Jomon are in between Australoids and Southeast Asians and related to Denisovans

[Goujian]

Ancient genomic DNA analysis of Jomon people

http://ir.soken.ac.jp/?action=repository_uri&item_id=4960&file_id=19&file_no=2

http://s9.postimg.org/rrbp2n4gf/Asian_Genetics.png


To investigate the genetic relationship among two Jomons and HGDP-CEPH East
Eurasians, Melanesians, and Native Americans I carried out PCA. I observed that two Jomon
individuals clustered with present-day East Eurasians, but they were relatively closer to
Melanesians than other East Eurasians (Figure 4.5a).

No European gene flow was observed in Shikkariabe Jomons as well as Sanganji
Jomons.

Finally, one of the most important discoveries is the existence of genetic
relationship between Jomon people and archaic humans. I observed the genetic relationship
between not only Jomon and Vindija Neanderthal but also Jomon and Denisovan.


The existence of Denisovan DNA material in Jomon people will be one of the center of debate
connected to not only the history of Japanese but also the origin and population structure of East
Eurasian.

[curupira]

Interesting, thanks for posting.

[easy772]

I’ve been seeing a lot of misinterpretation/oversimplification of this paper all over the internet. I thought I’d link to the actual paper and post the abstract to clarify. The author is not saying Jomon were primarily Melanesian or even Southeast Asian.

Abstract:
Clarifying the genetic relationship between Neolithic East Asian Hunter-Gatherers and modern human populations is one of the keystones to understand the complex history of modern East Eurasian populations. Neolithic hunter-gatherers, Jomon people, inhabited the Japanese Archipelago from 16,000 years ago, and while their origin and relationship with modern humans have been long debated, details remain unclear. To solve these questions, I investigated mitochondrial DNA and nuclear DNA of Jomon individuals excavated from Sanganji Shell Mound, Fukushima Prefecture, Tohoku region, Japan. I decided mitochondrial DNA haplotypes from four Sanganji Jomon individuals, and conducted statistical analyses. I found that their mitochondrial DNA haplotypes, M7a and N9b, were unique to modern Japanese. When I compared frequencies of mitochondrial DNA haplotypes of modern East Eurasians and other Jomon populations which were previously reported, I observed that Northern Jomon people were genetically closer to Udegey of Southern Siberia than other continental East Eurasians. This implies that Northern Jomon people originated from Northeast Asia. Microblade culture with Araya type burin was introduced from Northeast Asia into Japanese Archipelago via Sakhalin in the Upper Paleolithic period. The genetic similarity among Northern Jomon people and modern Southern Siberian is therefore plausible. I also found that Jomon people were genetically heterogeneous in terms of their geographical regions. It is not clear whether this heterogeneity indicates the multi-origin or sub-structure of Jomon people. For investigating their origin and relationship with modern humans based on genomic DNAs, I sequenced 60 million base pairs of nuclear Jomon genomes with next generation sequencer, GAIIx and Hiseq 2000. The Jomon genomic DNA clearly evidenced that Neolithic Jomon people were genetically isolated from modern East Eurasians for a long time, and they diverged from the ancestors of both northern and southern East Eurasians but postdated the divergence of East Eurasian and Melanesians. It implies that the genetic structure of modern East Eurasians was formed after the divergence of Jomon people ancestors and other East Eurasians. Another conclusion is that Jomon genomic DNAs were highly inherited to Ainu people and Okinawa people, who live in Northern and Southern part of the Japanese Archipelago, respectively, compared to Mainland people. The finding supports the dual structure model proposed by Hanihara Kazuro and others based on craniofacial data analyses. Another controversial issues are the genetic relationship between archaic humans and modern humans. Using phylogenetic network analysis and D-statistic analysis, I observed that Jomon people and other non-Africans shared more derived alleles with Vindija Neanderthal than Africans. The sharing confirms the existence of archaic gene flow from Vindija Neanderthal into the ancestors of modern non-Africans. Furthermore, I also detected Denisovan gene flow into not only Melanesians but also to Sanganji Jomon and Dai ethnic minority group of Southern China, while Ainu people as well as modern East Asians did not show a sign of the gene flow. This indicates that first migrants from Sundaland into East Asia had genetic components of Denisovan, but the remnants were diluted or disappeared in modern East Asians. The Denisovan DNA in East Eurasians and Melanesians is a footprint of early modern human migration into East Eurasia. The heterogeneity of Jomon people in mitochondrial DNA implies the complexity of the Jomon history. To investigate whether Jomon people from different regions and period were genetically heterogeneous, I sequenced more Jomon genomes from four samples; Shikkariabe Jomon from Aomori Prefecture, Yugura Jomon from Nagano Prefecture, Daizenno-Minami Jomon from Chiba Prefecture, and Odake Jomon from Toyama Prefecture, respectively. I successfully sequenced about 10% and 80% of Jomon nuclear genomes from Yugura Jomon and Shikkariabe Jomon DNA samples, respectively. Using principal component analysis, I found that Jomon people were homogeneous at least in northern part of the Japanese Archipelago. The small pairwise distance between Shikkariabe Jomon and Yugura Jomon also supports their homogeneity. I also investigated the genetic relationship between Shikkariabe Jomon and archaic humans to examine whether Jomon people really have more Denisovan DNA materials than other East Eurasians. Using principal component analysis, phylogenetic network, and D-statistic analysis, I confirmed the evidence of Denisovan gene flow into the ancestors of Shikkariabe Jomon people. I also sequenced the genome of Upper Paleolithic Ryukyuan, who lived ca. 20,000 years ago, to investigate the earlier stages of human migration into the Japanese Archipelago, and the genetic relationship between Upper Paleolithic humans and Jomon people. I obtained 0.03% of the whole genome, and informative SNPs were limited. Despite of this small dataset, I observed a genetic similarity between Jomon and Paleolithic Ryukyuan. I speculate that both Jomon people and Paleolithic Ryukyuan share same ancestors, who migrated from Southeast Asia into East Asia. In summary, I observed that Jomon people were genetically quite unique in East Eurasia, and it suggests that Jomon people were the descendants of early stage of humans who migrated into East Asia. The finding indicates that Jomon people are very important populations to clarify how early modern humans migrated into East Asia. A draft sequence of the Shikkariabe Jomon genome made me possible to compare the Jomon genome with other ancient and modern human genomes. This will certainly deepen the understanding the history of not only modern Japanese and Jomon people but also East Eurasians and Native Americans. Part of the Jomon genome from several individuals approached to the truth of their population structure (homogeneous or heterogeneous). In addition, genome sequences from 20,000 year-old Upper Paleolithic Ryukyuan will accelerate the elucidation of genetic relationship between Upper Paleolithic Japanese and Jomon/present-day individuals. Finally, one of the most important things is the genetic relationship between Jomon people and archaic humans. I observed the genetic relationship not only between Jomon and Vindija Neanderthal but also between Jomon and Denisovan. Since the conclusion of this study is based on partial sequences of the Jomon genome, further analyses with more genome sequence data and other statistical methods are necessary in future studies. The existence of Denisovan DNA material in Jomon people will be one of the main debates connected to not only the history of Japanese but also the origin and population structure of East Eurasians.

Full Paper:
http://www.docdroid.net/u5oq/a1684.pdf.html

[Iloko]

I'm reading the full paper now, this is mighty fascinating stuff!

[coolstorybro]

Tl:dr

I guess what this study says is that Jomon share an ancestry with the people who went on to colonize North America, the mixed Native Americans, who genetic testing proves to have as much as 1/3 west europe hunter gatherer. The mix took place in Siberia. Jomon went south and Amerindians went east.

[nicalandia]

Tl:dr

I guess what this study says is that Jomon share an ancestry with the people who went on to colonize North America, the mixed Native Americans, who genetic testing proves to have as much as 1/3 west europe hunter gatherer. The mix took place in Siberia. Jomon went south and Amerindians went east.
I agree

[Iloko]

The Jomon were Proto-Mongoloid: https://en.wikipedia.org/wiki/Proto-Mongoloid