Modern Japanese people arose from 3 ancestral groups, 1 of them unknown: DNA study

[Russki]

https://www.livescience.com/archaeology/...y-suggests

https://pubmed.ncbi.nlm.nih.gov/38630824/

Modern Japanese people largely originated from three ancestral groups and carry ancient DNA that may influence their risk of developing certain diseases, genetic analyses suggest.


A large new study has revealed new insight into the evolutionary history of Japanese people. (Image credit: Grant Faint via Getty Images)


Modern Japanese people largely descend from three ancestral groups, a new study suggests. The research also reveals genetic ties with our closest extinct relatives — the Neanderthals and Denisovans — and how these genes may affect present-day disease risk.

In one of the largest non-European analyses of its kind, scientists sequenced the DNA of more than 3,200 Japanese people across seven regions of the country, extending from the snowy mountains of Hokkaido in the north to the subtropical southern shores of Okinawa.

The researchers collated these genetic data, along with relevant clinical information, into a large new database called the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL).

The team discovered that modern Japanese people mostly descended from three ancestral groups: Neolithic Jomon hunter-gatherers; a group believed to have been the ancient predecessors of the Han Chinese; and an unidentified group with ties to Northeast Asia. This finding further challenges a contested, three-decades-long hypothesis that Japanese people originated from the Jomon people and, later, rice-farming Yayoi migrants from continental Asia.

The new analysis also revealed 42 pieces of DNA that Japanese people inherited from Neanderthals and two from Denisovans that could be linked to complex traits, meaning those that are encoded by multiple genes. This inheritance was likely the result of earlier interbreeding events between these ancient groups and early Homo sapiens, the authors wrote in the paper.

Denisovan-derived DNA within a gene called NKX6-1 was associated with the development of type 2 diabetes (T2D), and within the gene POLR3E, it was tied to height, the authors found. Eleven Neanderthal-derived DNA sequences were found to be associated with seven diseases, including T2D, coronary artery disease, prostate cancer and the inflammatory disorder rheumatoid arthritis. Most of these 44 chunks of ancient DNA are unique to East Asians, the authors said.

Until recently, large-scale genetic sequencing research has focused on analyzing DNA from people of European descent, leaving a significant gap in our understanding of other human populations, including those in Asia. Therefore, the new findings may provide some long-coveted answers.

"This comprehensive genetic dataset enables us to delve into uncharted territories concerning population and medical genetics of the Japanese population," the authors wrote in a paper describing their findings, published Wednesday (April 17) in the journal Science Advances.

These discoveries could even supplement research that could lead to the development of personalized medicine, the authors wrote.

For instance, the team identified gene mutations that could be clinically important within the Japanese population. One notable example is a mutation in a gene called PTPRD that was found in six people in the cohort. Clinical information was available for three of these individuals, who experienced several of the same health conditions, including having heart attacks, kidney failure and high blood pressure.

JEWEL will serve as a "reference for future genetic research within and beyond the Japanese population," the study authors concluded.

[qijia]

https://pubmed.ncbi.nlm.nih.gov/38630824/

The team discovered that modern Japanese people mostly descended from three ancestral groups: Neolithic Jomon hunter-gatherers; a group believed to have been the ancient predecessors of the Han Chinese; and an unidentified group with ties to Northeast Asia. This finding further challenges a contested, three-decades-long hypothesis that Japanese people originated from the Jomon people and, later, rice-farming Yayoi migrants from continental Asia.

I cannot access the paper. Considering chinese paper 2020, I think modern japanese has more common denominators with chinese than with korean:




 especially see C- present day : modern japanese has more brighter green color than modern chinese:


Fig. 3 Ancestry localized to the north and south in the Early Neolithic is found in admixed form across northern and southern East Asia today.
(A to C) A heatmap showing f4(Mbuti, X; Qihe, Bianbian), where Bianbian is the oldest northern East Asian sampled (~9500 cal yr B.P.) and Qihe is the oldest southern East Asian sampled (~8400 cal yr B.P.). X are East and Southeast Asians who date to the Early Neolithic (A), Late Neolithic (B), or present day ©. Green indicates more affinity to Early Neolithic northern East Asians, whereas blue indicates greater affinity to Early Neolithic southern East Asians. Numerical values can be found in table S5A. kBP, thousand calibrated years before the present. (D to F) Ancestry proportions estimated for Neolithic and present-day individuals. Possible ancestries are northern East Asian (green), southern East Asian (blue), Paleosiberian (light green), Hòabìnhian (orange), and Jōmon (light blue). Proportions were determined using qpAdm (15), with representative sources and outgroups described in (14). During the Neolithic, there was a division between East Asians north and south of the Qinling-Huaihe line (dark gray line on map) in ancestry; but in the present day, ancestries previously localized to only northern or southern East Asia can be found in appreciable frequencies in both regions. Results for present-day Han are in fig. S13 and point values are in table S6. Labels on the map indicate the populations listed in table S1.

https://www.science.org/doi/10.1126/scie...%200pubmed

[Neoroad]

I cannot access the paper.

https://www.science.org/doi/10.1126/sciadv.adi8419

[CLTVTE]

 especially see C- present day : modern japanese has more brighter green color than modern chinese:


Fig. 3 Ancestry localized to the north and south in the Early Neolithic is found in admixed form across northern and southern East Asia today.
(A to C) A heatmap showing f4(Mbuti, X; Qihe, Bianbian), where Bianbian is the oldest northern East Asian sampled (~9500 cal yr B.P.) and Qihe is the oldest southern East Asian sampled (~8400 cal yr B.P.). X are East and Southeast Asians who date to the Early Neolithic (A), Late Neolithic (B), or present day ©. Green indicates more affinity to Early Neolithic northern East Asians, whereas blue indicates greater affinity to Early Neolithic southern East Asians. Numerical values can be found in table S5A. kBP, thousand calibrated years before the present. (D to F) Ancestry proportions estimated for Neolithic and present-day individuals. Possible ancestries are northern East Asian (green), southern East Asian (blue), Paleosiberian (light green), Hòabìnhian (orange), and Jōmon (light blue). Proportions were determined using qpAdm (15), with representative sources and outgroups described in (14). During the Neolithic, there was a division between East Asians north and south of the Qinling-Huaihe line (dark gray line on map) in ancestry; but in the present day, ancestries previously localized to only northern or southern East Asia can be found in appreciable frequencies in both regions. Results for present-day Han are in fig. S13 and point values are in table S6. Labels on the map indicate the populations listed in table S1.

https://www.science.org/doi/10.1126/scie...%200pubmed

It should be mentioned that the above Chinese article from July 17, 2020, was accompanied by one more Chinese article from July 17, 2020:

Human evolutionary history in Eastern Eurasia using insights from ancient DNA
Ming Zhang, Qiaomei Fu
DOI: 10.1016/j.gde.2020.06.009

In this second article, it was shown that components, named here “Early East Asia” (Tibetan lineage), “Inland nEast Asia”, “Coastal sEast Asia”, separated from each other less than 20000 years ago, which means that these three components started to distribute well within the Chinese Late Paleolithic after the Last Glacial Maximum, so they are not suitable, for example, for understanding of the earlier distribution of Early Upper Paleolithic (that is, starting from ca. 38000 years ago) inland and sea coastal populations in China.

Since all ancient individuals of the three mentioned main lineages and related lineages were included in “populations of East Asian ancestry” in the main text of the first Chinese article, relative to the Chinese articles, it is intriguing to understand the meaning of the “Northeast Asian ancestry”, mentioned in the new Japanese article as distinct from “East Asian ancestry”, while both “Northeast Asian ancestry” and “East Asian ancestry” separated from “Japan Jōmon” in the new Japanese article’s Japanese references. In any case, neither this Japanese article, nor the Chinese article do not mention any existence of any “typically North Asian component”.

Some Jōmon period’s mtDNA lineages from Japan were reported as “mtDNA M7bc” in “Genetic structure of the Japanese and the formation of the Ainu population”, which may be hypothetically interpreted as the existence of cases of the deep and thus very ancient mtDNA M7bc (because “ancestors” of M7b and M7c split ca. 42000 years ago), unless some of these cases belong to already separated mtDNA M7b and M7c. In China, in “Human population history at the crossroads of East and Southeast Asia since 11,000 years ago”, already-separated cases of both mtDNA M7b and mtDNA M7c were only reported together from the ancient DNA of the Guangxi Province so far, while “the separation of Longlin-related and Baojianshan-related [Guangxi] ancestries from Early Neolithic Shandong and Fujian East Asians occurred more recently than that of Tianyuan-, Onge-, Papuan-, and Hòabìnhian-related ancestries. Longlin, Early Neolithic Shandong and Fujian East Asians, and the Jōmon, however, are similarly related.” In that article, the existence of the deep Early Upper Paleolithic period’s Baojianshan-related ancestry was mediated by the Early Neolithic Dushan specimen, whose site had an earlier Late Palaeolithic layer.

In addition to mtDNA M*-related Minatogawa specimen (possibly akin to mtDNA M32’56, since one of its mtDNA relatives from “Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences” was reported as belonging to mtDNA M32’56 https://www.theytree.com/mttree/M32'56), the most ancient DNA from the Pre-Jōmonese period of Japan was reported from the site of Shiraho Saonetabaru of the Ryukyu Islands. Its specimens had the age, comparable to the age of separation of “Northeast Asian ancestry” and “East Asian ancestry” from “Japan Jōmon” in the new Japanese article’s Japanese references. They include (https://press-files.anu.edu.au/downloads...f/ch03.pdf):
[1] Three mtDNA M7a specimens dated to 20000 years ago (uncalibrated), 9000-16000 years ago (uncalibrated) and 4574-4452 years ago (calibrated). However, basal subclades of mtDNA M7a* were not reported from mainland East Asia and geographic mainland Northeast Asia so far.
[2] An mtDNA B4e specimen dated to 24558-23997 years ago.
[3] An mtDNA R specimen dated to 25521-24558 years ago (perhaps, a branch, being close to basal branches of mtDNA R*).

Cases of ancient “plain” mtDNA R were reported from:
[1] 7 cases of “plain” mtDNA R from ancient Taiwan in “Genomic insights into the formation of human populations in East Asia”, and it is not implausible that the Pre-Jōmon Shiraho Saonetabaru’s case of “plain” mtDNA R separated to the Ryukyu Islands via Taiwan;

[2] 1 case of “plain” mtDNA R from the Northeast Asia’s Boisman culture in “Genomic insights into the formation of human populations in East Asia”. However, in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, it was shown that this particular case of mtDNA R specimen formed a cline with modern and ancient East Asians. Consequently, this case might have migrated to ancestors of the sea coastal Boisman culture in the Late Palaeolithic or Early Neolithic, even if its ancestors might have been related to ancient Taiwanese bearers of mtDNA R* and might have been migrating along the eastern sea coast, inhabited by bearers of "East Asian ancestry", in the northern direction in parallel to the maritime island distribution of mtDNA R* bearers between Taiwan and the Ryukyu Islands. In any case, modern Han Chinese were shown to possess quite a few cases of the “plain” mtDNA R*, thus, the existence of such an mtDNA R*-related population can account for the shared component with the population of modern Han Chinese. Moreover, “Bronze and Iron Age population movements underlie Xinjiang population history” showed that the ANE-related Altai Mountains Afontova Gora had a similar component, which is perhaps consistent with the reporting of “plain” mtDNA R* from the Afanasievo culture of Mongolia in “Genomic insights into the formation of human populations in East Asia”, while it is known that the Afanasievo culture bearers migrated to Mongolia from the vicinity of the Altai Mountains. Regarding the Boisman culture, it should be added that the Boisman culture's pottery bears similarity to the Chulmun pottery of ancient Osan-ri, Munam-ri and Seopohang Korean settlements, which might be relevant for the persistence of bearers of this “East Asia ancestry” component also in Korea.

[3] 1 case of mtDNA R* from the Slab Grave culture of Eastern Mongolia; 1 case of mtDNA R* from the Mongun Taiga culture of the Uvs aimag of Mongolia, Ulaangom sum, Chandman Uul, Ulaangom cemetery, in association with the “eastern” ancient mtDNA C4b1 from the same location.
Indeed, mtDNA B4e, a case of which was reported from Shiraho Saonetabaru of the Ryukyu Islands, should share a mutation G6026A with the quite “young” “Northeast Asian” mtDNA C4 as a whole, and the article “Bronze and Iron Age population movements underlie Xinjiang population history” supported the existence of such a shared autosomal component for populations, having mtDNA C4. However, “Bronze and Iron Age population movements underlie Xinjiang population history” suggested that this particular Northeast Asia’s mtDNA C4 population-related component, being quite young, did not contribute to the known cases of Paleolithic ANE-related populations. Indeed, in “Human genetic history on the Tibetan Plateau in the past 5100 years”, ancient specimens from Northeast China (including the West Liao River basin), including ones belonging to lineages, such as, for example, mtDNA D4m, whose bearers would have had mtDNA C4-related “Northeast Asian” relatives among their ancestors, did not show evidence of Western Eurasian ANE/Yana-related components in the Admixture model, which also points to the Northeast Asia-related origin of mtDNA C4 prior to the coming of the “Coastal sEast Asia”-admixed population from the Chinese article from year 2020, whose ANE/Yana-admixed descendants died out in Siberia during the Holocene climatic deterioration and did not contribute to the West Liao River basin-related population, which is more closely related to modern living individuals, different from the Japan_Kofun-related population, and which did not have the ANE/Yana component in “Human genetic history on the Tibetan Plateau in the past 5100 years”.

Unlike the “derived” Northeast Asia’s component, described above, the “Bronze and Iron Age population movements underlie Xinjiang population history” pointed to the existence of mtDNA lineages, also observed in South Siberia, which carried mutations, often occurring in mtDNA M7bc-related lineages; consequently, it would be consistent that, in the Palaeolithic, an eastern part of the southern deeply diverged mtDNA M7bc*-related population (perhaps, a “parallel” population to some ancestors of the Japan Jōmon and Pre-Jōmonese Shiraho Saonetabaru population) migrated along the coastal and island route as far as the latitude of the Japanese Archipelago, and, being associated with some rare and quite ancient mtDNA branches of the East Asian origin in South Siberia, much later some of these migrants were gradually distributed towards South Siberia from the sea coastal zone via Korea and Northeast China, including the West Liao River basin.

[CLTVTE]

Since one of the ways of the formation of Koreans according to the model of “Ancient DNA indicates human population shifts and admixture in northern and southern China” has already been shown in this topic (see the pictures in the previos posts), it is convenient to mention the role of non-A2 branches of mtDNA A in this topic.

Regarding mtDNA A, in “Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago”, it is pointed that mtDNA A5a ( a relative of the Korean mtDNA A5) was only found in the coastal area during the “Beiqian period” (5500–5300 years before present), and during the later period other branches of mtDNA A appeared in the coastal sites starting from 3100 years ago.
The article stated that:
“These results suggest that exchange between populations from the coastal and inland regions was less frequent before 3100 BP, which is consistent with archaeological findings that there were cultural differences between coastal and inland regions before and during the Longshan culture [39], [40], [41]. An alternative explanation could be due to the influx of people with ancestry from other parts of East Asia that introduced haplogroups M8 and A [6], [13], [33]. ”

[6] M.A. Yang, X. Fan, B. Sun, et al. Ancient DNA indicates human population shifts and admixture in northern and southern China. Science, 369 (2020), pp. 282-288
[13] Y. Yao, Q. Kong, X. Man, et al. Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA. Mol Biol Evol, 20 (2003), pp. 214-219
[33] Q.P. Kong, Y.G. Yao, M. Liu, et al. Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China. Hum Genet, 113 (2003), pp. 391-405

Thus, “Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago” suggests the association of mtDNA A and ancestry from other parts of East Asia. In [33] (Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China), the Korean population contained the highest amount of various branches of mtDNA A (except for mtDNA A2) (8,3% mtDNA A5 plus 6,3% other branches of mtDNA A, that is, the total of 14,6% of mtDNA A in the sample of the Korean population).

Nonetheless, zero cases of ancient mtDNA A was reported in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene” from one of the region of Northeast China (the Songhua river basin, which partially includes the Jilin Province). It implies that regions could experience gradual population changes, and it implies the possibility of the gradual influx of populations from other parts of East Asia.

In “Ancient DNA indicates human population shifts and admixture in northern and southern China”, the Korean population has ca. 40% of additional “Early East Asian” ancestry (see pictures in the posts above), and it is not shown whether such an ancestry may have separated from ancient East Asians closer to the “Southern-Northern East Asian” split less than 20000 years ago, or such an ancestry may have separated from ancient East Asians closer to the Tianyuan individual. Consequently, it should be added that, in “Human genetic history on the Tibetan Plateau in the past 5100 years”, those ca.40% ancestry in the ancient Miaozigou specimen of Inner Mongolia, belonging to mtDNA A14 and yDNA C2-F1067, were “fully “East Asian”” in the admixture model without any substantial North Asian drift, shared with mtDNA A2 populations, which points to the possibility of the development of a particular branch of mtDNA A in one of the Early East Asian populations. The TMRCA of mtDNA A is 33700 years ago in “A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes”, while yDNA C2-L1373 separated ca. 34100 years ago. Nonetheless, in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, some China-specific cases of mtDNA A form clines with members of a very ancient population, connected to the basal yDNA O-M175*. The Qinghai-Tibetan-specific case of ca.40% “Early East Asian” ancestry (of which ancient Xinjiang’s mtDNA A12 was reported in “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China”) distributed between a more ancient Early East Asian part (which should have separated closer to Tianyuan), contributing to the Neolithic Iran specimens (possible Elamite or Elamo-Dravidian speakers, also contributing to Mesopotamian members and western Altaic-speaking populations), a younger Early East Asian part, contributing to the Himalayan populations and even a small Early East Asian part, which should have contributed to the Paleolithic AfontovaGora specimen (if the data from “Bronze and Iron Age population movements underlie Xinjiang population history” are added) as a non-ANE Early East Asian population, and this AfontovaGora-related ancestry should have been distributed between Afanasievo yDNA Q-related specimens and BedouinB (which is similar to the distribution of the AfontovaGora component in “Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry”) in accordance with “Human genetic history on the Tibetan Plateau in the past 5100 years”.

Nonetheless, the Korean population was described in “Ancient DNA indicates human population shifts and admixture in northern and southern China” as a population, which did not form a cline with the “Himalayan-related” Sherpa population. Consequently, the appearance of mtDNA A branches in Korea and nearby Jilin Province should have happened due to the gradual penetration of mtDNA A-related populations from closer locations, comparable with the Miaozigou population, where yDNA C2-F1067 was also observed.

On the other hand, the Japanese population was described as the one, sharing the genetic connection with the Himalayan Sherpa population, which is similar to implications of “Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations”. However, the data of “Human genetic history on the Tibetan Plateau in the past 5100 years” suggest that this connection was caused by the Upper Paleolithic Eastern Eurasian contribution to the ANE Yana_RHS-related population (as in Allentoft’s “Population Genomics of Stone Age Eurasia”), which contributed to the Mesolithic Kolyma, and the Kolyma-related population contributed to some Himalayan populations: according to “Human genetic history on the Tibetan Plateau in the past 5100 years”, it is also possible, however, that yDNA D-M64-related population shared a common ancient substratum with a population, contributing to Yana_RHS and Ust-Ishim, and it was implied that mtDNA mutation T11809C had a fitting distribution:

T11809C L2b1 (EU092766)
T11809C L0a4
T11809C L5b2
T11809C L7

T11809C A2s
T11809C A13b2a1a


T11809C B4b1a2c1
T11809C B2 (MK860678)

T11809C D4h3a8

T11809C M2a1a-a3
T11809C H1ao-a
T11809C H5a1b2
T11809C H5a3a1b
T11809C H27a7
T11809C H27-a1
T11809C J1d7b

The linguistic influence of such a population on ancestors of modern individuals is still too a larger degree enigmatic. In “Population Genomics of Stone Age Eurasia”, a component, sharing a very small genetic drift with Japan Jomon, might have insignificantly reached the Neolithic Iran via the ANE.


One of the most interesting cases is the case of Yushu2.8K from the Qinghai-Tibetan Plateau (“Human genetic history on the Tibetan Plateau in the past 5100 years”):

CSP134 Pukagongma ~2800 years ago b Yushu,Q 33,5 95,4 4177 0,01 14 552 M 1,6 - mtDNA A15c1 yDNA CT (D-M174) Yushu2.8k

According to “Human genetic history on the Tibetan Plateau in the past 5100 years”, the Yushu specimen (yDNA D-M174, mtDNA A15c1) should have the component, responsible for the Japanese-Sherpa genetic connection. Some Austroasiatic populations, speaking Austroasiatic Waic (“Wa”) languages, also have mtDNA A lineages, mediated by the Qinghai-Tibetan Plateau.

[CLTVTE]

Regarding yDNA O-M122>…>O-M188>…>O-M159, this subclade is a relative of the ancient Dushan specimen from the Guangxi Province of China.The ancient Dushan specimen was dated to 8593-8974 years ago and was on the verge of the formation of the southern Neolithic.

However, in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", the Dushan site was reported to have a Late Paleolithic layer, dated to less than 15000 years ago, which was dominated by small flake tool-based industry, and the Dushan specimen additionally showed the participation of two ancestries, one of these ancestries was relatively estimated to separate from the Eastern Eurasians ca. 38100 years ago (which is comparable to the age of yDNA NO-M214 on theytree.com site) and another one of these ancestries was relatively estimated to separate from the Eastern Eurasians somewhat less than 38000 years ago in that article. According to "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", “all of these stone artifacts are produced from medium sized fluvial cobbles that were transported from the ancient Youjiang River, more than 10 km north of the cave”, and it is known from archaeology that medium sized cobbles were used to produce flaked artifacts in the locality of the Yi river basin of the Huai river system (Shandong), whose ancient inhabitant was the ancient Bianbian individual from one more population.

Thus, the ancestors of yDNA O-M188-related Dushan (yDNA O-M7) should have interacted with representatives of these earlier deeply diverged Guangxi populations less than 15000 years ago. Dushan was named a southern ancient individual in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago". Today yDNA O-M7 is observed in populations, speaking Miao-Yao languages. Among other Miao-Yao-related lineages, the HuatuyanNL17 from an ancient (medieval) Guangxi Miao-Yao-related population was reported to belong to yDNA O-M122>O-IMS-JST002611* (a basal branch of yDNA O-IMS-JST002611). Moreover, on the PCA of "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", some of the Miao-Yao-related specimens, belonging to yDNA O-IMS-JST002611, participated in clines along with individual from a very ancient population, connected to the basal yDNA O-M175*. Thus, yDNA O-IMS-JST002611* (coupled with yDNA O*), yDNA O-M188 individuals played a certain role in the formation of the originality of the ancient Miao-Yao populations.


On the other hand, nevertheless, on one of PCAs from “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, where most ancient specimen Tianyuan and AR33K (both belonging to mtDNA R) were used, the HGDP00819 yDNA O-M122>…>O-M188>…>O-M159 specimen formed a cline with one Tai-Kadai individual (the most Dushan-related one in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago"). This cline passed not far from the yDNA O-IMS-JST002611-rich Miao-Yao She individuals. Consequently, members of different yDNA O-M122>…>O-M188>…>O-M159 populations, ancestral to HGDP00819, might have interacted with ancestors of Miao-Yao to a greater degree, or they might have interacted with ancestors of the Miao-Yao to a lesser degree. Indeed, the yDNA O1b2-47z Japanese individual, who was the most shifted to the HGDP00819 yDNA O-M122>…>O-M188>…>O-M159 specimen on the PCA, additionally aligned with the yDNA O-IMS-JST002611-related individual and individuals from a very ancient population, connected to the basal yDNA O-M175*, that is, populations, contributing to the Miao-Yao.

[This Japanese article (“Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing”) hinted at a role, which migrants (the notion of which should also include ancient Miao-Yao-related individuals) should have had in ancient Japan and in which sort of area (that is, the peripheral area) they are expected in modern Japan to have settled during the ancient period.]

Consequently, there should have been one more kind of the yDNA O-M122>…>O-M188>…>O-M159 population, related to the ancestors of the HGDP00819 yDNA O-M122>…>O-M188>…>O-M159 specimen, whose members interacted with the Miao-Yao ancestors to a lesser degree and, as a result, to a larger degree preserved their initial closeness to the yDNA O-M122>…O-M134-related Sino-Tibetan population. Indeed, on one of the PCAs from “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, the HGDP00819 yDNA O-M122>…>O-M188>…>O-M159 specimen formed a cline, bypassing individuals, whose ancestors were likely related to the population of the rice-farming Liangzhu culture, and including a specimen from Shandong, who clustered with more southern Jiangsu specimens and who clustered with one of ancient Longshan culture’s Pingliangtai specimens, and who had the mtDNA, which shared a mutation with the fairly southern mtDNA R9b1a2a2:

https://www.yfull.com/mtree/R9b1a2a2/

It is striking that mtDNA R9b1a2a2, being so South China’s, has representatives in Russia, sharing the most recent common ancestor 5000 years ago. Indeed, “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China”, pointed to the mtDNA D4+195 from the Yangtze River basin’s Hunan Province, which shared a mutation with mtDNA R9b1a2a. “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China” only pointed to the Altai Mountains’ Okunevo EMBA as the second specimen having mtDNA D4+195, listed in that article. It is known from archeology, that the Lower Yangtze River basin’s Liangzhu culture, being influenced by the Hongshan-influenced Lingjiatan culture, was characterized by jade artifacts, whose production methods combined typically mainland China’s ways of jade processing with ways of jade processing, characteristic of the ancient cultures of Northeast China. Interestingly, the early Hongshan culture’s jade working was initially also characterized by mainland China’s ways of jade processing, and the interaction with a more northeastern Zuojiashan culture enriched the Hongshan culture’s jade working with ways of jade processing, characteristic of the ancient cultures of Northeast China, and thus, those Northeast China’s ways of jade working reached as far as the Liangzhu culture of the Lower Yangtze River basin, while mixed sites of the Yangshao culture (for example, one of female specimens of the Yangshao’s Wanggou site was shifted from other Yangshao specimens in the direction of both Hongshan and Shandong’s most northeastern Xiaojingshan specimens, clustering somewhat close to each other on the PCA of “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”) served as intermediaries for migration at first as far as the Anhui Province’s Lingjiatan culture followed by the migration to the Lower Yangtze River basin, in the vicinity of which the Liangzhu culture formed. The Pingliangtai site of the Longshan culture showed the presence of the combined mainland China/Northeast China jade processing technology in a southern Shijiahe-style jade artifact, while the Shijiahe culture’s jade working was characterized by the Liangzhu culture’s influence, which means the backmigration of bearers of such technologies from the Yangtze river basin to the more northern area of the Henan Province, where the Pingliangtai site of the Longshan culture later formed.
Interestingly, the Pingliangtai site was one of the early sites in China, which had evidence that its inhabitants were acquainted with the wheeled transportation. It may help to explain the striking appearance of the 5000-year-old clades of mtDNA R9b1a2a2 in Russia. However, yDNA O-M159 was not reported from the sites of the Okunevo culture, while a rare branch of yDNA N was reported from one of the Okunevo sites (https://www.yfull.com/tree/N-B187/ ).

Nonetheless, there is no evidence for any considerable distribution of mtDNA R9b1a2a2 in Japan so far. Moreover, the more northeastern Xiaojingshan-related Japanese-specific branch of yDNA N (https://www.yfull.com/tree/N-Y23749/) was never reported from Russia. It means that the groupings of individuals were not a part of exactly the same population. Instead of this, the mentioned northeast-shifted mixed Yangshao Wanggou female specimen formed a cline with one of individuals, whose ancestors were likely related to the population of the rice-farming Liangzhu culture, and this cline also bypassed two Longshan culture’s Pingliangtai specimens in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”. Moreover, one of the specimens, belonging to the described cline in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, clustered extremely closely to the Pingliangtai PLTM312 specimen in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", which may mean marriages between representatives of those populations, whereas the Pingliangtai PLTM312-specific lineage is not directly represented in Japan, where there is yDNA N-Y23749 instead. Similarly, “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China” reported the yDNA O-M188 Japanese individual, who should be a distant relative of the yDNA O-M159-related population, and the mtDNA of this yDNA O-M188 Japanese individual was the “northeastern” mtDNA F1b1a (https://www.yfull.com/mtree/F1b1a/ ).

Regarding the mtDNA N9a, while the most ancient case so far (N9a2'4'5'11) was observed in ancient Shandong in a more “northern” Xiaogao specimen, “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China” listed other more northern non- N9a2'4'5'11 branches of N9a, in Korea, where mtDNA O1b2-L682 is also observed on the territory of the Gaya Confederacy. “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China” selected mtDNA M7a1a4a, which shares a mutation T11368C with mtDNA N9a8, which is observed in the Hunan Province of China among other locations, and the Hunanese N9a8 carries some mutations, observed in rice farming populations, while mtDNA N9a9 is observed in Western Eurasians and carries some mutations, shared with mtDNA M7c-related populations (including some Taiwanese Austronesians) and Western Eurasians.

[CLTVTE]

It should be added to the last paragraph of the previous post that “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China” pointed to this rare branch of mtDNA N9a, which is quite rare, since basal mtDNA branches should be rare, and deeply diverged representatives of the "basal" y chromosome branch, born in such a population, should be rare as well, unlike the most widely distributed (in Japan) modern individuals of the same y chromosome lineage, belonging to much more frequent younger derived branches

mtDNA N9a1+G12007A

https://www.yfull.com/mtree/N9a1-a*/ TMRCA 5300 years before present

AP008261.1 Japanese N9a1 16-JUL-2005 A73G C150T T195C A263G 309.1C 315.1C A750G A1438G A2706G T4386C A4769G G5231A G5417A C7028T T8265C A8860G G11719A G12007A A12358G G12372A C12705T G13810A C14766T A15326G C16111T G16129A C16223T C16257A C16261T

Korean_JN857052 Korean Korean Korea Korea JN857052 N9a1 Derenko et al., 2012

AP008726.1 Japanese N9a1 16-JUL-2005 A73G C150T A263G 309.1C 315.1C A750G A1438G A2706G T4386C A4769G G5231A G5417A C7028T A8860G G11719A G12007A A12358G G12372A C12705T C14766T A15326G C16111T G16129A C16223T C16257A C16261T T16519C


P.S. One should warn that mtDNA N9a is not considered to be related to yDNA O1b2-P49 as a whole in the IVPP articles. For example, in “Insights into human history from the first decade of ancient human genomics”, Tianyuan did not contribute to modern populations, but AR33K contributed to modern populations. In “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, the individual, who was related to the basal mtDNA N9a* and participated in the cline together with mtDNA N9a1’3 and N9a2'4'5'11-related individuals, clustered not so distantly from ancient Naga-related populations, in whose descendants basal yDNA O-M175* was detected, but he also clustered even more closely to AR33K on the PCA, thus, the basal mtDNA N9a* started to distribute in yDNA O-M175*-related populations, which were described as “populations, akin to Tianyuan” (as opposed to yDNA O-M175 populations, ancestral to modern yDNA O-M175 individuals), while the mentioned mtDNA N9a1’3 and N9a2'4'5'11-related individuals of the derived lineages already clustered with the Han Chinese (the population, rich in yDNA O-M122) in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”.

[CLTVTE]

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia

Abstract

Previous genomic studies understanding the dispersal of Homo sapiens have suggested that present-day East Eurasians and Native Americans can trace their ancestry to migrations from Southeast Asia. However, ineluctable adaptations during the Last Glacial Maximum (LGM) remain unclear. By analyzing 42 genomes of up to 30-fold coverage from prehistoric hunter-gatherers, Jomon, we reveal their descent from Upper Paleolithic (UP) foragers who migrated to and isolated in the Japanese archipelago during Late Pleistocene. We provide compelling evidence suggesting that these UP people underwent positive selection for cold environments, aiding their survival through the LGM facilitated by non-shivering thermogenesis and detecting it polygenically across multiple loci in the Jomon lineage. Our study pioneers the close estimation of the physiological adaptation of ancient humans by the paleogenomic approach.

https://www.biorxiv.org/content/10.1101/...91810v1?ct=

Could not find the data but it should be available at some point.

All raw genomic data (fastq files) are available for download in the DNA DataBank of
Japan (DDBJ) Sequence Read Archive (DRA. https://www.ddbj.nig.ac.jp/index-e.html)
under the accession numbers PRJDB14637, PRJDB18003 and PRJDB18005.

The Jomon population is one of groups, ancestral to the Japanese population. In any case, “Human genetic history on the Tibetan Plateau in the past 5100 years” has already happened to point to a relevant individual, who carries an mtDNA mutation, which should be widely distributed in Western and Eastern Eurasians and beyond, and which is present in the Greenland Inuit, and which is present in aboriginals of Northern Australia, and which is present in the San population (that is, a “Bushman-related” population), whereas its presence in mtDNA L0a-related individuals appears to be limited to African mtDNA branches, which had managed to settle close to the Near East during the later period, and some of representatives of one of these mtDNA L0a branches have even managed to settle in the Near East, that is, this mutation appears in mtDNA L0a branches, whose rather recent ancestors interacted with the Eurasians, while the mtDNA mutation in question is additionally present in other African mtDNA branches, some of which were also observed in the San population. Consequently, if one starts to think over the possibility that different kinds of human cold adaptations in different populations became possible due to the presence of the shared genetic components, the relevant individual, to which “Human genetic history on the Tibetan Plateau in the past 5100 years” pointed, who carries an mtDNA mutation, which is widely distributed in Western and Eastern Eurasians, suggests that such a common component may be widely distributed in different parts of the world, including gigantic Western and Eastern Eurasian populations. In general, a mentioned commentary from the Institute of Vertebrate Paleontology and Paleoanthropology (Ancient genomes and the evolutionary path of modern humans E. Andrew Bennett, Qiaomei Fu https://doi.org/10.1016/j.cell.2024.01.047 ) already contains the graphic material, suggesting a separate origin of cold adaptation in the Northeast China-related territory and a separate origin of cold adaptation in Greenland.


It is suggested by this new Japanese article “Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia” that the Chugoku-Shikoku Jomon contributed to the Japanese population. It is thought by some in China that the importance of the Jomon lineage for the formation of ancestors of Japanese individuals surpasses the geographic scope of the Japanese Archipelago.
For example, the most ancient mtDNA B4e (24558-23997 years ago) was reported from the Ryukyu Islands (https://press-files.anu.edu.au/downloads...f/ch03.pdf). mtDNA B4e bearers should have blended into the Jomon-related population as well.
One branch of mtDNA B4e remains in Japan https://www.yfull.com/mtree/B4e2/
One more branch of mtDNA B4e, having TMRCA 5200 years ago, became distributed in China, including rather southern areas https://www.yfull.com/mtree/B4e1/
It appeared that some mtDNA B4e1 cases, observed in China, share a mutation with a branch of mtDNA B4c1b2a (https://www.yfull.com/mtree/B4c1b2a4a/), which migrated to the north from an area closer to the Austronesian homeland (mtDNA B4c1b2a is especially observed in the yDNA O-M119-only Taiwan Austronesian Thao population, according to “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China”), and was detected in the Beiqian settlement of the Jiaodong Peninsula in Shandong, dated to 5500-4600 years ago. Indeed, in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, the available yDNA O1b2 Chinese individual (most likely having yDNA O1b2-47z>O1b2-BY45877 members among its relatives, whereas yDNA O1b2-BY45877 is a lineage of yDNA O1b2-47z, mostly observed in China and Korea) participated in a cline, encompassing the O1b2-L682 inividual from Japan, who clustered with the Japanese and thus should be mixed with the Jomon ancestry relative to the Koreans and Han Chinese, an individual with a mutation, shared with mtDNA B4e1 in China, and one of the very ancient individuals, having the mtDNA B* component, which shoud be relevant for the origin of the deep mtDNA B4e lineage. However, since the most ancient mtDNA B4e case and some modern deeply diverged mtDNA B4e cases were detected in Japan, and the TMRCA of the modern mtDNA B4e is only 14800 years (https://www.yfull.com/mtree/B4e/), there should have been the “Jomon-related” migration from the Japanese Archipelago via Korea, reaching at least the Jiaodong Peninsula of Shandong in the beginning, and the results of such a Jomon-related migration can be attested from other materials of “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”. Consequently, the different population history between some continental lineages, which contributed to the Japanese, and some lineages, which remained in China, may be affected by the presence or absence of connections to a migrating population, whose ancestors were mixed with some Jomon-derived individuals, in ancestors of such initially ancient Chinese individuals.



Though mtDNA N9a2 is almost entirely found in Japan today and, in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, Japanese mtDNA N9a2 individuals, Longshan culture’s ca 4500-year-old WT1H16 Wadian mtDNA N9a2-related individual participate in meaningful clines with their “progenitor” Shandong Houli culture’s Xiaogao mtDNA N9a2’4’5’11* individual (who formed a cline (in “The deep population history…”) with yDNA O-M134 individual of the Yangshao culture and thus Xiaogao was named an ancient Chinese individual in “Ancient DNA indicates human population shifts and admixture in northern and southern China”, though yDNA N-M231 Boshan of the same Houli culture as Xiaogao was named an ancient Chinese individual as well in “Ancient DNA indicates human population shifts and admixture in northern and southern China”), additionally, the careful analysis of those mtDNA N9a2-related materials in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene” should provide an insight, where individuals, sharing important mutations with mtDNA B2 (B4b*), A2, D1, C1 of the Native Americans, had gathered in the Lower Huanghe river basin long before the arrival of ancestors of the Houli culture’s Boshan, Bianbian, Xiaojingshan (3 individuals) and Xiaogao there, because the mentioned Houli culture’s individuals (Boshan, Bianbian, Xiaojingshan (3 individuals) and Xiaogao) do not have the Native American-related ANE/Western Eurasian component in “Human genetic history on the Tibetan Plateau in the past 5100 years”.

Despite the lack of the Western Eurasian component in Xiaogao, the article “Ancient DNA indicates human population shifts and admixture in northern and southern China” suggested that mtDNA N9a2’4’5’11* Xiaogao from the population, ancestral to mtDNA N9a2 branches of Japan, despite aligning with yDNA O-M134 Yangshao individual, had an increased affinity to the Paleosiberian ancient individual, and, moreover, the same article suggested that the Paleosiberian and Native American ancestries were closely related, whereas the already mentioned accompanying article “Human evolutionary history in Eastern Eurasia using insights from ancient DNA” (Ming Zhang, Qiaomei Fu DOI: 10.1016/j.gde.2020.06.009) suggested the difference between the contribution to Paleosiberians of ancestry, which separated from Northern East Asians (for example, Shamanka_EN individuals were classified as individuals, belonging to the Northern East Asian ancestry in article “Human evolutionary history in Eastern Eurasia using insights from ancient DNA”) and the “East Asia-derived” ancestry, which separated to ancestors of Paleosiberians 27500 years ago in the article’s scheme, that is, prior to the split between Southern and Northern East Asians ca.19000 years ago, that is, the Eastern Eurasian part of the Paleosiberian ancestry should have separated from ancestors of East Asians to Paleosiberian and Native American ancestors roughly 27500 year ago, which is not the period of the Last Glacial Maximum, but, on the contrary, is the period of the flourishing of some more northern subclades of yDNA O-M175, when representatives of some subclades, such as some yDNA O-M122* clades (whose descendants in China should have been later substituted by yDNA O-L465, judging by the materials of “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”) and yDNA O1b2 clades started to expand in the northeastern direction. Consequently, the mentioned Xiaogao’s affinity to the Paleosiberian (“Native American”) ancestry should have been caused by the interaction between Xiaogao and the ancient individuals, whose remote ancestors contributed to that ca.27500-year-old Paleosiberian (“Native American”) component.

The article “Human evolutionary history in Eastern Eurasia using insights from ancient DNA” used the the Shandong Houli culture’s 8100-year-old individual Boshan (who was named “ancient Chinese” along the yDNA O-M134-affiliated Xiaogao in “Ancient DNA indicates human population shifts and admixture in northern and southern China”) to date the interaction between Shandong’s ancient ancestry and the Paleosiberian-like ancestry to as early as 8000 years ago. In “Ancient DNA indicates human population shifts and admixture in northern and southern China”, the affinity of both Boshan and “N9a2-affiliated” Xiaogao to the Paleosiberian individual decreases relative to the series of Late Neolithic individuals of Xitoucun. If one checks, which clines Boshan and Xiaogao form with Xitoucun individuals, it will appear that two clines pass through individuals, carrying the Shandong autosomal component, both of whom shared an mtDNA mutation with mtDNA A2, and one of whom shared an mtDNA mutation with mtDNA B2 (mtDNA B4b*). These two individuals formed a cline of their own with the nearby mtDNA A2-related individual, which may suggest that an mtDNA A2-related population once also lived in the close vicinity of Shandong (most likely in Northeast China). It is surprising that mtDNA N9a2’4’5’11* “N9a2-affiliated” Xiaogao formed one cline with one “mtDNA A2-affiliated/ mtDNA B2-affiliated” mentioned individual, which passed through an yDNA O1b2-47z/mtDNA N9a2 Japanese individual, and mtDNA N9a2’4’5’11* “N9a2-affiliated” Xiaogao formed another cline with another mtDNA A2-related mentioned individual, which passed through a Korean female individual, who, however, aligned with yDNA O-M134 individuals on the PCA (the ones, slightly shifted to yDNA O-L465 members) and who participated in a meaningful cline with WT1H16 Wadian mtDNA N9a2-related individual in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”.

The “mtDNA A2-affiliated/ mtDNA B2-affiliated” described individual not only showed a connection to an yDNA O1b-47z/mtDNA N9a2 Japanese, but also aligned with the Austroasiatic HtinMal population, which is rich in yDNA O1b, but is dominated by mtDNA R11’B6 in “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China”, which is different from mtDNA B4b, ancestral to mtDNA B2; consequently, the reason for this alignment may be caused by the shared male ancestors between the “mtDNA A2-affiliated/ mtDNA B2-affiliated” individual and yDNA O1b-rich HtinMal population.

One should recall the linguistic article by Jager, 2017 (http://www.sfs.uni-tuebingen.de/~gjaeger...esHITS.pdf), where a tentative non-trivial linguistic classification of numerous languages, based on automatic reconstructions, appeared. As an explaining example, in Jager, 2017, the Native American Kawesqar language from Chile (South America), being accompanied by the African language, coded as BAINOUK_GUNYAAMOLO, unexpectedly clustered in a group, comprising the Indo-European languages. The Kawesqar speakers are rich in mtDNA D4h3a, and no European and African lineages were reported from the Kawesqar people proper, so the question about the role of an mtDNA D4-related population may appear. However, the neighbouring Native American populations from Chile appeared more mixed with Europeans and Africans ("Ancestry and admixture of a southernmost Chilean population: The reflection of a migratory history" : “Non-Amerindian haplogroups represented 15.5% (n = 20) of the lineages: D4p (14.29%), H* (50%), I1* (14.29%), K1a4a1a + 195 (14.29%), L3d1b2 (7.14%), T2* (14.29%), U* (21.42%), and X2 (7.14%).”). Therefore,, the question of loanwords to the Kawesqar language from languages of more creolized Native American populations may also appear. However, the Kawesqar-Bainouk Gunyaamolo-Indo-European cluster is so unusual that it still cannot escape making an impression of the result of “wishful thinking”.

It was already mentioned in the previous posts that the deep “geographically Qinghai-Tibet-related” mtDNA A branches (that is, more than 30000-year-old branches) were viewed in “Human genetic history on the Tibetan Plateau in the past 5100 years”: consequently, the ancestor of mtDNA A clade, ancestral to mtDNA A2, might have also arrive to Northeast China more than 30000 years ago from such a “geographically Qinghai-Tibet-related” location, which also opens the possibility to suggest the arrival of some deep mtDNA M and mtDNA R branches (another part of whose relatives had been distributing in India), being accompanied by yDNA D-M174 (D-M174*) . Indeed, in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene” the relevant mtDNA A2-affiliated individual slightly more loosely aligned with “Qinghai-Tibet Plateau-related” yDNA D-M174 individuals, which suggests that the described ancient clade of yDNA D-M174 more than 30000 years ago was different from the modern Himalayan D-M174 (alternatively, this non-precise alignment may imply the participation of the ancient yDNA C haplogroup, since it is sometimes suggested that yDNA D and some yDNA C populations sometimes migrated along similar routes and the TMRCA of mtDNA A is 33700 years ago in “A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes”, while yDNA C2-L1373 separated ca. 34100 years ago).


In Jager, 2017, a part of Native American Otomanguean languages clustered with the Austronesian languages (a mixed mtDNA M/mtDNA B4a-related population), but they clustered even more closely with the languages of yDNA O1b-related Austroasiatic population, which suggests that the Austroasiatic population once had an yDNA O1b-related relative, associated with another clade of mtDNA B4 (mtDNA B4b, ancestral to mtDNA B2 of Native Americans). Another part of Otomanguean languages clustered with the Ainu languages, and the materials “The deep population history of northern East Asia from the Late Pleistocene to the Holocene” suggested the presence of an “India-like” deep mtDNA R branch in the described vicinity of Northeast China, which should have appeared along the ancestor of mtDNA A2 and should have been accompanied by some clade of yDNA D-M174. One Otomanguean language clustered with Western Eurasian languages as a whole. In one of western articles, it was suggested that speakers of one of Dravidian languages contained mtDNA M61 in their population, which would be the “Eastern Eurasian-related” influence on the formation of the Dravidian languages already in India, and the materials of “The deep population history of northern East Asia from the Late Pleistocene to the Holocene” suggested the appearance of an mtDNA M61-related haplogroup in the described vicinity of Northeast China along with the ancestor of mtDNA A2 more than 30000 years ago. The arrival of such populations should explain one of sorts of “Western Eurasian-like” affinity in Paleosiberian and Native American-related languages, which is not accounted for by the presence of mtDNA X2, for example.

In accordance with the materials of “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, the predominance of such an “mtDNA A2-related” affinity over the original “mtDNA B2-related” affinity in the previously mentioned population, arriving to Shandong at least since 8000 years ago and contacting Houli culture’s “ancient Chinese” Boshan and “ancient Chinese” “mtDNA N9a2-affiliated” Xiaogao may be helpful to explain the picture of Jager, 2017, where the Korean and Japanese languages, having local yDNA O1b-related populations as their speakers, clustered with languages of mtDNA A2-rich populations, but did not immideately clustered with languages of Austroasiatic, Austronesian and Tai-Kadai-related populatios, as some of Native American Otomanguean languages did in Jager, 2017.

Since “mtDNA N9a2-affiliated” Xiaogao aligned with the yDNA O-M134-related Yangshao individual, the name “ancient Chinese”, given to her in “Ancient DNA indicates human population shifts and admixture in northern and southern China”, should be fully applicable to her. Unlike this, though Boshan was named “an ancient Chinese” as well in “Ancient DNA indicates human population shifts and admixture in northern and southern China”, Sinitic or Sino-Tibetan was not the initial language of his remote ancestors. Whereas the Szarvas inscription, which can be tentatively “read” either in ancient Hungarian or in a Turkic language, is applicable to the language, spoken by Boshan’s distant relatives, one more ancient inscription, which may be relevant for determining the initial language of such individuals as Boshan, exists in Asia. Surprisingly, a non-negligible amount of more distant relatives of Boshan (their y chromosomes constitute 5-7% out of the total number of male individuals in Tibeto-Burman-speaking Chakma and Tripura populations) appeared in the coastal Chittagong area of Bangladesh, bordering Myanmar (“Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal”). However, in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”, relatives of such individuals formed a cline, leading to the individuals of the Himalayan region, which included the Hongshan culture’s related individual as an intermediary. It is known from archaeology, that the earlier Houli culture, to which Boshan belonged, contributed to some of its neighbouring cultures, which later also contributed to the Hongshan culture. In “Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal”, a more close relative of Boshan appeared in neighbours of Tibeto-Burman-speaking Chakma and Tripura populations, that is, he appeared in the Tibeto-Burman-speaking Marma population. The ancient/medieval Pyu civilization of Myanmar left partially undeciphered inscriptions. A set of inscriptions from the Myazedi Pagoda of the Pagan area of Myanmar contains an inscription, in which only a few dozens of words can be deciphered as belonging to the Tibeto-Burman Marma (Mranma) language, whose speakers arrived at the end of the Pyu civilization, while the linguistic affinity of the remaining words is unknown ("A preliminary reassessment of the PYU faces of the Myazedi inscriptions at Pagan"), therefore, it is speculated that they may belong to the language of one of the Pyu populations, interacting with the incoming Mranma/Marma speakers. After arriving to the territory of Myanmar, Mranma/Marma speakers continued to distribute as far as modern Bangladesh, and one of their modern populations is attested in “Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal”. Consequently, the sampled Mranma/Marma population may also include individuals, whose ancestors joined the ancestors of the sampled Mranma/Marma population after its arrival to the area of the Pyu civilization. All male lineages of the sampled Mranma/Marma belong to populations, which speak clearly definable languages: Tibeto-Burman languages, Austroasiatic languages, Dravidian languages, Indo-Aryan languages. Therefore, the y chromosome relative of Boshan may be a candidate to be a descendant of speakers of the language, whose words in one of the Myazedi Pyu inscriptions cannot find the clear correspondence in the well-known languages (Tibeto-Burman languages, Austroasiatic languages, Dravidian languages, Indo-Aryan languages). The researcher of the Japanese descent Marc Miyake is also trying to decipher this Myazedi Pyu inscription. When musing on the language of this Pyu civilization’s Myazedi inscription, which appears to be related to a less distributed and less known substratum of Tibeto-Burmans, one may combine the results of Marc Miyake‘s attempts with the fact that the ancestors of the Japanese interacted with the Houli culture in the past, and this culture indirectly contributed the part of its population to the ancestors of founders of the Hongshan culture, whose representatives are considered to migrate as far as the Southern Himalayas in accordance with the materials of “The deep population history of northern East Asia from the Late Pleistocene to the Holocene” and thus should have become bearers of the substratum language for Tibeto-Burman languages there.

[TanTin]

The Jomon population is one of groups, ancestral to the Japanese population.

You put a lot of information and you connect many ancient populations:
San, Jomon, China, Xiaogao, Tibetan Plateau, Korea, Austronesian , Greenland Inuit.

For me the most important is the link starting from San ( “Bushman-related” population).
If you can make some graphic diagram to show these connections would be great !

[qijia]

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia
Abstract
Previous genomic studies understanding the dispersal of Homo sapiens have suggested that present-day East Eurasians and Native Americans can trace their ancestry to migrations from Southeast Asia. However, ineluctable adaptations during the Last Glacial Maximum (LGM) remain unclear. By analyzing 42 genomes of up to 30-fold coverage from prehistoric hunter-gatherers, Jomon, we reveal their descent from Upper Paleolithic (UP) foragers who migrated to and isolated in the Japanese archipelago during Late Pleistocene. We provide compelling evidence suggesting that these UP people underwent positive selection for cold environments, aiding their survival through the LGM facilitated by non-shivering thermogenesis and detecting it polygenically across multiple loci in the Jomon lineage. Our study pioneers the close estimation of the physiological adaptation of ancient humans by the paleogenomic approach.
https://www.biorxiv.org/content/10.1101/...91810v1?ct=

Actually I doubt that Jomon people adapted to cold environment. 
Modern north east asians had got two traits of Neotany and ABCC11 gene under cold environment.
I don't think the Jomon people has this kind of factors. 30% of japanese allele frequency below must be an effect of Jomon. Considering those, yangshao and west liao valley people would not be ancestors to modern northern east asian also.

According to Clive Bromhall who has a Ph.D. in zoology from Oxford University, "Mongoloid races are explained in terms of being the most extreme pedomorphic humans."
Mongoloid Race - Features - Neoteny (liquisearch.com)