Two papers excerpted here below reveal the complexities and difficulties of determining the origins of Jomon peoples of Japan:
Gakuhari 2019, Jomon genome sheds light on East Asian population history
From the abstract
Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.
First, we characterized IK002 in the context of worldwide populations after the out-of-Africa expansion using principal component analysis (PCA)[31,32].We found that IK002 clusters between present-day Southeast and East Asians and the Upper-Paleolithic human remain (40 kya) from Tiányuán Cave[28,33](Fig.1A). Second, when using a smaller number of SNPs (41,264 SNPs) including the present-day Ainu from Hokkaido (Fig.S1), IK002 clusters with the Hokkaido Ainu (Fig.S4), supporting previous findings that they are direct descendants of the Jomon people[14,34–41].Thus, the PCA plot showed that IK002 is slightly different from present-day people in East Eurasia and Japan except for the Hokkaido Ainu. [1. The simpler explanation might simply be that proto-N9b ancestor arrived via the Sakhalin-to-Hokkaido route to establish the N9b as it has been shown before that N9b has a Northeast to southwest cline, i.e. that N9b entered from the northern route along with the microblade culture (and possibly with a variation of D haplogroup-bearing people than that which entered Japan from the south)]
[…we carried out model-based unsupervised clustering using ADMIXTURE (Fig.S5). Assuming K = 10 ancestral clusters (Fig.1B), an ancestral component unique to IK002 appears, which is the most prevalent in the Hokkaido Ainu (average 79.3%). This component is also shared with present-day mainland Japanese as well as Ulchi (9.8% and 6.0%, respectively) (Fig.1C). Thus, the results of ADMIXTURE showed the strong genetic affinity between IK002 and the Hokkaido Ainu.
We next used ALDERto investigate the timing of admixture in populations with Jomon ancestry. Using IK002 and present-day Han Chinese as source populations, we estimate the admixture in modern Japanese to date to between 42 and 57 generations ago (~1,200 – 1,700 years ago …
For the Ulchi we estimate a more recent timing (8-33 generations ago) consistent with the higher variance in Ikawazu Jomon admixture proportions, albeit with overall weaker statistical support.Finally, using IK002 and present-day Japanese as source populations, we detect very recent (2-4 generations ago) admixture for the Hokkaido Ainu, likely a consequence of still ongoing gene flow between the Hokkaido Ainu and mainland Japanese.
To further explore the deep relationships of Jomon and other Eurasian populations, we used TreeMixto reconstruct admixture graphs of IK002 and 18 ancient and present-day Eurasian and Native American groups (Fig.1C & Fig.S6). We found the IK002 lineage placed basal to the divergence between ancient and present-day Tibetans[7,29]and the common ancestor of the remaining ancient/present-day East Eurasians[29,46]and Native Americans[47,48].These genetic relationships are stable across different numbers of migration incorporated into the analysis. Major gene flow events recovered include the well-documented contribution of MA-1 to the ancestor of Native Americans,as well as a contribution of IK002 to present-day mainland Japanese (m=3~6; Fig.S6). IK002 can be modelled as a basal lineage to East Asians, Northeast Asia/East Siberians, and Native Americans, supporting a scenario in which their ancestors arrived through the southern route and migrated from Southeast Asia towards Northeast Asia[6,49].The divergence of IK002 from the ancestors of continental East Asians therefore likely predates the split time between East Asians and Native Americans, which has been previously estimated at 26 kya.Thus, the TreeMixstrongly supported that IK002 is the direct descendant of the people who brought the Upper Paleolithic stone tools 38,000 years ago into the Japanese archipelago.
Testing the impacts of the northern route migration into East Asia
Taking advantage of the earliest divergence of the IK002 (Fig.1C & Fig.S6), we address a question if the Upper-Paleolithic people who took the northern route of the Himalayas mountains to arrive east Eurasia made genetic contribution to populations migrated from Southeast Asia. Under the assumption that MA-1 is a descendant of a northern route wave, we tested gene flow from MA-1 to IK002, as well as to the other ancient and present-day Southeast/East Asians and Northeast Asians/East Siberians by three different forms of D statistics: D(Mbuti, MA-1; X,Ami), D(Mbuti, X; MA-1, Ami), and D (Mbuti, Ami; X,MA-1).
The first D statistics (shown as red in Fig.2) provides results consistent with previous findings on the prevalence of MA-1 ancestry in the present-day Northeast Asians/East Siberians (Z< -3; Table S4),while none of Southeast/East Asians, except for Oroqen, shows a significant deviation from zero. The tree relationships observed in Fig. 1Care confirmed from the other two different forms between Ami and all of the tested populations with some variation that is mostly explained by the MA-1 gene flow (cyan and green in Fig.2, Table S5 & Table S6). Therefore, we concluded that no gene flow from MA-1 to the ancient/present-day Southeast/East Asians including IK002 was detected.
Remnant Jomon-related ancestry in the coastal regions of East Asia
The basal divergence of IK002 (Fig.1C) suggests a negligible contribution to later ancient and present-day mainland East Asian groups. To further test this prediction we conducted f4 s tatistics with the form of (Mbuti, IK002; X,Chokhopani). If IK002 were a true outgroup to later East Asian groups, this statistic is expected to be zero for any test population X. However, #we find that together with Japanese, present-day Taiwan aborigines (Ami and Atayal), as well as minorities in the Okhotsk-Primorye region (Ulchi and Nivhk) also showed a significant (Z < -3) excess of allele sharing with IK002. Populations in the inland of the eastern part of the Eurasian continent on the other hand were consistent with forming a clade with Chokhopani (Fig.3), suggesting the presence of remnant Ikawazu Jomon-related ancestry in present-day coastal populations in East Asia. The signal is also present in the Neolithic individuals from Devil’s Gate Cave in the Primorye region (Z < -3; Fig.S7a), suggesting that at 8 kya IK002-related ancestry in the region had already been largely but not completely replaced by later migrations. Interestingly, the genetic affinity to IK002 was found, thus, only in the coastal region but not in the inland for both ancient and present-day populations (Fig.3).
This study takes advantage of whole-genome sequence data from the 2,500-years old Jomon individual, IK002, dissecting the origins of present-day East Asians. IK002 is modelled as a basal lineage to East Asians, Northeast Asians/East Siberians, and Native Americans (basal East Eurasians: bEE)(Fig.4), supporting a scenario in which their ancestors came through south of the Himalayas mountains and migrated from Southeast Asia towards the north[6,49].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 kya,the divergence of the lineage leading to IK002 is likely to have occured before this time but after 40 kya when the Tiányuán appeared (Fig.4). Therefore, our results support the archaeological evidence that the Jomon are direct descendants of the Upper-Paleolithic people who started living in the Japanese archipelago 38 kya.
Here, 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 period.This microblade culture also reached the Hokkaido island ~25 kya and the mainland of the Japanese archipelago ~ 20 kya (Text S5). If this culture was brought by demic diffusion, IK002 may 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 (NS-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 was brought to the Japanese archipelago by the NS-NA population who must have had substantial gene flow from MA-1. The first and second possibilities can be examined by obtaining genome data of the Upper-Paleolithic specimens hopefully accompanying with microblade excavated from around Lake Baikal and from the Primorye region, respectively.
The genome of the Ikawazu Jomon (IK002) strongly supports the classical hypothesis concerning peopling history in the Japanese archipelago. 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 & S6). The PCA and ADMIXTURE showed the close relationship between IK002 and the Hokkaido Ainu even in the genome-wide structure reflected by linkage blocks.
(Fig.S4 & 5). These results fit the hypothesis that the Ainu and the Jomon share the common ancestor: the present-day mainland 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 migrants[35,40](Text S5).
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 & Fig.S7). There are two explanations for the genetic affinity to IK002: (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 important [3,50–53].The use of water craft could support such explanation for the expansions through the islands and the coastal region,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). 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 peoplewho were morphologically close related to Ulchi and Nivkh currently inhabit in the the Primorye region[55–57], which are supported by mtDNA[58,59]and genome-wide SNP data (Matsumae et al., unpublished data). 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 kya,though the origin of Igorot is not well known.
We carried out admixture graph modelling to further characterize the contributions of IK002-related ancestry (Fig. S8). To that end, we first fit a backbone graph including ancient genomes representative of major divergences among East Asian lineages: IK002 (early dispersal); Chokhophani (later dispersal, East Asia) and Shamanka (later dispersal, Siberia). Test populations of interest were then modelled as three-way mixtures of early (IK002) and later (Chokhopani, Shamanka) dispersal lineages, using a grid search of admixture proportions within qpGraph. Consistent with the results from the f4s tatistics, we find that models without contribution from IK002 result in poor model fit scores for Japanese, Devil’s Gate Cave and Ami, as opposed to inland groups such as Han which do not require IK002-related ancestry (Fig. S7). The range of admixture fractions with good model fit is generally quite wide, with best fit models show IK002-related contributions of 8%, 4% and 41% into Japanese, Devil’s Gate Cave and Ami, respectively (Fig. S8). We note that while the substantial contribution into Ami seems at odds with the lower f4 statistics compared to Japanese, the lineage admixing with Ami shares only a very short branch with IK002, suggesting a contribution from a distinct group with an early divergence from the IK002 lineage. As IK002 also shares ancestry with early Hòabìnhian hunter-gatherers,a contribution of those to the ancestors of Ami would also be compatible with this result. …
Using TreeMix and qpGraph (16, 19) to explore admixture graphs that could poten- tially fit our data, we find that group 1 individuals are best modeled as a sister group to present-day Önge (Fig. 3, and figs. S21 to S23 and S35 to S37). Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be mod- eled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29).
The remaining ancient individuals are modeled in fastNGSadmix as containing East Asian and Southeast Asian components present in high pro- portions in present-day Austroasiatic, Austronesian, and Hmong-Mien speakers, along with a broad East Asian component. A PCA including only East Asian and Southeast Asian populations that did not show considerable Papuan or Önge-like ancestry (fig. S11) separates the present-day speakers of an- cestral language families in the region: Trans- Himalayan (formerly Sino-Tibetan), Austroasiatic, and Austronesian/Kradai (20). The ancient individ- uals form five slightly differentiated clusters (groups 2 to 6) (Fig. 1B), in concordance with fastNGSadmix and f3 results (Fig. 2 and figs. S12 to S19) (11).
Group 2 contains late Neolithic and early Bronze Age individuals (4291 to 2184 cal B.P.), from Vietnam, Laos, and the Malay Peninsula who are closely related to present-day Austroasiatic lan- guage speakers such as the Mlabri and Htin (Fig. 1) (11). Compared with groups 3 to 6, group 2 indi- viduals lack a broad East Asian ancestry compo- nent that is at its highest proportion in northern EA in fastNGSadmix. TreeMix analyses suggest that the two individuals with the highest cover age in group 2 (La364 and Ma912) form a clade resulting from admixture between the ancestors of East Asians and of La368 (Fig. 3 and figs. S24 to S27). This pattern of complex, localized admix- ture is also evident in the Jehai, fitted as an ad- mixed population between group 2 (Ma912) and the branch leading to present-day Önge and La368 (fig. S28). Consistent with these results, La364 is best modeled as a mixture of a population an- cestral to Amis and the group 1/Önge-like popu- lation (Fig. 3). The best model for present-day Dai populations is a mixture of group 2 individuals and a pulse of admixture from East Asians (fig. S39).
Group 6 individuals (1880 to 299 cal B.P.) orig- inate from Malaysia and the Philippines and cluster with present-day Austronesians (11) (Fig. 2). Group 6 also contains Ma554, having the highest amounts of Denisovan-like ancestry relative to the other ancient samples, although we observe little variation in this archaic ancestry in our samples from MSEA (11).
Group 5 (2304 to 1818 cal B.P.) contains two indi- viduals from Indonesia, modeled by fastNGSadmix as a mix of Austronesian- and Austroasiatic- like ancestry, similar to present-day western Indonesians, a finding consistent with their po- sition in the PCA (Fig. 2) (11). Indeed, after Mlabri and Htin, the present-day populations sharing the most drift with group 2 are western Indonesian samples from Bali and Java previously identified as having mainland Southeast Asian ancestry (21) (fig. S13). Treemix models the group 5 individuals as an admixed population receiving ancestry related to group 2 (figs. S30 and S31) and Amis. Despite the clear relationship with the mainland group 2 seen in all analyses, the small ancestry components in group 5 related to Jehai and Papuans visible in fastNGSadmix may be remnants of ancient Sundaland ancestry. These results sug-gest that group 2 and group 5 are related to a mainland migration that expanded southward across MSEA by 4 ka ago and into island South- east Asia (ISEA) by 2 ka ago (22–24). A similar pattern is detected for Ma555 (fig. S33) in Borneo (505 to 326 cal B.P., group 6), although this may be a result of recent gene flow.
Group 3 is composed of several ancient individuals from northern Vietnam (2378 to 2041 cal B.P.) and one individual from Long Long Rak (LLR), Thailand (1691 to 1537 cal B.P.). They cluster in the PCA with the Dai, Amis, and Kradai speakers from Thailand, consistent with an Austro- Tai linguistic phylum, comprising both the Kradai and Austronesian language families (20, 25). Group 4 contains the remaining ancient individuals from LLR in Thailand (1570 to 1815 cal B.P.), and Vt778 from inland Vietnam (2750 to 2500 cal B.P.). These samples cluster with present-day Austro- asiatic speakers from Thailand and China, in sup- port of a South China origin for LLR (26). The genetic distinction between Austroasiatic and Kradai speakers is discussed further in (11).
Present-day Southeast Asian populations derive ancestry from at least four ancient populations (Fig. 4). The oldest layer consists of mainland Hòabìnhians (group 1), who share ancestry with present-day Andamanese Önge, Malaysian Jehai, and the ancient Japanese Ikawazu Jōmon. Consistent with the two-layer hypothesis in MSEA we observe a change in ancestry by ~4 ka ago, supporting a demographic expansion from EA into SEA during the Neolithic transition to farming. However, despite changes in genetic structure coinciding with this transition, evi- dence of admixture indicates that migrations from EA did not simply replace the previous occupants. Additionally, late Neolithic farmers share ancestry with present-day Austroasiatic- speaking hill tribes, in agreement with the hypotheses of an early Austroasiatic farmer expansion (20). By 2 ka ago, Southeast Asian individuals carried additional East Asian ancestry compo- nents absent in the late Neolithic samples, much like present-day populations. One component likely represents the introduction of ancestral Kradai languages in MSEA (11), and another the Austronesian expansion into ISEA reaching Indonesia by 2.1 ka ago and the Philippines by 1.8 ka ago. The evidence described here favors a complex model including a demographic transition in which the original Hòabìnhians admixed with multiple incoming waves of East Asian mi- gration associated with the Austroasiatic, Kradai, and Austronesian language speakers..
Figure 3. Model for migration routes into Southeast Asia uncovered by genomic data of prehistoric skeletons
Current evidence suggests that Southeast Asia was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, but the human occupation history of Southeast Asia thereafter with farming economies developed and expanded remains heavily debated. By sequencing 26 ancient human genomes (25 from Southeast Asia, 1 Japanese Jōmon), we show that Southeast Asian history is more complex than previously thought; both Hòabìnhian hunter-gatherers and East Asian farmers with further migrations contributed to current Southeast Asian diversity. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
Uncovering the expansion processes of human habitats in the past is of great importance for understanding the origins and establishment of present-day populations and the acquisition of genetic characteristics of individuals as well as for investigating mechanisms of resistance against diseases and pathogens. Previous genetic/genomic studies aimed to uncover the expansion processes using present-day human genomes of different individuals and locations. However, it is not always possible to elucidate the expansion processes based on the genomic similarity of present-day populations due to the possibility of migrations of populations between regions in various periods. It is therefore impossible to uncover the precise expansion processes of populations in the past without knowledge of the genomic information existing in a designated region and period. Thus, expansion processes hypothesized so far were nothing but speculations based on assumptions about present-day genomes.
Recent developments of DNA analysis technology have made it possible to obtain whole genome information from ultratrace amounts of DNA; we are now in an era where whole genome information can be obtained directly from ancient human skeletons discovered at archaeological sites. There remain, however, technical problems for obtaining whole genome information of ancient human skeletons. In particular, there are two main problems: first, genomic analyses*1) of poorly-preserved ancient remains in hot and humid regions of the world have up until now failed (Figure 1). Secondly, there is the risk of contamination of present-day human DNA in the DNA samples of ultratrace amounts from prehistoric remains. To evaluate objectively the possibility of such contamination, several different research groups must cross-check*2) one another in order to achieve exact genome sequencing; in other words, establishment of a collaborative research system is a prerequisite for attaining the highest level of scientific authenticity.
In order to cope with these problems, the present international research team, led by researchers from the University of Copenhagen with the participation of three researchers from Kanazawa University has established technologies to efficiently extract human DNA from skeletons discovered at prehistoric remains even under very poor conditions for DNA preservation. At the same time, an international system of research collaboration has been established for objectively evaluating the effects of contamination by present-day human DNA. Thanks to these efforts, the team has uncovered the expansion processes of human habitats and genetic interactions in hot and wet Southeast Asia, which was not possible previously with conventional technologies and research systems (Figure 2).
Worthy of special mention, the present study has been successful in determining the “whole genome” sequence of an individual with typical Jōmon culture, while previous studies were only able to show a very limited “partial genome” sequence of two Jōmon individuals. Thus, the present study is the first successful example to show the possibility of whole genome sequencing of prehistoric individuals in regions like Japan where preservation conditions are quite poor, possibly leading to further major progress in prehistoric genome studies.
In the present study, the international research team succeeded in extracting and sequencing DNA from 25 ancient individuals’ skeletons from Southeast Asian remains, where the condition of DNA preservation is very poor, and from one Japanese Jōmon female skeleton. Upon comparison of the genomic data of ancient human skeletons with those of present-day human skeletons, it has become clear that those prehistoric populations in Southeast Asia can be classified into six groups (Figure 3).
Group 1 contains Tahara, Aichi), a female adult*4), than other present-day Southeast Asians. In addition, the Ikawazu Jōmon genome*5) is best modelled contributing genetically present-day Japanese.
On the other hand, Groups 2-6 consist of ancient skeletons from the Neolithic Age, when farming started, until ~500 years ago. It is now found that they are genetically much different from Hòabìnhians, each group having histories of migration and genetic interaction, i.e., inter-population mixture. Group 2 is found to be genetically close to the present-day Austroasiatic language-speaking groups such as Mlabri, but to have few genetic components common with the present-day East Asian populations. Group 3 is found to be genetically close to Kradai, Thailand, in the present-day Southeast Asian populations and to the Austronesian language-speaking groups. Group 4 is found to be genetically close to the present-day populations in South China. Group 5 is genetically close to the present-day populations in the western part of Indonesia. Group 6 is most closely related to present day Austronesian populations, with one individual showing slightly elevated Denisovan ancestry, an archaic hominin which is classified as a sister group of Neanderthals.
As above, Neolithic Southeast Asians are found to have been partially genetically influenced by ethnic groups in South China and to have had a genetic connection with populations in Taiwan; Neolithic Southeast Asians are found not to have been indigenous hunter-gatherers passively accepting farming but to have accepted farming gradually in the process of migrations of populations between the continent and islands. Conventional archaeology proposed the two-layer hypothesis that, in those periods, a large population with farming culture with rice and millet migrated into Southeast Asia and that they replaced the indigenous population. Additionally, the present study indicates that the genetic influence from South China with rice farming was only partial and that the migrating population did not replace the indigenous population completely. The present analysis shows that there were at least four big migration waves; migrations of Southeast Asians should be investigated with a new “complex model” framework. …
*3) Ikawazu kaizuka (shellmound)
A kaizuka (shellmound) site at Tahara city, Aichi prefecture, dating back to late and final Jōmon period. One of the best known archaeological site of Jōmon period, where more than 200 individual skeletons have been discovered from Meiji era till today. A number of renowned anthropologists like Profs. Yoshikiyo KOGANEI and Hisashi SUZUKI performed morphological research on prehistoric skeletons from this site. There are also other kaizuka sites in Tahara city, such as Yoshigo kaizuka and Hobi kaizuka, representative Jōmon sites. Those sites have been well studied and many skeletons have been excavated.
*4) A female skeleton dating back to late Jōmon period, ~2500 years ago.
A Jōmon skeleton discovered from Ikawazu kaizuka site in 2010. Recent studies indicate the beginning of Yayoi period to be ~3000 years ago, but the arrival of Yayoi culture differed depending on regions. The female adult skeleton from Ikawazu kaizuka site is accompanied with a pottery that is validated to date back to the period of Gokanmori type pottery, indicating that the period was still Jōmon at those sites in Atsumi peninsula, Aichi prefecture. In addition, the female skeleton analyzed here shows typical Jōmon morphology.
#it was suggested by Melton et al., Genetic evidence for the Proto-Austronesian Homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes that the affinity seen between the Ami and the northern Asian coastal regions could be geneflow from those places into Taiwan as well:
“…an AMOVA of 11 Asian populations revealed that the Taiwanese account for more Asian substructure than does any other single population (Melton and Stoneking 1996). Second, the Taiwanese have a deep position with respect to Asian mtDNA control-region variation, as evidenced by the appearance of their sequences throughout neighbor-joining phylogenies of the most commonly shared types. This may indicate that they are derived from an early diverse pool of types that spread, from a centralized location, throughout Asia; certainly, the mismatch expansion times indicate that this substantial diversity has temporally deep roots. In fact, the four shared lineages without the deletion were observed to be from central Asia, northeast coastal Asia, island Southeast Asia, and Mongolia. The presence of related types in Taiwan, Japan, Korea, Ryukyu, and the Ainu is quite intriguing, and, although nothing suggests tight associations among any of these populations, we cannot rule out more recent introduction directly onto Taiwan, via migration, of mtDNAs from these northern coastal regions (however, the flow of mtDNAs could have been in the other direction).
Overall, for the markers we have described, the Taiwanese most resemble populations from the Philippines, but this probably is the result of migration from Taiwan—and perhaps especially from the Ami—south to the Philippines, as suggested by an earlier analysis of mtDNA diversity (Melton et al. 1995). However, although a connection between Taiwanese with the deletion and Southeast Asia is robust, mainland Asian connections for the deletion are present as well and have been found in additional mtDNAs observed primarily in north Asia and Taiwan. mtDNA substitutions associated with the Polynesian motif (e.g., 16217 and 16261) were also observed in China and Mongolia (as well as in Indonesia and the Philippines), providing another mainland link. Curiously, although the 9-bp deletion and related control-region motifs are easily detectable in Southeast Asia, there is little evidence of Taiwanese mtDNAs without the deletion in this region. Only one haplotype of Taiwanese without the 9-bp deletion was shared with another island Southeast Asian population, although there were a number of similar lineages. Unfortunately, at the present time, we lack mtDNA sequence data from Vietnam, Thailand, and other areas of mainland Southeast Asia, and, since theories about Taiwanese origins emphasize both south China and northern Indochina as potential sources, these would be valuable populations to sample.