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Thread: Ancient genomics reveals tripartite origins of Japanese populations

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    Ancient genomics reveals tripartite origins of Japanese populations

    Ancient genomics reveals tripartite origins of Japanese populations

    https://www.science.org/doi/10.1126/sciadv.abh2419

    Abstract

    Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.

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    Last edited by Shuzam87; 09-18-2021 at 03:37 AM.

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    The coverage for those two Yayoi looks terrible. I'm not sure I'd trust any conclusions based on those.
    Ελευθερία ή θάνατος.

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    Possible influences from Northeast Asia and Mainland China for the Kofun Culture. Kofun ancient samples were also closer to modern-day Japanese ancestry wise.

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    Last edited by Shuzam87; 09-18-2021 at 06:09 AM.

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    Quote Originally Posted by Michalis Moriopoulos View Post
    The coverage for those two Yayoi looks terrible. I'm not sure I'd trust any conclusions based on those.
    I think those two samples were from the previous journal "Genetic characteristics of Yayoi people in Northwestern Kyushu" https://doi.org/10.1537/asj.1904231
    Last edited by Shuzam87; 09-18-2021 at 03:43 AM.

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    Quote Originally Posted by Shuzam87 View Post
    Ancient genomics reveals tripartite origins of Japanese populations

    https://www.science.org/doi/10.1126/sciadv.abh2419

    Abstract

    Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.
    This makes intuitive sense to me, although I didn't expect the "Later East Asian" component to be so much bigger than the "NE Asian rice farmer" component.

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  12. #7
    There is a strange finding in this article:
    Rice cultivation was introduced by people with Northeast Asian ancestry.

    While the West Liao populations used in our admixture models did not themselves practice rice farming, they are situated just north of a hypothesized route of agricultural spread into Japan, to which our results lend weight. This follows the Shandong Peninsula (northeastern China) into the Liaodong Peninsula (northwestern part of the Korean Peninsula) and then reaches the archipelago via the Korean Peninsula (41).

    Our findings imply that wet rice farming was introduced to the archipelago by people who lived somewhere around the Liaodong Peninsula but who derive a major component of their ancestry from populations further north, although the spread of rice agriculture originated south of the West Liao River basin (55).
    However, later they write:

    There are caveats to this analysis. First, we are limited to only two Late Yayoi individuals from a region where skeletal remains associated with Yayoi culture are morphologically similar to Jomon (16). Yayoi individuals from other regions or other time points may have different ancestral profiles, e.g., continental-like or Kofun-like ancestry.
    We then explore the possibility that the continental ancestry observed in both the Yayoi and Kofun periods derives from the same source, with intermediate levels of Northeast and East Asian ancestry (table S12). Only one candidate was found to better fit a two-way mixture for Kofun, a population of the Late Bronze Age and Iron Age individuals from the Yellow River basin (YR_LBIA) (20), although this was not consistent across the reference sets (nested, P = 0.100; table S13). Despite not showing statistically significant gene flow with Yayoi to the exclusion of Jomon (Z = 2.487) (Fig. 4A and fig. S16), we find that a two-way model between YR_LBIA and Jomon also fits the Yayoi (table S14). This Yellow River population has an intermediate genetic profile with approximately 40% Northeast Asian and 60% East Asian (i.e., Han) ancestry, as estimated by qpAdm. Thus, this is an intermediate genetic profile that fits both Yayoi and Kofun in certain models, with an input of 37.4 ± 1.9% and 87.5 ± 0.8% in these populations (table S14). These results imply that continuous gene flow from a single source may be sufficient to explain the genetic changes between the Yayoi and Kofun.
    They model Kofun as admixed with Han Chinese, but:

    The three Kofun individuals sequenced in this study were not buried in those tumuli (see note S1), which suggests that they were lower-ranking people. Their genomes document the arrival of people with majority East Asian ancestry to Japan and their admixture with the Yayoi population (Fig. 5 and fig. S17). This additional ancestry is best represented in our analysis by Han, who have multiple ancestral components. A recent study has reported that people became morphologically homogeneous in the continent from the Neolithic onward (56), which implies that migrants during the Kofun period were already highly admixed.

    K. Okazaki, H. Takamuku, Y. Kawakubo, M. Hudson, J. Chen, Cranial morphometric analysis of early wet-rice farmers in the Yangtze River Delta of China. Anthropol. Sci., 210325 (2021).

    In conclusion, the cranial morphometric analysis conducted in this study suggests that by the fourth millennium BC, wet-rice farmers in the Yangtze Delta contained significant numbers of individuals who were migrants from the millet
    agricultural societies of northern China or else were people who had received genetic influences from those societies. The impact of the gene flow from northern China gradually increased over time as shown by the fact that the morphometric differences seen in the Neolithic had disappeared by the Eastern Zhou–Han Dynasty. These people participated in the population diffusion and movement associated with the spread of rice farming to surrounding areas including the Japanese archipelago. (cf. This Yellow River population has an intermediate genetic profile with approximately 40% Northeast Asian and 60% East Asian (i.e., Han) ancestry, as estimated by qpAdm.)
    They pay so much attention to finding Northeast Asian ancesry in places, where rice was cultivated in China. Perhaps, they think that Kofun migrants with prominent Northeast Asian ancestry brought modern varieties of Japonic languages to the Japanese archipelago, not early Yayoi migrants.

    Rice is prominent in Japanese mythology:
    6. Rice
    The Kojiki calls the earthly world "Toyoashihara no chiaki no nagaihoaki no mizuho no kuni," while the Nihon shoki calls it "Chiihoaki no mizuho no kuni," IV appelations idealizing it as an ideal land where forever ripen bountiful ears of rice. Further, the Kojiki and Nihongi include the motif of rice within both names and attributes of figures in the lineage from Amaterasu to the first emperor Jimmu, thus indicating how closely rice cultivation was linked to kingship. For example, Amaterasu cultivates rice in her sacred paddies on the Plain of High Heaven. And the names of her child Oshihomimi and his younger brother Amenohohi --- who was sent on the first mission to Izumo in preparation for the "transfer of the land"V --- both include the character ho, which means "rice ears." Oshiho means "stalwart rice ears" or "teeming rice ears," while hohi means the "spiritual power of the rice ears".

    The child of Oshihomimi was Ho no Ninigi, the grandchild of Amaterasu who finally descended to Japan, and his name likewise means something akin to "luxuriantly ripening ears of rice." The place where Ho no Ninigi descended was called Takachiho-mine, or "high-thousand rice-ears peak," with the similar meaning of a place where innumerable ears of rice are piled up. Finally, the three children produced by Ho no Ninigi and Konohanasakuya-bime[Glossary: konohanasakuyahime_no_mikoto] (Kamuatakashitsu-hime), namely, Hoderi, Hosuseri, and Hoori (also called Hikohohodemi), all contain the common "ho," which originally did not mean "fire,"VI but "rice ear," with the result that their three names mean "rice-ear-shining" (hoderi), "rice-ear advancing" (hosuseri or hosusumi), and "rice-ear breaking" (hoori, from being so heavily weighted down with the ripe rice grain).

    Further, the child of Hoori (Hikohohodemi) was Ugayafukiahezu[Glossary: ugayafukiaezu_no_mikoto], whose offspring were named Itsuse, Inahi, Mikenu, and Wakamikenu (also called Toyomikenu). These deities' names all contain elements related to rice and foodstuffs; for example, the se of Itsuse came from the primitive word sa which meant the spirit of the rice grain, and thus indicated "divine rice." The hi of Inahi, on the other hand, was the same hi (bi) of the word musibi, which referred to the creative power of becoming and thus indicated the rice spirit, while the mike of Mikenu meant "food," or "food offering."

    Also, in the second alternate "one writing" relating the "descent of the heavenly grandchild" in the Nihon shoki,VII Amaterasu orders Amanokoyane and Futotama to "take the rice from my gardens in the Plain of High Heaven and present it to my offspring," thus indicating that the divine rice from heaven was entrusted by Amaterasu to Oshihomimi. However, since it later came about that Ho no Ninigi descended in place of Oshihomimi, it appears that in the end, rice was brought to the earthly world by Ninigi.

    According to a fragmentary passage from the Hyuga no kuni fudoki[Glossary: fudoki], at the time Ho no Ninigi descended from heaven, the earth was in a condition of chaos, with "a darkened sky lacking any distinction of night and day, so that people lost their way and could not discriminate things." But Ho no Ninigi plucked a thousand stalks of rice and scattered the unhulled grain in the four directions, whereupon "the sky was brightened, and the sun and moon shone brightly," thus showing that rice and king were viewed as equivalent, both conceived as possessing the power to change darkness to light and chaos to order.

    Further, the third alternate "one writing" provided by the NihongiVIII as a description of Ho no Ninigi's descent relates that Ho no Ninigi's wife Kamuatakashitsu-hime "selected a field by divination, giving it the name Sanada. From the rice of that field she brewed sweet rice wine of heaven, which she gave [him] to drink. And using the rice of the field Nunata, she prepared cooked rice which she gave him to eat." In short, sake and steamed rice were produced from the rice grain and presented as offerings to the ruler of the divine land, reflecting a concept similar to that evident in the previous passage.

    As the embodiment of the rice grain, Ho no Ninigi thus represented not only the ancestor of the imperial family, but also the spirit of rice and grains presented from heaven to the world of human beings. In this context, it should be noted that the rice cultures around Southeast Asia frequently treat rice as a sacred grain unique in status compared to other agricultural products. Many of those cultures also personify the spirit of the rice as a goddess, calling it "grain mother," or "mother of the rice."6

    The divine genealogy from Amaterasu to Jimmu is intimately linked to rice, thus revealing a conceptual identification of rice with kingship. Forming the basic structural motif of the kingship myths of Kojiki and Nihongi, this linkage identifies the king (i.e., tennô) with the rice spirit, thus suggesting one factor that motivated the identification of the imperial ancestral deity Amaterasu with the goddess "rice mother."

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    There's some intriguing stuff in this paper, but I would want more Yayoi samples to back up these author's conclusions. Hopefully they will be forthcoming.

    Evidence of higher Liao basin ancestry vs Yellow River ancestry in early Japanese farmers compared to later ones is possibly circumstantial evidence in favor of some kind of Altaic/Transeurasian hypothesis for Japonic, but again, things are still too fuzzy with these limited samples. Let's hope for more with good coverage.

  15. #9
    Quote Originally Posted by Psynome View Post
    There's some intriguing stuff in this paper, but I would want more Yayoi samples to back up these author's conclusions. Hopefully they will be forthcoming.

    Evidence of higher Liao basin ancestry vs Yellow River ancestry in early Japanese farmers compared to later ones is possibly circumstantial evidence in favor of some kind of Altaic/Transeurasian hypothesis for Japonic, but again, things are still too fuzzy with these limited samples. Let's hope for more with good coverage.
    Ancient spread of Yellow River ancestry is firmly connected to Sino-Tibetan languages. But at a certain point the genetic expansion culminated to cultural and linguistic influence rather than replacement. From that aspect there’s no controversy. We also have no way of knowing how much influence the Jomon languages in Kyushu had on Japonic.

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    I only skimmed it yet, but I think this paper underestimates the contribution of mainland East Asian ancestry to Japanese individuals post-Yayoi, at least going by what I have read on Japanese uniparentals and what other members here (who know about them a lot better than me) have posted about recent sharing of Y lineages between Han Koreans and Japanese.

    Perhaps these Yayoi genomes are not very typical of the average Yayoi population. There was of course later migration to Japan from mainland Asia but it's odd that so much of it seemed to have arrived during the Kofun period.

    Also, their ADMIXTURE results in Fig 2 do not make much sense , Yellow_River_MN (Yangshao-related genomes) as a mix of southern East Asian ancestry +Okunevo (?) and Yayoi as mostly Jomon (?)
    Last edited by Max_H; 09-18-2021 at 02:11 PM.

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