(05-06-2024, 09:17 AM)teepean Wrote: [ -> ]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.