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Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve...
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... blood or saliva specimens were collected from 1660 unrelated male individuals from 35 ethnic groups in ISEA, Taiwan, the east coast of China and Indochina (Vietnam and Thailand) ( Table 1 and Figure 1). ...
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... data with other populations of south China, ISEA and Oceania were taken from the literature and comprised Yueh/Daic-speaking populations [27,30,[36][37][38], Malayo-Polynesians and Papua New Guineans [39], and Han Chinese [7,8,12,29,30,40,41]. These datasets are shown in Additional file 1: Table S1. ...
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... the PCR-SSP method, a combination of 81 markers, the majority of which are slowly evolving SNPs [8], were used to genotype in a hierarchical fashion the NRY of 1660 individuals. Altogether, these 81 markers define 68 Y-SNP haplogroups: CDEF-M168, C*-M216, C1-M8, C2-M38, C3-M217, C4-M247, C5-M356, C6-P55, DE- M145, D*-M174, D1-M15, E-M96, F*-M89, G-M201, , H- M69, H1-M52, H1a-M82, H2-Apt, I-M170, J-P209, K-M9, K1-M147, L-M20, M-P256, NO-M214, N-M231, N1- LLY22g, N1a-M128, N1c*-Tat, N1c1-M178, O-M175, O1a*-M119, O1a1*-P203, O1a1a-M101, O1a2-M50, O2*-P31, O2a*-PK4, O2a1*-M95, O2a1a-M88, O2b-SRY465, O3*M122, O3a*-M324, O3a1*-KL1, O3a1a-M121, O3a1b- M164, O3a1c*-IMS-JST002611, O3a1c1-P103, O3a2*-P201, O3a2a-M159, O3a2b*-M7, O3a2b1-M113, O3a2c*-P164, O3a2c1*-M134, O3a2c1a-M133, O3a2c1a1-M162, O3a2c1b- P101, O3a3-M300, O3a4-M333, PQR-M45, Q-M242, R*-M207, R1-M173, R1a1*-SRY10831.2, R1a1a-M17, R1b-M343, R2a-M124, S-M230, and T1-M70. ...
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... samples were further subjected to genotyping with 17 microsatellites (DYS19, DYS385I, DYS385II, DYS389I, DYS389II, DYSS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y GATA-H4) and analyzed using Y-filer kit (Applied Table 1 Information on the 35 population samples genotyped in the present study Sample number 1 Country Ethnicity ISO639-3 (or local) Sample numbers as in Figure 1. Biosystems). ...
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... the contour map interpolation (which includes published data, see Additional file 1: Table S2 for a more detailed frequency table. Table S1) indicates its presence in Western Sumatra, towards the Indian Ocean ( Figure 3). The internal STR diversity of O1a*-M119 decreases gradually from mainland China towards the south, although a second, somewhat lower peak of diversity is observed around the Moluccas. ...
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... MJ network of O1a*-M119 ( Figure 4) clearly differ- entiates TwMtA and TwPlt from Indonesia (Indonesian STR haplotypes are all included in the lower left reticula- tion of the O1a*-M119 network), whereas most Filipinos O1a*-M119 haplotypes are shared or very similar to those Figure 3 Spatial distributions of the O1, O2 and O3 clades using haplogroup frequency and associated STR diversity (rho statistic). Maps are based on data from Additional file 1 : Tables S1 and S2 and from literature data [12,27,30,36,39,40,62]. Panels are labeled according to ISOGG2011 [8,42,43]. ...
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... estimates of the diversity of these two haplogroups all point to the early Neolithic period (i.e. < 10,000 Kya), with the notable exception of estimates for the Han groups (Table 2 and Additional file 1: Table S3). Accordingly, the contour maps of O3a2c1*-M134 display a general location of higher fre- quency and diversity related to Han populations, in mainland SEA (Figure 3). ...
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... a second MDS analysis, we included earlier published data (Additional file 1: Table S1) to investigate the genetic relationships of populations represented in our dataset to other East Asian groups. The resulting 2-dimensional plot is provided in Additional file 1: Figure S4. ...
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... also genotyped 17 Y-specific STR markers, in order to gain insights into the distribution of the Y-chromosome variation in this region of the world. Since only one population from the mainland east coast of China (Fujian Han) was analyzed, data from other populations of SEA were obtained from the literature (Additional file 1: Table S1). ...
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... the lack of a clear clinal pattern of frequency variation of this haplogroup between regions, the low frequency but high diversity observed in Indonesia ( Figure 2 and Table 2) and the rather faint star-like shape of the MJ network showing numerous long branches and low frequency nodes (Figure 4) all suggest a recent spread of O3a1c* from mainland SEA. Thus the O3a1c* high frequency observed for the Ivatan (25%) of the Batan archipelago, north of the Philippines, associated to a low age estimate (0.9 Kya, Table 2 and Additional file 1: Table S3), is con- sistent with a recent introduction of this haplogroup by gene flow with TwHan or TwPlt. The presence of Han lin- eages at most nodes of the star-like MJ network supports this hypothesis (Figure 4). ...
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... another hand, haplogroup O3a2c*-P164, whose origins also likely trace back to mainland SEA, is quite fre- quent in Taiwan (especially so among the Amis), whereas the derived O3a2c1*-M134 and O3a2c1a-M133 are rather rare among TwMtA. In our dataset we observed that they often occurred together (Additional file 1: Table S2), and given the recent dates estimated for their STR di- versification (~8 to 6 ± 4 Kya ago) ( Figure 3, Table 2 and Additional file 1: Table S2), it is likely that their spread southwards to Vietnam, Laos and Thailand, as well as to Taiwan, the Philippines and Indonesia, concomitant with a northward spread to Japan [26,77], occurred during Neolithic times. ...
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... patterns of genetic diversity observed in this study are consistent with this scenario in that several haplogroups displaying a cline with lower Y-STR diversity over Western Indonesia (i.e. O1a*-M119, O1a1*-P203 and O1a2-M50) or lower diversity over Taiwan (O2a1*-M95) show diversity higher than expected in the Philippines, as attested by the corresponding age estimates (Table 2 and Additional file 1: Table S3). ...
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... S4. MDS plot (stress 0.203) using our data and literature data from Additional file 1: Table S1 (over 6000 chromosomes). Haplogroup frequencies were adjusted to 20 basal haplogroups (low definition SNP). ...
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... frequencies were adjusted to 20 basal haplogroups (low definition SNP). See Additional file 1: Table S1 for correspondence of numbers and populations. Table S1. ...
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Background: Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used...
Citations
... We then extracted a total of 2088 SNPs on the non-recombining region of the Y chromosome (MSY) for this study (S1 and S2 Datasets); analyses of the autosomal SNP data for these individuals are part of a further study. For subsequent analysis, these SNPs were aligned with~2.3 million bases of the MSY of 600 previously published Vietnamese samples [24], resulting in 2079 overlapping SNP positions (S3 and S4 Datasets [42,43] based on reported Y-chromosomal SNP datasets (S4 Table). We use the term haplotype throughout this paper to refer to the Y chromosome SNP sequences and not to STR profiles. ...
Austronesian (AN) is the second-largest language family in the world, particularly widespread in Island Southeast Asia (ISEA) and Oceania. In Mainland Southeast Asia (MSEA), groups speaking these languages are concentrated in the highlands of Vietnam. However, our knowledge of the spread of AN-speaking populations in MSEA remains limited; in particular, it is not clear if AN languages were spread by demic or cultural diffusion. In this study, we present and analyze new data consisting of complete mitogenomes from 369 individuals and 847 Y-chromosomal single nucleotide polymorphisms (SNPs) from 170 individuals from all five Vietnamese Austronesian groups (VN-AN) and five neighboring Vietnamese Austroasiatic groups (VN-AA). We found genetic signals consistent with matrilocality in some, but not all, of the VN-AN groups. Population affinity analyses indicated connections between the AN-speaking Giarai and certain Taiwanese AN groups (Rukai, Paiwan, and Bunun). However, overall, there were closer genetic affinities between VN-AN groups and neighboring VN-AA groups, suggesting language shifts. Our study provides insights into the genetic structure of AN-speaking communities in MSEA, characterized by some contact with Taiwan and language shift in neighboring groups, indicating that the expansion of AN speakers in MSEA was a combination of cultural and demic diffusion.
... Table 1 exhibits the coalescence time estimations based on the available 15-loci Y-STR haplotypes under subhaplogroup O2a2-P 164 of populations with sufficient number of individuals. The time estimations were calculated from Y-STR genotypes generated in the original studies 13,26,[37][38][39] . Due to the limitations and assumptions associated with the current calibrations of Y-STR mutation rates [40][41][42][43] , as well as the differences in methodology among studies, the dates generated in this study should only be taken as relative estimates for comparisons among the populations examined in this report. ...
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... The maps of population haplogroup frequencies were supplemented with measures of haplogroup diversity, generated from a dataset of over 5,000 STR profiles ( Fig. 3; points). These techniques have a long history of use in human population genetics [29][30][31][32]57 and allow researchers to infer likely origin points of haplogroups from regions of high diversity [58][59][60][61] . ...
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... It was also the dominant haplogroup in our study, except for the Kyrgyz population. Haplogroup O1a-M119 is dominant in Austronesian-speaking populations of Southeast Asian islands, but rare in Austronesian-speaking populations from the Pacific islands [26]. Previous studies have showed that haplogroup O1a is one of the paternal lineages of the Han, Tai-Kadai-speaking and Austronesian-speaking populations. ...
China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literature were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1-F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time with the most recent common ancestor (TMRCA), we found that haplogroups C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.
... Перейдем к гаплогруппе Т на территории Индостана. Гаплогруппа Т у аустро-азиатских народов по (Chaubey, Metspalu et al. 2011: Suppl., tab.1;Trejaut et al. 2014: 23, fi g.2) отсутствует. По (Trivedi et al. 2007: 398, tab. ...
... The Highland groups of Taiwan have been the primary focus of genetic studies, while the Lowland groups have received much less attention. There is evidence of genetic diversity among Taiwanese Austronesians, as shown by studies of the Highland groups using uniparental genetic makers (6,(22)(23)(24)(25), although few of these studies included the Lowland groups (6,24,25). Furthermore, genome-wide studies, which can provide much more detailed insights into population histories, are very limited. ...
... The Highland groups of Taiwan have been the primary focus of genetic studies, while the Lowland groups have received much less attention. There is evidence of genetic diversity among Taiwanese Austronesians, as shown by studies of the Highland groups using uniparental genetic makers (6,(22)(23)(24)(25), although few of these studies included the Lowland groups (6,24,25). Furthermore, genome-wide studies, which can provide much more detailed insights into population histories, are very limited. To our knowledge, genome-wide data have only been generated for the Atayal, Amis, Paiwan, and Tao (Yami) (17,(26)(27)(28). ...
... The fact that the Atayal exhibit the highest levels of within-group IBD sharing (Fig. S5) may also explain why they are the most distinct of the THI/TOI groups in PCA and ADMIXTURE analyses (Figs. 2 and 3C). The Atayal have their own distinct haplotype network, according to a previous Y-chromosomal DNA study (24), suggesting they experienced founder/isolation events. The genetic structure observed within Taiwan could have formed (or strengthened) within the past 3 kya, as the signal can be identified in all size ranges of IBD sharing between/within the THI/TOI group (Figs. ...
The origin and dispersal of the Austronesian language family, one of the largest and most widespread in the world, have long attracted the attention of linguists, archaeologists, and geneticists. Even though there is a growing consensus that Taiwan is the source of the spread of Austronesian languages, little is known about the migration patterns of the early Austronesians who settled in and left Taiwan, i.e. the “Into-Taiwan” and “out-of-Taiwan” events. In particular, the genetic diversity and structure within Taiwan and how this relates to the into-/out-of-Taiwan events are largely unexplored, primarily because most genomic studies have largely utilized data from just two of the 16 recognized Highland Austronesian groups in Taiwan. In this study, we generated the largest genome-wide data set of Taiwanese Austronesians to date, including six Highland groups and one Lowland group from across the island and two Taiwanese Han groups. We identified fine-scale genomic structure in Taiwan, inferred the ancestry profile of the ancestors of Austronesians, and found that the southern Taiwanese Austronesians show excess genetic affinities with the Austronesians outside of Taiwan. Our findings thus shed new light on the Into- and Out-of-Taiwan dispersals.
... Histo-leukocyte-Antigen (HLA-A, -B and -DRB1) [11][12][13][14][15][16]. In this study, we aim to use these gene systems further by focusing on the genetic differentiation and the admixture patterns between the Truku and Atayal tribes. ...
... 16 Y-chromosomes short tandem repeats (Y-STRs haplotypes) in a sample of 258 Atayal indigenous people from the northern central mountain ranges and 64 men from the Truku tribe living on the northeast coast of Taiwan [11,15]. Individuals were unrelated, spoke either Truku or Atayal languages [11]. ...
... The Atayal and Truku indigenous people were compared to a dataset of 1,607 Y-chromosomes from East and island Southeast Asia [15]. The Y-SNPs and Y-STRs data of Atayal and Truku are shown in Supplement Table S1. ...
Background: The Truku indigenous people of Taiwan share strong cultural and genetic relationships with the Atayal tribe. Archaeological and linguistic studies show that their line of descent is associated to Proto-Austronesian speaking groups from Southeast Asia who settled in Taiwan in the early Neolithic, 6000 years ago.
... This scenario differs markedly from Bellwood's widely-publicised 'Out of Taiwan' model for the origin of the Austronesians (see Bellwood and Dizon, 2008), which seemed to be supported by the early genetic evidence (e.g. see Ko et al., 2014;Mörseburg et al., 2016;Tabbada et al., 2010;Trejaut, 2014). But, even then, some prehistorians were uncomfortable about the mismatch between the genetic and the archaeological evidence, pointing out that none of the early supposedly Austronesian sites in the Philippines had pigs, dogs, pottery or evidence of rice cultivation (e.g. ...
... These uni-parental gene systems never recombine; they are exclusively inherited maternally or paternally. In addition to the linguistic relationship with genetics, many studies have used these gene systems to characterize gene flow, mixture, and the origin of many autochthonous groups 17,18 and have more recently used DNA from ancient human remains to retrace the origin of archaic humans in East Asia 19,20 . ...
Many studies have described the diversity of Austronesian-speaking Taiwanese people to shed more light on their origin and their connection with the “Out of Taiwan” migrations. However, the genetic relationship between the non-Austronesian-speaking groups of Taiwan and the populations of continental Asia is still unclear. Here, we studied the diversity of mtDNA in 767 non-Austronesian speakers from 16 locations in Taiwan using partial sequencing obtained from the hypervariable segment I (HVS-I) and coding regions 8,001-9,000 and 9.801–10,900 and 85 complete mtDNA genome sequences. Bayesian analysis of population structure was used to examine their relationship with over 3662 individuals representing indigenous groups of Taiwan, continental East Asia, Japan, and Island Southeast Asia. The whole analysis identified 278 haplotypes. Complete genomes revealed 62 novel subhaplogroups, of which 31 were exclusive to Taiwan. Estimates of coalescence times of all subhaplogroups showed peaks of diversification greater than 5.0 kya, likely characterizing gene flow from continental East Asian groups but not excluding in situ Taiwanese ancestry. Furthermore, a significant number of clades exclusive to non-Austronesian speakers of Taiwan (NAN_Tw) showed coalescence peaks between 1.0 and 2.6 kya, suggesting possible late Neolithic to early metal age settlements of NAN_Tw and local expansion in Taiwan.
... we constructed a simplified phylogenetic tree that showed the overall distribution of Handan Han samples. To better understand the distribution of prevailing haplogroups in the studied population, we integrated data from previously published papers (Shi et al. 2005;Xue et al. 2006;Park et al. 2012;Trejaut et al. 2014;Ning et al. 2016;Li et al. 2020;Zhou et al. 2020) and constructed contour maps by Surfer 15 (https://www.goldensoftware.com/products/ surfer). ...
We analysed the forensic characteristics and substructure of the Handan Han population based on 36 Y-STR (short tandem repeat) and Y-SNP (single nucleotide polymorphism) markers. The two most dominant haplogroups in Handan Han, O2a2b1a1a1-F8 (17.95%) and O2a2b1a2a1a (21.51%), and their abundant downstream branches, reflected the strong expansion of the precursor of the Hans in Handan. The present results enrich the forensic database and explore the genetic relationships between Handan Han and other neighbouring and/or linguistically close populations, which suggests that the current concise overview of the Han intricate substructure remains oversimplified.
