by DRC1 variants. Among these 39 cases, biallelic DRC1 exon 1-4 deletions were detected in 38 (97.4%). These DRC1 deletions exhibited an identical breakpoint in all PCD cases in the Japanese and Korean populations, strongly suggesting a founder effect. In this study, we performed haplotype analysis, using a whole-exome sequencing dataset of 18 Japanese PCD patients harboring large biallelic DRC1 deletions. We estimated that the founder allele likely emerged 115.1 generations ago (95% confidence interval: 33.7-205.1), suggesting an origin of approximately 3050 years ago, coinciding with the transition from the Jomon period to the early Yayoi period in Japan. Considering the formation of the modern Japanese population, the founder with the DRC1 exon 1-4 deletion likely lived on the Korean peninsula, with the allele later transmitted to Japan through migration. This study provides insights into the origin of the DRC1 copy number variant, the most frequent PCD variant in the Japanese and Korean populations, highlighting the importance of understanding population-specific genetic variations in the context of human migration and disease prevalence.

Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations.

Culinary continuity in central Japan across the transition to agriculture

Rice and millet arrived in Western Japan from Korea around 3,000 years ago and spread eastwards across the archipelago in the next 700 years. However, the extent to which agriculture transformed traditional Jōmon hunter-gatherer-fisher communities is debated. Central Japan is a key area of study as remodelling of radiocarbon dates shows a slowdown in the dispersal rate of rice agriculture in this area. Here, we examine and compare the use of pottery by Final Jōmon and Early to Middle Yayoi communities in the Tōkai and the Central Highland regions of central Japan, using lipid residue analysis. Although the identification of specific biomarkers for rice remains elusive, an increase in the ratio of E/H C18 APAAs with the arrival of rice and millet indicates a potential change in plant processing and consumption. We were also able to identify biomarkers for broomcorn millet (miliacin) in both Final Jōmon and Yayoi pottery. However, evidence for millet consumption is sparse and in all cases was likely mixed with wild hunted and foraged foods. We conclude therefore that, despite the introduction of rice and millet agriculture in central Japan, pre-existing diets and culinary habits of Jōmon hunter-gatherers remain important.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12520-024-01992-9.

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.

The importance of wild resources as a reflection of the resilience and changing nature of early agricultural systems in East Asia and Europe

We examine the changing importance of wild starch rich plant staples, predominantly tree nuts, in early agricultural societies in East Asia and Europe, focusing on Korea, Japan, and Britain. A comparative review highlights variations in the importance of wild plant staples compared to domesticated crops. The Korean Middle to Late Chulmun periods (c. 3,500–1,500 BC) was characterized by a high reliance on nuts alongside millet. This declines with the transition to rice agriculture, but remains significant during the Mumun period (c. 1,500–300 BC). In Japan, the arrival of rice and millets in the Yayoi Period (c. 1,000 BC−250 AD) saw continued evidence for high levels of reliance on wild resources, which declines only in the Kofun and early historical periods. In Early Neolithic Britain (c. 4,000–3,300 BC) cereal agriculture is accompanied by high evidence for wild plant foods. But during the Middle to Late Neolithic (3,300–c. 2,400/2,200 BC) cereals were abandoned on the mainland with hazelnuts becoming a prominent plant staple. Agriculture returned in the second half of the 3rd millennium BC, followed by a strong decline in wild plant food use during the Middle to Late Bronze Age (1,700–700 BC). Such patterns have previously been attributed to the slow adoption of farming by indigenous peoples, with a continued reliance on wild resources. In light of evidence demonstrating that the dispersal of agriculture was largely driven by a mixture of demic-diffusion and introgression of hunter-gatherers into agricultural groups, a reinterpretation of the role of wild foods is needed. It is argued that the relative importance of wild plant staples provides an indicator of the stability and dependability of agricultural and social systems. A heavy reliance on wild foods in early agricultural societies is tied to the slow adaptation of domesticated crops to new environments, where agricultural and social landscapes are yet to be firmly established, and social systems that could mitigate for poor harvests and storage were often absent. The retained lengthy persistence of wild plant staples in East Asian subsistence systems compared to the British Isles likely reflects differences in the ecological and labor demands for rice compared to Western Asiatic cereals.

Bayesian analyses of direct radiocarbon dates reveal geographic variations in the rate of rice farming dispersal in prehistoric Japan

The adoption of rice farming during the first millennium BC was a turning point in Japanese prehistory, defining the subsequent cultural, linguistic, and genetic variation in the archipelago. Here, we use a suite of novel Bayesian techniques to estimate the regional rates of dispersal and arrival time of rice farming using radiocarbon dates on charred rice remains. Our results indicate substantial variations in the rate of dispersal of rice within the Japanese islands, hinting at the presence of a mixture of demic and cultural diffusion, geographic variations in the suitability of its cultivation, and the possible role of existing social networks in facilitating or hindering the adoption of the new subsistence economy.

Demography, trade and state power: a tripartite model of medieval farming/language dispersals in the Ryukyu Islands

Hunter-gatherer occupations of small islands are rare in world prehistory and it is widely accepted that island settlement is facilitated by agriculture. The Ryukyu Islands contradict that understanding on two counts: not only did they have a long history of hunter-gatherer settlement, but they also have a very late date for the onset of agriculture, which only reached the archipelago between the eighth and thirteenth centuries AD. Here, we combine archaeology and linguistics to propose a tripartite model for the spread of agriculture and Ryukyuan languages to the Ryukyu Islands. Employing demographic growth, trade/piracy and the political influence of neighbouring states, this model provides a synthetic yet flexible understanding of farming/language dispersals in the Ryukyus within the complex historical background of medieval East Asia.

The emergence of 'Transeurasian' language families in Northeast Asia as viewed from archaeological evidence

From a linguistic standpoint, Proto-Japonic and Proto-Koreanic are assumed to have split off the Transeurasian languages in southern Manchuria. The linguistic idea that Proto-Japonic came earlier than Proto-Koreanic in the chronological scheme means that the Proto-Japonic language first entered the Korean Peninsula, and from there spread to the Japanese archipelago at the beginning of the Yayoi period, around the ninth century BC, while the arrival of Proto-Koreanic in southern Korea is associated with the spread of the rolled rim vessel culture around the fifth century BC. The genealogical sequence of the Pianpu, Mumun and Yayoi cultures, which shared the same pottery production techniques, indicates the spread of Proto-Japonic. On the other hand, migrants moved from Liaodong to the Korean Peninsula and established the rolled rim vessel culture. This population movement was probably due to social and political reasons as the Yan state enlarged its territory eastward. The Proto-Koreanic of the rolled rim vessel culture later spread to the Korean Peninsula and gradually drove out Proto-Japonic, becoming the predecessor of the Koreanic. In this paper, I examine the spread of Proto-Japonic and Proto-Koreanic in Northeast Asia based on archaeological evidence, focusing especially on the genealogy of pottery styles and pottery production techniques.

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.

Some observations on the transeurasian language family, from the perspective of the Farming/Language Dispersal Hypothesis

During my attendance at the 'Transeurasian Millets and Beans, Words and Genes' conference in Jena (January 2019), Martine Robbeets invited me to comment on the articles that are published in this Special Collection in the journal Evolutionary Human Sciences. My comments are focused on the seven articles that deal with the 'Farming/Language Dispersal Hypothesis', one of the key theoretical constructs discussed during the conference. I consider how the hypothesis might aid an understanding of the prehistory and early history of the Transeurasian language family.

About millets and beans, words and genes

In this special collection, we address the origin and dispersal of the Transeurasian languages, i.e. Japonic, Koreanic, Tungusic, Mongolic and Turkic, from an interdisciplinary perspective. Our key objective is to effectively synthesize linguistic, archaeological and genetic evidence in a single approach, for which we use the term 'triangulation'. The 10 articles collected in this volume contribute to the question of whether and to what extent the early spread of Transeurasian languages was driven by agriculture in general, and by economic reliance on millet cultivation in particular.