Quantifying Yayoi and Jomon ancestry in Japanese

This paper attempts a difficult task: quantifying the relative influence of Yayoi agriculturalists and Jomon hunter gatherers on the population of Japan. While relatives to the early farmers of Japan can be traced to Korea or China, there are no known relatives of the Jomon people. This is different from the case of Latin Americans, where Amerindians have been largely absorbed in the Mestizo population, but populations with minimal European or African admixture persist. It is also different from the case of Indians, where the Ancestral South Indians have also been largely absorbed but their distant relatives in the Andaman Islands still exist.

This is an issue that will come up time and again: in Europe, for example, the hunter-gatherers disappeared thousands of years ago, and the extant population is apparently a mix of the two in proportions that remain to be determined. And, there were probably older, pre-Neolithic, episodes of admixture, as well, when different groups of modern humans expanded across the globa and mixed with older groups of modern humans, or, as it seems increasingly likely, with archaic humans as well.

It is sometimes possible to obtain ancient DNA from pre-contact individuals and determine their contribution to modern populations directly. However, there is still value in trying to extract this signal in the absence of ancient DNA, as was attempted for archaic Africans, and, in the current paper for the pre-agricultural Japanese. Hopefully, the latter can be eventually studied directly, and their genetic makeup can then be compared with their reconstruction in this paper.


The authors link the Jomon to modern Altaic populations of Siberia. There has already been ancient mtDNA work on the Jomon tying them to Siberia. On the other hand, the link to Altaic populations is intriguing, and I am wondering whether the authors' model (which uses Chinese and Koreans as farmer representatives) may not be actually representing as a substratum of the farmers, what may in fact be -at least partially- an Altaic superstratum.

Scientific Reports 2, Article number: 355 doi:10.1038/srep00355

Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data 

Yungang He et al.

The genetic origins of Japanese populations have been controversial. Upper Paleolithic Japanese, i.e. Jomon, developed independently in Japanese islands for more than 10,000 years until the isolation was ended with the influxes of continental immigrants about 2,000 years ago. However, the knowledge of origin of Jomon and its contribution to the genetic pool of contemporary Japanese is still limited, albeit the extensive studies using mtDNA and Y chromosomes. In this report, we aimed to infer the origin of Jomon and to estimate its contribution to Japanese by fitting an admixture model with missing data from Jomon to a genome-wide data from 94 worldwide populations. Our results showed that the genetic contributions of Jomon, the Paleolithic contingent in Japanese, are 54.3∼62.3% in Ryukyuans and 23.1∼39.5% in mainland Japanese, respectively. Utilizing inferred allele frequencies of the Jomon population, we further showed the Paleolithic contingent in Japanese had a Northeast Asia origin.

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