Jomon: Paleolithic Contingent in Modern Japanese

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Jomon: Paleolithic Contingent in Modern Japanese Jan 2, 2022 2:13:16 GMT

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Post by Admin on Jan 2, 2022 2:13:16 GMT

Discussion
This study takes advantage of whole-genome sequence data from the 2500 years old Jomon individual, IK002, dissecting the origins of present-day East Asians. IK002 is modeled as a basal lineage to East Asians, Northeast Asians/East Siberians, and Native Americans (basal East Eurasians, bEE) after the divergence between Tiányuán and the ancestor of hunters-gatherers in Southeast Asia (Fig. 4)7,17. We clearly show the early divergence of IK002 from the common ancestor of the other ancient and present-day East Eurasian and Native Americans (Fig. 1c). Given that the split between the East Asian lineage and the Northeast Asians/East Siberian and Native American lineage was estimated to be 26 kya49, the divergence of the lineage leading to IK002 is likely to have occurred before this time but after 40 kya when the Tiányuán appeared (Fig. 4). Therefore, our results support the archaeological evidence based on lithic industry that the Jomon are direct descendants of the Upper-Paleolithic people who started living in the Japanese archipelago 38 kya (Supplementary Discussion).

Fig. 4: Schematic of peopling history in Southeast and East Asians, Northeast Asian/East Siberians and Native Americans.

The basal East Eurasians (bEE) are an ancient population that had no divergence among the ancestors of East Asians, Northeast Asians/East Siberian, and Native Americans. NA-ES-NA presents another ancient population that had no split between the ancestors of Northeast Asians/East Siberian and Native Americans.

We use the MA-1 ancestry as a proxy for ancestral populations who took the northern route of Himalaya mountains to come to East Eurasia. The fine stone tool, i.e., microblade, is a representative technology that was originally developed around Lake Baikal in Central Siberia during the Upper-Paleolithic period9. This microblade culture was also reached the Hokkaido island ~25 kya and the main island of the Japanese archipelago ~20 kya. If this culture was brought by demic diffusion, IK002 should still retain the MA-1 ancestry. However, we find no evidence on the genetic affinity of MA-1 with ancient and present-day Southeast/East Asians including Devil′s Gate Cave (8.0 kya), Chokhopani (3.0–2.4 kya), and IK002 (2.5 kya) (Fig. 2). Therefore, we conclude that MA-1 gene flow occurred after the divergence between the ancestral populations of Northeast Asians/East Siberians/Native Americans (NA-ES-NA) and East Asians (Fig. 4): namely, East Asians originated in Southeast Asia without any detectable genetic influence from the ancestor who took the northern route. There are two hypothetical possibilities to explain the contradiction between genome data and archaeological records. The first possibility is that MA-1 may not be a direct ancestor who invented the microblade culture. The second is that, if the assumption is correct, then the northern-route culture represented by microblade was brought to the Japanese archipelago by the NA-ES-NA population who must have had substantial gene flow from MA-1, which was a typical “cultural diffusion.” The first and second possibilities can be examined by obtaining genome data of Upper-Paleolithic specimens hopefully accompanying with microblade newly excavated from around Lake Baikal and from the Primorye region, respectively.

The genome of the Ikawazu Jomon (IK002) strongly supports the dual structure model of the origins of modern Japanese37. The PCA plot and phylogenetic tree showed that the present-day Japanese fell in the cluster of present-day East Asians (e.g., Han Chinese) but not clustered with IK002 (Fig. 1a & c), while a signal of gene flow was detected from IK002 to present-day Japanese (Fig. 1c & Supplementary Fig. 8). The PCA and ADMIXTURE showed the close relationship between IK002 and the Hokkaido Ainu even in the genome-wide structure reflected by linkage blocks (Supplementary Fig. 4 & Supplementary Fig. 6). These results fit the hypothesis that the Ainu and the Jomon share the common ancestor: the present-day Honshu Japanese are the hybrid between the Jomon and migrants from the East Eurasian continent, and the Hokkaido Ainu have less influence of genetic contribution of the migrants37,42.

IK002 gave new insights into the migration route from south to north in East Eurasia. The f4-statistics suggest that both the ancient and the present-day East Asians are closer to IK002 than Chokhopani (ancient Tibetans, 3.0–2.4 kya) in the coastal region but not in the inland region (Fig. 3 & Supplementary Fig. 9). Recent archaeological evidence shows little cultural influence from ancestral Austronesians to the Ryukyu islands (i.e., southernmost islands in the Japanese archipelago) in the last 10,000 years51. Given this cultural continuity, it is unlikely that this extra genetic affinity to IK002 was formed due to recent gene flow as shown in a previous study52 (see Supplementary Discussion). Here, we provide two explanations for this signal: (1) the earliest-wave of migration from south to north occurred through the coastal region, and/or (2) the migration occurred in both the coastal and inland regions, but the genetic components of the earliest-wave were drowned out by back-migration(s) from north to south occurred in the inland region. In the early migration of anatomically modern humans, the route along the coast has been primarily thought to be important3,53,54,55,56. The use of water craft could support such explanation for the expansions through the islands and the coastal region3, which supports the first explanation. There could be, however, potential criticisms: such archaeological evidence of craft boat is hardly found. Ulchi and Nivkh show significantly negative values of f4-statistics (Z = −4.541 and −10.148, respectively. p < 0.000006). This could be an influence of the Hokkaido Ainu who are likely to be direct descendants of the Jomon people. The ancestor of the Ainu people could have admixed with the Okhotsk people57 who were genetically as well as morphologically close to Ulchi and Nivkh in the the Primorye region58,59,60,61,62. The second explanation is that the track of the earliest-wave was erased in the inland but left over in the coastal region. Taiwan aborigines (Ami and Atayal) and Igorot are the Austronesian minorities. Taiwan aborigines are thought to have come from the East Eurasian continent 13.2 ± 3.8 kya63, though the origin of Igorot (which can be derogatory, and could be best referred as Kankanaey) is not well-known.

The coastal-migration hypothesis would be supported by morphological traits of the Jomon individuals excavated from the Hobi shell-mound site, which is geographically very close to the Ikawazu shell-mound site in the Atsumi peninsula. Kaifu and Masuyama (2018) examined spatiotemporal variation in humeral shaft thickness using a sample of 1003 prehistoric individuals from various sites in the Japanese Archipelago, including 797 Jomon individuals64. The results showed that the Jomon humeri were thicker in coastal populations than in inland populations. Kaifu and Masuyama (2018) hypothesized that this was caused by not only fishing in the outer sea, but also active marine transportation by rowing boats. This previous study suggests the Hobi Jomon individuals in the Atsumi peninsula were the people who adapted to coastal environment.

However, there is still lack of ancient genome data in East Asia critical to understand the peopling history of East Eurasians. Although our data support the idea that IK002 was the direct descendant of the Upper-Paleolithic people, how/where those Upper-Paleolithic people migrated to the Japanese archipelago remains unanswered. It is required to analyze more ancient genome data in order to fill the gap and to prove the hypothetical migration routes.

Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The manuscript focuses on genomic analysis of the 2.5 kya Jomon individual, IK002, an important piece of evidence that can inform us on the demographic history of eastern Eurasia. The authors concluded that IK002 is basal to all modern and ancient eastern Eurasians, and that, based the genetic affinity to Taiwanese aborigines, Jomon-related ancestry migrated into Japan from Southeast Asia likely via the coastal route.

2) Paragraph 2, Line 12 of Introduction: ‘This direct evidence on the link between the Jomon and Southeast Asians, thus, confirms the southern route origin of East Asians.’ The evidence only shows genetic affinity between Jomon and Hoabinhian-related ancestry. Most ancient and present-day Southeast Asians and East Asians do not show strong genetic affiliations with Hoabinhian individuals. The finding can only support southern route origin of Jomon individual, and not all of East Asians. The populations of Southeast Asia and East Asia are already structured since the Paleolithic (Hoabinhian-related, Siberian-related, and ancestors of Austronesian-related and Austroasiatic-related populations), and some of this may have migrated from north of the Himalayan arc.

7) Paragraph 5, Line1 or Resutls. The basal position of IK002 relative to the selected East Asian and Native American groups can be attributed to genetic affiliation of IK002 to Hoabinhian-related ancestry, which was not accounted for in the Treemix run. Figure S38 of McColl et al., 2019 models IK002 as an admixture between Hoabinhian-related and East Asian related ancestry (represented by Ami). How do you reconcile the difference between the result of this treemix run and the earlier published qpGraph analysis? Would the topology be consistent if you include other present-day Southeast Asians, Siberian (Koryak, Yakut, etc), and Papuans in the Treemix analysis?

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Last Edit: Apr 29, 2023 19:26:27 GMT by Admin

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Jomon: Paleolithic Contingent in Modern Japanese Feb 23, 2024 20:44:48 GMT

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Post by Admin on Feb 23, 2024 20:44:48 GMT

Japan considered from the hypothesis of farmer/language spread
Published online by Cambridge University Press: 05 May 2020

Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC–AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jōmon peoples (14,000–300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC–AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kantō region.

www.cambridge.org/core/journals/evolutionary-human-sciences/article/japan-considered-from-the-hypothesis-of-farmerlanguage-spread/BD91E69AEA3CCAEDC567519EF7F5AA97

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Jomon: Paleolithic Contingent in Modern Japanese Feb 25, 2024 21:41:33 GMT

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Post by Admin on Feb 25, 2024 21:41:33 GMT

Introduction
The Jōmon period (see Figure 1) is one of the longest post-Palaeolithic archaeological periods in the world, sustained by a hunting–gathering–fishing–horticultural subsistence pattern (Habu, Reference Habu2004). The introduction of rice agriculture into the Genkai Bay area of North Kyushu (Figure 1) from around 1000 BC marks the beginning of the Yayoi period. Wet-rice technology was introduced by Mumun (‘plain pottery’) culture migrants from the southern Korean Peninsula relatively early, ca. 1000 BC, in the Peninsula's Mumun period (1500–300 BC). These migrants were not Yayoi, they were Mumun.

The term Yayoi has four uses, which can create much confusion. First, it is the designation of the period beginning with the introduction of rice agriculture around 1000 BC until the advent of the Mounded Tomb Culture in the third century AD. Yayoi is a period designation exclusive to Japan; it includes both farmers and hunter–gatherers and entails the agricultural transition in a time-transgressive and regionally disparate process. Second, ‘Yayoi people’ may refer to anyone living in the Japanese Islands in the Yayoi period, or third, Yayoi may refer specifically to admixed people (Mumun + Jōmon in varying in proportions and across great distances). Fourth, Yayoi may indicate acculturation: the adoption of (rice) agriculture (and other continental material culture) by Jōmon-lineage people in the Yayoi period. All of these conflicting aspects of Yayoi must be kept in mind and clearly defined in any discussion.

Upon the Mumun migrants’ arrival, it is assumed from artefactual, skeletal morphological, and genetic evidence that many took partners from the resident Jōmon population, leading to mixed descendants – and to cultural transformation. These generational ‘admixed’ farmers then spread out from North Kyushu into the rest of the Japanese Islands, meeting more local Jōmon-lineage peoples with further admixing taking place. It is common in the literature to label the admixed farmers as ‘Yayoi’ because they carried the new culture based on rice, while increasingly recognizing that Jōmon-lineage peoples (distinguished as Epi-Jōmon in the north, but included within ‘Yayoi’ in the south) survived well into historical times without substantial admixture. The mixing of these two populations is recognized as the Dual Structure Hypothesis of the modern mainland Japanese population (Hanihara, Reference Hanihara1991, Reference Hanihara and Omoto2000).

The first section below reports on Jōmon genetics as a basis for further research on Yayoi admixtures. Despite the 13,000-year Jōmon history entailing multiple cultural formations and temporal trends, archaeologists tend to treat the Jōmon as a homogeneous people unadmixed with mainland East Asians and Austronesians since their separation from each other in the Palaeolithic. Genetic research is disabusing us of that approach, revealing potential Jōmon contacts with coastal mainland East Asians before the arrival of Mumun migrants; these data mirror archaeological evidence of contact. This is enlightening for its own sake, particularly in tracing connections between the Jōmon and continental peoples. However, in terms of investigating Yayoi admixtures, it makes the issue much more complicated. As more Yayoi-period genomic data becomes available, we may then be able to track the regional spread of continental genes through the Japanese archipelago. The addition of new Yayoi-period genomic data is vital, as new waves of immigration from the Korean Peninsula in the succeeding Kofun and Nara periods have enhanced the continental contribution in the modern Japanese, making it difficult to use present-day genomes to effectively study population movement and admixture in the Yayoi period.

The second section focusses on the spread of agriculture from west to east through the Japanese Islands. The major topic of study in this spread has been the adoption of irrigated wet-rice agriculture. It has been assumed that this technology was spread by admixed farmer-migrants. In contrast, new studies are documenting instances of non-irrigated (swamp, dryland) rice and millet cultivation that may be earlier (e.g. Nasu & Momohara, Reference Nasu and Momohara2016; Shitara & Takashe [sic], 2014). These authors assume that local Final Jōmon and Epi-Jōmon peoples were the cultivators, although some may have become farmers of irrigated wet rice later. The relationships between cultivation technologies and ethnic populations are often unclear, making the next step in the analysis, on language spread, difficult.

The third section deals with language spread. Prehistoric language as such is inaccessible, but the fact that nowadays all languages on the islands except Ainu are related to Japanese makes it absolutely clear that the population that brought wet-rice agriculture to Japan must have been speakers of proto-Japanese. (Proto-Japanese is the ancestral language from which all modern varieties of Japanese descended.) Proto-Japanese split into several dialects, and then Ryūkyūan split off from the Kyūshū dialect. Evidence for the latter scenario has been growing in recent years. (For an overview see De Boer Reference De Boer2017.) Although the Ryūkyūan varieties form independent languages now, their split from the Kyūshū dialect makes them in origin dialects of Japanese.

Proto-Japanese is postulated to have developed on the continent (Whitman, Reference Whitman2011; Miyamoto, Reference Miyamoto2016; Robbeets, Reference Robbeets2005, Reference Robbeets2017), and it is hypothesized to have had spread throughout the archipelago with the admixed Yayoi people practising irrigated rice agriculture. This accords well with the farming/language dispersal hypothesis (Renfrew, Reference Renfrew1987; Bellwood & Renfrew, Reference Bellwood and Renfrew2002). Problems, however, include exactly when and how this spread took place, whether it was indeed only associated with rice agriculture or also with other grain crops, and what Jōmon or Epi-Jōmon language(s) might have been replaced or pushed out by which dialect of Japanese. With the general lack of Yayoi DNA and written linguistic data, it is difficult to match food production techniques, genomic identity and language type.

Jōmon genetics

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Jomon: Paleolithic Contingent in Modern Japanese Feb 27, 2024 20:34:20 GMT

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Post by Admin on Feb 27, 2024 20:34:20 GMT

The transition from the Jōmon to the Yayoi periods marked a transition in the material culture of Japan, with the appearance and increase of tools, artefacts and archaeobotanical remains associated with agriculture. Studies have long associated this transition with the migration of Mumun people through the Korean peninsula into the closest island in the Japanese archipelago, Kyushu (Hammer & Horai, Reference Hammer and Horai1995; Hanihara, Reference Hanihara1991). Early assessments using cranial and dental morphology and genetics of humans and their commensals led to the Dual Structure model (Hanihara, Reference Hanihara1991), for which a key component is the argument that present-day Japanese are a mixture of populations indigenous to Japan since the Palaeolithic and later migrants from mainland Asia. Many studies, mostly using present-day genomes of indigenous populations in the archipelago (i.e. Ainu, Ryūkyū) as a proxy for Jōmon-related ancestry, found genetic patterns that suggest that the present-day Japanese populations are admixed, supporting that aspect of the Dual Structure model (Jeong, Nakagome, & Di Rienzo, Reference Jeong, Nakagome and Di Rienzo2016a; Jinam et al., Reference Jinam, Kanzawa-Kiriyama, Inoue, Tokunaga, Omoto and Saitou2015; Nakagome et al., Reference Nakagome, Sato, Ishida, Hanihara, Yamaguchi, Kimura and Consortium2015).

Advances in DNA sequencing methods have allowed access to genetic material for studying population demographic history in the Japanese archipelago. Uniparental markers were some of the earliest used to infer population history; these include mitochondrial DNA (mtDNA), which exists outside the nucleus, and the non-recombining portion of the Y-chromosome. The primary units considered when studying these markers are haplogroups, which are variants of a DNA segment that derives from the same common ancestor, and they can provide information on a population's genetic history.

Since uniparental transfer results in no recombination, it is straightforward to reconstruct phylogenetic trees and assign a haplogroup to the mtDNA or Y-chromosome region (Haber, Mezzavilla, Xue, & Tyler-Smith, Reference Haber, Mezzavilla, Xue and Tyler-Smith2016). Sets of haplogroups are now well annotated and easily identifiable in newly sequenced individuals using many tools and databases (e.g. ISOGG, 2019; Weissensteiner et al., Reference Weissensteiner, Pacher, Kloss-Brandstätter, Forer, Specht, Bandelt and Schönherr2016). If they are identified to be at high frequency in a localized area but in low frequency elsewhere, the origin of the haplogroup, or the common ancestor, can be inferred to have derived from that region. While the lack of recombination allows simple haplogroup assignation, it also means that it is a single data point representing population history, and stochastic events or sex-biased migration patterns can lead to inaccurate inference of the true population history (Nordborg, Reference Nordborg1998; Rosenberg & Nordborg, Reference Rosenberg and Nordborg2002).

In contrast, the nuclear genome undergoes recombination, which means that small segments of each chromosome have effectively independent histories. Study of a single diploid genome (i.e. the 23 pairs of chromosomes in the cell nucleus) can be interpreted as study of small portions of thousands of different individuals, resulting in high statistical power for inferring the history of the population(s) represented by those individuals. Thus, sampling genome-wide is imperative for assessing the accuracy of the demographic relationships inferred from uniparental markers.

The ability to extract and sequence ancient DNA (aDNA) has revolutionized the study of human prehistory, allowing direct sampling of past populations and revealing genetic variation no longer observed today. Post-mortem degradation of DNA makes it very difficult to sequence aDNA, so the greater numbers of mtDNA makes it much easier to extract and sequence. The earliest ancient DNA studies in humans were for mtDNA (e.g. Krings et al., Reference Krings, Stone, Schmitz, Krainitzki, Stoneking and Pääbo1997), including from a Jōmon individual as early as 1989 (Horai et al., Reference Horai, Hayasaka, Murayama, Wate, Koike and Nakai1989) and Yayoi individuals as early as 1995 (Oota, Saitou, Matsushita, & Ueda, Reference Oota, Saitou, Matsushita and Ueda1995). In fact, the majority of ancient DNA studies on Jōmon individuals have been on mtDNA (Schmidt & Seguchi, Reference Schmidt and Seguchi2014).

Only recently have ancient nuclear genomes been retrieved from individuals from Japan. Ancient genomes have been published from human remains at different sites (Sanganji, Ikawazu, and Funadomari associated with Jōmon material culture; Shimo-Motoyama associated with Yayoi material culture; Figure 1). Two partial genomes sequenced from the Sanganji shellmound in Tōhoku were of 3000-year-old individuals (Kanzawa-Kiriyama et al., Reference Kanzawa-Kiriyama, Kryukov, Jinam, Hosomichi, Saso, Suwa and Saitou2017). Genome-wide data have also been retrieved for a 2700-year-old individual from Ikawazu (McColl et al., Reference McColl, Racimo, Vinner, Demeter, Gakuhari, Moreno-Mayar and Willerslev2018) and two 3900-year-old individuals from the Funadomori site in Hokkaido (Kanzawa-Kiriyama et al., Reference Kanzawa-Kiriyama, Jinam, Kawai, Sato, Hosomichi, Tajima and Shinoda2019). Sampling of nuclear genomes is still sparse, but a rough understanding of the ancestry associated with the Jōmon is taking shape with each study.

Characterizing Jōmon-period ancestry is fundamental to understanding the genetic composition of humans that lived during the Yayoi period, who ostensibly represent various degrees of mixture between Jōmon and continental peoples. This in turn will improve our understanding of population migration on the archipelago and its role in the spread of agriculture across the archipelago. Here, we highlight some key features and emerging questions observed to date on Jōmon-related ancestry, which allow us to better understand the challenges (and rewards!) in interpreting the genetics of the Yayoi in future studies.

Analyses of both uniparental (Y and mtDNA) and nuclear DNA of present-day populations have highlighted that ancestry persists in Japan that is deeply diverged from ancestry found in mainland East Asian populations. The distribution of haplogroup frequencies across multiple populations is often used to determine where haplogroups originated. For example, those that occur in high frequency in present-day populations from Japan but low frequency elsewhere (e.g. N9b, M7a, G1b) were proposed as candidate haplogroups of Jōmon origin (Adachi, Shinoda, Umetsu, & Matsumura, Reference Adachi, Shinoda, Umetsu and Matsumura2009; Adachi et al., Reference Adachi, Shinoda, Umetsu, Kitano, Matsumura, Fujiyama and Tanaka2011; Kanzawa-Kiriyama, Saso, Suwa, & Saitou, Reference Kanzawa-Kiriyama, Saso, Suwa and Saitou2013; Kivisild et al., Reference Kivisild, Tolk, Parik, Wang, Papiha, Bandelt and Villems2002).

The most prominent of these is N9b, which is the most frequent mtDNA haplogroup assigned to Jōmon individuals. An estimate of the time to the most recent common ancestor (t MRCA) is ca. 22,000 years ago, which is older than the t MRCA for several other haplogroups found in East Asians (Adachi et al., Reference Adachi, Shinoda, Umetsu, Kitano, Matsumura, Fujiyama and Tanaka2011). The non-recombining region of the Y-chromosome has also been extensively studied in Japan. Y-haplogroup D1b is exceptionally interesting as it is found in high frequency in the Japanese archipelago and the Tibetan Plateau but not elsewhere (Hammer & Horai, Reference Hammer and Horai1995; Tajima et al., Reference Tajima, Hayami, Tokunaga, Juji, Matsuo, Marzuki and Horai2004; Watanabe et al., Reference Watanabe, Naka, Khor, Sawai, Hitomi, Tokunaga and Ohashi2019). The estimated t MRCA for D1b is ca. 19,400 years ago (Hammer et al., Reference Hammer, Karafet, Park, Omoto, Harihara, Stoneking and Horai2006), similar to that estimated for N9b mtDNA. These dates, if corresponding to the expansion of Jōmon ancestry on the archipelago, suggest that Jōmon ancestry separated fairly early from mainland East Asian ancestry.

One mtDNA haplogroup found in many Jōmon-associated individuals (e.g. Kanzawa-Kiriyama et al., Reference Kanzawa-Kiriyama, Saso, Suwa and Saitou2013; Adachi et al., Reference Adachi, Shinoda, Umetsu, Kitano, Matsumura, Fujiyama and Tanaka2011; Kim et al., Reference Ae-Jin, Kijeong, Jee-Hye, Eun-Ha, Yu-Jin, Na Young and Keun-Cheol2010) as well as Yayoi-associated individuals (Igawa et al., Reference Igawa, Manabe, Oyamada, Kitagawa, Kato, Ikematsu and Rokutanda2009) is D4, which is widespread in northern East Asia both in past and present-day populations (e.g. Tanaka et al., Reference Tanaka, Cabrera, Gonzalez, Larruga, Takeyasu, Fuku and Shimodaira2004; Zhao et al., Reference Zhao, Li, Cai, Li, Zhang, Zhu and Zhou2010; Hong et al., Reference Hong, Kim and Kim2014; Jeong et al., Reference Jeong, Wilkin, Amgalantugs, Bouwman, Taylor, Hagan and Warinner2018; Lan et al., Reference Lan, Xie, Jin, Fang, Mei, Yang and Zhu2019). Its widespread presence, however, suggests that it was found in the common ancestral population of all East Asians, making it difficult to evaluate its role in more recent migrations and interactions.

In genomic studies of ancient Asians, both a 40,000-year-old individual found in Tianyuan Cave, Beijing, China (Fu et al., Reference Fu, Meyer, Gao, Stenzel, Burbano, Kelso and Paabo2013; Yang et al., Reference Yang, Gao, Theunert, Tong, Aximu Petri, Nickel and Fu2017) and 8000-year-old individuals from Southeast Asia associated with Hòabìnhian foragers (McColl et al., Reference McColl, Racimo, Vinner, Demeter, Gakuhari, Moreno-Mayar and Willerslev2018) show an early split time from other East Asians, including from ancient Jōmon genomes (Kanzawa-Kiriyama et al., Reference Kanzawa-Kiriyama, Kryukov, Jinam, Hosomichi, Saso, Suwa and Saitou2017, Reference Kanzawa-Kiriyama, Jinam, Kawai, Sato, Hosomichi, Tajima and Shinoda2019). Thus, we denote them as ‘basal Asians’. In contrast, humans living in Southeast Asia, the eastern steppes of Siberia and the southwest edges of the Tibetan Plateau from the Neolithic to historic periods (e.g. Sikora et al., Reference Sikora, Pitulko, Sousa, Allentoft, Vinner, Rasmussen and Willerslev2019; Jeong et al., Reference Jeong, Ozga, Witonsky, Malmstrom, Edlund, Hofman and Warinner2016b) share a closer relationship to present-day East Asians than the Jōmon individuals, confirming that Jōmon are distantly related to mainland East Asian ancestry (Yang, MA and Fu, Q unpublished observations).

In fact, the Jōmon sampled thus far probably separated earlier than the split time of East Asians and the early Asian population that contributed to Native Americans (Gakuhari et al., Reference Gakuhari, Nakagome, Rasmussen, Allentoft, Sato, Korneliussen and Oota2019; Kanzawa-Kiriyama et al., Reference Kanzawa-Kiriyama, Kryukov, Jinam, Hosomichi, Saso, Suwa and Saitou2017, Reference Kanzawa-Kiriyama, Jinam, Kawai, Sato, Hosomichi, Tajima and Shinoda2019). Estimates of when ancestral Native Americans separated from the East Asian lineage is ca. 36,000–25,000 years ago (Moreno-Mayar et al., Reference Moreno-Mayar, Potter, Vinner, Steinrücken, Rasmussen, Terhorst and Willerslev2018), and a direct estimate of the split time between the Jōmon and mainland East Asians ranges from 38,000–18,000 years ago (Kanzawa-Kiriyama et al., Reference Kanzawa-Kiriyama, Jinam, Kawai, Sato, Hosomichi, Tajima and Shinoda2019). These estimates are broad, indicating there is still high uncertainty as to the exact date. However, studies of both uniparental and nuclear markers all highlight Jōmon ancestry separated from mainland East Asian ancestry in the Palaeolithic, with dates ranging from 38,000–18,000 years ago.

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Jomon: Paleolithic Contingent in Modern Japanese Feb 29, 2024 22:11:44 GMT

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Post by Admin on Feb 29, 2024 22:11:44 GMT

Figure 2. F4-tests surveying the relationship of populations with East Asian ancestry (on the x-axis, ‘X’) to the Ikawazu Jōmon, relative to ancient Southeast Asian foragers (Hòabìnhian, HB), an ancient Tibetan (Chokhopani, CH), and an inland ancient northern East Asian (Shamanka_EN, SH) (graphs by Melinda Yang). Numerical values for the data visualized here can be found in Table S3. F4-statistics are tests of symmetry of the form f4(Out, P1; P2, P3), where it is assumed that P2 and P3 form a clade with espect to P1. Our statistics take the form (A) f4(Mbuti, HB; Ikawazu Jōmon, ‘X’ East Asians) or (B, C) f4(Mbuti, Ikawazu Jōmon; CH or SH, ‘X’ East Asians), with the underlying tree structure verified by other genetic analyses. Central African Mbuti were used as the outgroup (Out).

Key: tree models showing relationships of f4 values are placed to the right of the plot: f4 > 0 corresponds to the highest tree; f4 = 0 corresponds to the middle tree (clarified by dashed grey arrow); and f4 < 0 corresponds to the lowest tree for each figure. The presence of gene flow in the model is indicated by the red arrow. A significantly positive value highlights gene flow between the outgroup (P1) and ‘X’ East Asians (P3). A significantly negative value highlights gene flow between the outgroup (P1) and the other population in the tree (P2). Two standard errors are indicated by the thin grey bar, while one standard error is indicated by the thick grey bar. Points are coloured (colour online) by region of origin, with darker colours for ancient populations and lighter colours for present-day populations. East Asians for whom all or part of their population live near coastal East Asia are shaded grey. *Ancient islanders were sampled from Southeast Asian and Southwest Pacific islands, but were previously shown to share a close relationship to present-day Austronesians (McColl et al., Reference McColl, Racimo, Vinner, Demeter, Gakuhari, Moreno-Mayar and Willerslev2018; Skoglund et al., Reference Skoglund, Posth, Sirak, Spriggs, Valentin, Bedford and Reich2016).

Interpretation: in Figure 2A, 8000-year-old Hòabìnhian (HB) foragers from Laos and Malaysia are an outgroup to the Ikawazu Jōmon individual and present-day and ancient populations of East Asian ancestry. A connection between the Ikawazu Jōmon individual and the Hòabìnhians would result in a significantly negative statistic (f4 < 0), which is not observed. In all cases, the Ikawazu Jōmon shows no connection to Hòabìnhians (f4 ≈ 0).

In Figure 2B, we compare against a 3100-year-old Tibetan (Chokhopani, CH), and in Figure 2C, we compare against a 7500-year-old northern East Asian from the eastern steppe region of Siberia (Shamanka_EN, SH). The Ikawazu Jōmon is an outgroup to all East Asians, including these ancient inland East Asians. Thus, a significantly positive statistic (f4 > 0) indicates that the Ikawazu Jōmon shares connections with that East Asian (X) that the ancient inland East Asian Chokhopani or Shamanka_EN do not possess. No connections are observed between the Ikawazu Jōmon and ancient inland East Asians, which would be indicated by a significantly negative statistic (f4 < 0). A symmetric relationship to Ikawazu is observed when comparing with other non-coastal ancient and present-day East Asians (f4 ≈ 0). Coastal East Asians from northern and southern East Asia tend to show significantly positive results (f4 > 0), indicating a connection to the Ikawazu Jōmon that ancient inland East Asians do not share.