Wednesday, February 1, 2017

Genetic Continuity From The Mesolithic Near Border Of Russia and Korea

Genetic continuity from the first wave farmers of the Neolithic era to the present is uncommon in Europe (Sardinia comes closest), and continuity from Mesolithic hunter-gatherer DNA to modern populations is almost unheard of in Europe. But, remarkably, two Mesolithic ancient DNA samples gathered near the border of Russia and North Korea are genetically similar to modern populations in the area.

I use the Western convention of calling hunter-gatherers on the eve of the food production era Mesolithic, rather the Neolithic, a term which in the Eastern convention is based upon pottery and basket use as a key litmus test. The paper notes that:
Early Neolithic societies in the Russian Far East, Japan, and Korea started to manufacture and use pottery and basketry 10.5 to 15 ka, but domesticated crops and livestock arrived several millennia later.  . . .
This site dates back to 9.4 to 7.2 ka, with the human remains dating to ~7.7 ka, and it includes some of the world’s earliest evidence of ancient textiles. The people inhabiting Devil’s Gate were hunter-fisher-gatherers with no evidence of farming; the fibers of wild plants were the main raw material for textile production. We focus our analysis on the two samples with the highest sequencing coverage, DevilsGate1 and DevilsGate2, both of which were female. The mitochondrial genome of the individual with higher coverage (DevilsGate1) could be assigned to haplogroup D4; this haplogroup is found in present-day populations in East Asia and has also been found in Jomon skeletons in northern Japan. For the other individual (DevilsGate2), only membership to the M branch (to which D4 belongs) could be established. . . .
We compared the individuals from Devil’s Gate to a large panel of modern-day Eurasians and to published ancient genomes. On the basis of PCA and an unsupervised clustering approach, ADMIXTURE, both individuals fall within the range of modern variability found in populations from the Amur Basin, the geographic region where Devil’s Gate is located, and which is today inhabited by speakers from a single language family (Tungusic). This result contrasts with observations in western Eurasia, where, because of a number of major intervening migration waves, hunter-gatherers of a similar age fall outside modern genetic variation.
We further confirmed the affinity between Devil’s Gate and modern-day Amur Basin populations by using outgroup f3 statistics in the form f3(African; DevilsGate, X), which measures the amount of shared genetic drift between a Devil’s Gate individual and X, a modern or ancient population, since they diverged from an African outgroup. Modern populations that live in the same geographic region as Devil’s Gate have the highest genetic affinity to our ancient genomes, with a progressive decline in affinity with increasing geographic distance (r2 = 0.756, F1,96 = 301, P < 0.001), in agreement with neutral drift leading to a simple isolation-by-distance pattern. 
The Ulchi, traditionally fishermen who live geographically very close to Devil’s Gate and are the only Tungusic-speaking population from the Amur Basin sampled in Russia (all other Tungusic speakers in our panel are from China), are genetically the most similar population in our panel. Other populations that show high affinity to Devil’s Gate are the Oroqen and the Hezhen—both of whom, like the Ulchi, are Tungusic speakers from the Amur Basin—as well as modern Koreans and Japanese. Given their geographic distance from Devil’s Gate, Amerindian populations are unusually genetically close to samples from this site, in agreement with their previously reported relationship to Siberian and other north Asian populations. . . . 
By analyzing genome-wide data from two early Neolithic East Asians from Devil’s Gate, in the Russian Far East, we could demonstrate a high level of genetic continuity in the region over at least the last 7700 years. The cold climatic conditions in this area, where modern populations still rely on a number of hunter-gatherer-fisher practices, likely provide an explanation for the apparent continuity and lack of major genetic turnover by exogenous farming populations, as has been documented in the case of southeast and central Europe. Thus, it seems plausible that the local hunter-gatherers progressively added food-producing practices to their original lifestyle. However, it is interesting to note that in Europe, even at very high latitudes, where similar subsistence practices were still important until very recent times, the Neolithic expansion left a significant genetic signature, albeit attenuated in modern populations, compared to the southern part of the continent. Our ancient genomes thus provide evidence for a qualitatively different population history during the Neolithic transition in East Asia compared to western Eurasia, suggesting stronger genetic continuity in the former region. These results encourage further study of the East Asian Neolithic, which would greatly benefit from genetic data from early agriculturalists (ideally, from areas near the origin of wet rice cultivation in southern East Asia), as well as higher-coverage hunter-gatherer samples from different regions to quantify population structure before intensive agriculture. 
The paper also conducts some interesting analysis of Korean and Japanese genetic informed by these new ancient genomes that largely support existing paradigms and suggest genetic connections between the Devil's Gate Mesolithic population and the Jomon of Japan.
The close genetic affinity between Devil’s Gate and modern Japanese and Koreans, who live further south, is also of interest. It has been argued, based on both archaeological and genetic analyses, that modern Japanese have a dual origin, descending from an admixture event between hunter-gatherers of the Jomon culture (16 to 3 ka) and migrants of the Yayoi culture (3 to 1.7 ka), who brought wet rice agriculture from the Yangtze estuary in southern China through Korea. The few ancient mtDNA samples available from Jomon sites on the northern Hokkaido island show an enrichment of particular haplotypes (N9b and M7a, with D1, D4, and G1 also detected) present in modern Japanese populations, particularly the Ainu and Ryukyuans, as well as southern Siberians (for example, Udegey and Ulchi). The mtDNA haplogroups of our samples from Devil’s Gate (D4 and M) are also present in Jomon samples, although they are not the most common ones (N9b and M7a). Recently, nuclear genetic data from two Jomon samples also confirmed the dual origin hypothesis and implied that the Jomon diverged before the diversification of present-day East Asians. 
We investigated whether it was possible to recover the Northern and Southern genetic components by modeling modern Japanese as a mixture of all possible pairs of sources, including both modern Asian populations and Devil’s Gate, using admixture f3 statistics. The clearest signal was given by a combination of Devil’s Gate and modern-day populations from Taiwan, southern China, and Vietnam, which could represent hunter-gatherer and agriculturalist components, respectively. However, it is important to note that these scores were just barely significant (−3 < z < −2) and that some modern pairs also gave negative scores, even if not reaching our significance threshold (z scores as low as −1.9). 
The origin of Koreans has received less attention. Also, because of their location on the mainland, Koreans have likely experienced a greater degree of contact with neighboring populations throughout history. However, their genomes show similar characteristics to those of the Japanese on genome-wide SNP data and have also been shown to harbor both northern and southern Asian mtDNA and Y chromosomal haplogroups. Unfortunately, our low coverage and small sample size from Devil’s Gate prevented a reliable estimate of admixture coefficients or use of linkage disequilibrium–based methods to investigate whether the components originated from secondary contact (admixture) or continuous differentiation and to date any admixture event that did occur. 
The abstract and citation to the paper are as follows: 
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. 
We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
Siska et al., Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago, 3(2) Science Advances e1601877 (February 1, 2017) (open access).

Hat Tip to Eurogenes.

No comments: