Unique characteristics of the Ainu population in Northern Japan

Jinam, Timothy A.; Kanzawa-Kiriyama, Hideaki; Inoue, Ituro; Tokunaga, Katsushi; Omoto, Keiichi; Saitou, Naruya

doi:10.1038/jhg.2015.79

Cited by 28 publications

(46 citation statements)

References 29 publications

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“…This was further supported by a genome-wide single nucleotide polymorphism (SNP) study that showed the Ainu and Ryukyuans cluster with 100% bootstrap probability on the phylogenetic tree (Jinam et al, 2012). Furthermore, autosomal SNP data also revealed signs of recent admixture between the Ainu and Hondo Japanese (Jinam et al, 2015).…”

Section: The Indigenous Groups Of Japanmentioning

confidence: 49%

“…2). The indigenous Ainu and Ryukyuan populations retain a genetic identity that most likely traces back to Jomon ancestors, while at the same time show indications of recent admixture with the Hondo Japanese (Jinam et al, 2015). Some questions remain unanswered, however, such as the origins of the Jomon people and the genetic affinities of the Yayoi people.…”

Section: Resultsmentioning

confidence: 99%

“…A follow-up to that study used a formal test for admixture (Patterson et al, 2012) to show that the Hondo Japanese are indeed the result of admixture between the ancestors of the Ainu and Han Chinese or Korean: the Jomon and Yayoi people, respectively. Furthermore, they estimated the proportion of Jomon component in the Hondo Japanese to be approximately 18% and that the admixture event occurred at least 1.4 KYA (Jinam et al, 2015). Other studies have tried to estimate the proportion of Jomon ancestry in the Japanese population.…”

Section: Origins Of the Hondo Japanese And Their Genetic Substructurementioning

confidence: 99%

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Human genetic diversity in the Japanese Archipelago: dual structure and beyond

2015

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The Japanese Archipelago stretches approximately 3,000 kilometers from Hokkaido in the north to the Ryukyu Islands in the south, and has seen human activity since at least 30 thousand years ago (KYA). The Jomon period from 16 to 3 KYA is associated with cord-marked pottery and the people at that time, who were hunter-gatherers, occupied a range of locations across the Japanese Archipelago. The Yayoi period from 3 to 1.7 KYA saw the introduction of migrants from the Asian Continent who brought rice agriculture to the archipelago. The dual-structure model, which is based on craniofacial measurements, proposes that admixture between the Jomon and Yayoi people resulted in current-day Japanese. Subsequent genetic studies using uniparental and autosomal markers in currentday and ancient human samples are widely in support of the dual-structure model. These genetic data have also unveiled the uniqueness of the indigenous Ainu and Ryukyuan people while further demonstrating the genetic substructure within the Mainland Japanese.

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Section: The Indigenous Groups Of Japanmentioning

confidence: 49%

Section: Resultsmentioning

confidence: 99%

Section: Origins Of the Hondo Japanese And Their Genetic Substructurementioning

confidence: 99%

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Human genetic diversity in the Japanese Archipelago: dual structure and beyond

2015

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“…We think this is an artifact of including close relatives in PCA, a well-known phenomenon. Indeed, a recent reanalysis by Jinam et al (2015) also found that exclusion of close relatives from the analysis removed this clustering pattern (Jinam et al 2015). We discuss this issue in more detail in Text S1.…”

Section: Discussionmentioning

confidence: 98%

Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu

2015

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Despite recent advances in population genomics, much remains to be elucidated with regard to East Asian population history. The Ainu, a hunter-gatherer population of northern Japan and Sakhalin island of Russia, are thought to be key to elucidating the prehistory of Japan and the peopling of East Asia. Here, we study the genetic relationship of the Ainu with other East Asian and Siberian populations outside the Japanese archipelago using genome-wide genotyping data. We find that the Ainu represent a deep branch of East Asian diversity more basal than all present-day East Asian farmers. However, we did not find a genetic connection between the Ainu and populations of the Tibetan plateau, rejecting their long-held hypothetical connection based on Y chromosome data. Unlike all other East Asian populations investigated, the Ainu have a closer genetic relationship with northeast Siberians than with central Siberians, suggesting ancient connections among populations around the Sea of Okhotsk. We also detect a recent genetic contribution of the Ainu to nearby populations, but no evidence for reciprocal recent gene flow is observed. Whole genome sequencing of contemporary and ancient Ainu individuals will be helpful to understand the details of the deep history of East Asians. KEYWORDS Jomon; Tibet; migration; demography T HE rapid development of genomic technologies has greatly enhanced our understanding of the history of modern human dispersal out of Africa and the peopling of different continents (Li et al. 2008;Green et al. 2010;Reich et al. 2010). However, the history of populations in East Asia, including Siberia, remains poorly understood even though they account for a large fraction of the human population (Stoneking and Delfin 2010;Oota and Stoneking 2011). There is still no clear consensus regarding basic questions such as when, where, and how many times modern humans migrated into East Asia and Siberia. For example, several previous studies based on contemporary samples concluded that one migration from south to north could explain the genetic structure of East Asians (Li et al. 2008; HUGO Pan-Asian SNP Consortium 2009). However, recent studies indicate that this scenario is too simplistic: a recent study detected western Eurasian ancestry in an individual in southern Siberia 24,000 years ago as well as a substantial contribution of this ancestry to the gene pool of Native Americans (Raghavan et al. 2014), and several studies detected a clear genetic differentiation between northeast Siberians and central-south Siberians, with the latter being more closely related to northeast Asians (Rasmussen et al. 2010;Fedorova et al. 2013). Indigenous high-altitude populations of the Tibetan plateau provide another example of East Asian populations that do not fit into the simple one migration hypothesis. Tibetans and Sherpa show a divergent history from lowland East Asian populations such as Han Chinese (Jeong et al. 2014), and their adaptive haplotype spanning the EPAS1 (endothelial PAS domain-containing prote...

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“…The first is that almost all of these studies (Hammer et al, 2006; Harihara, Hirai, & Omoto, 1986; Harihara et al, 1988; Horai et al, 1996; Jinam et al, 2015, 2012; Tajima et al, 2004) were based on modern‐day samples. Historically, after the Meiji government started sending settlers to Hokkaido as a national policy in 1869 (Fumoto, 2004), an enormous number of mainland Japanese migrated to Hokkaido, and their apparent genetic influence on the modern‐day Ainu was confirmed by a genome‐wide single‐nucleotide polymorphism (SNP) analysis by Jinam et al (2012).…”

Section: Introductionmentioning

confidence: 99%

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Adachi

Kakuda

Takahashi

et al. 2017

American J Phys Anthropol

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ObjectivesThe Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern‐day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large‐scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido.Materials and methodsMitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup‐defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations.ResultsOur findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.DiscussionOur results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual‐structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.

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Unique characteristics of the Ainu population in Northern Japan

Cited by 28 publications

References 29 publications

Human genetic diversity in the Japanese Archipelago: dual structure and beyond

Human genetic diversity in the Japanese Archipelago: dual structure and beyond

Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

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