Delineating the dispersal of Y-chromosome sub-haplogroup O2a2b-P164 among Austronesian-speaking populations

This article reports on an exploration of the Y-chromosome sub-haplogroup O2a2b-P164 in Austronesian-speaking populations. Moderate to high abundance of the P 164 mutation is seen in the West Pacific including the Amis of Formosa (36%) and the Filipinos of Mindanao (50%) as well as in the Kiritimati of Micronesia (70%), and Tonga and Samoa of West Polynesia (54% and 33%, respectively), and it drops to low frequencies in populations of East Polynesia. The communities of Polynesia and Micronesia exhibit considerable inter- and intra-population haplotype sharing suggesting extensive population affinity. The observed affinities, as well as the ages and diversity values within the P 164 sub-haplogroup among Austronesian-speaking populations signal an ancestral migration route and relationships that link the Amis of Taiwan with distant communities in West and East Polynesia, Micronesia, and the Maori of New Zealand. High resolution sequencing of the Austronesian Y chromosome indicate that the P 164 lineage originated about 19,000 ya and then split into three branches separating the Ami aborigines, Southeast Asian and Polynesian/Micronesian populations about 4700 ya, roughly coinciding with the initiation of the Austronesian diaspora. The Y-chromosomes of all the Polynesian and Micronesian population examined belong to the new FT 257096 haplogroup.

On the Y chromosome of Chennai, Tamil Nadu and the Indian subcontinent

Several migratory waves from various origins along with cultural practices restricting marriages between people of different castes and tribes as well as continued endogamy have led to a complex and diverse society in the Indian subcontinent. Despite being widely represented in genetic studies, several interrogatives remain with regards to India's current genetic constituents and distributions, source populations and population relationships. To identify the forces that may have shaped Indian population's genetic relationships, we undertook a comprehensive comparative study of the Y-chromosomes across India utilizing Y-STR and Y-SNP chromosomal markers using the general population of Chennai in the state of Tamil Nadu as a point of reference. Our analyses identify differences in source populations for different regions within India, unique linguistic characteristics as well as demographic and cultural forces that may have shaped population structure.

Bidirectional dispersals during the peopling of the North American Arctic

It is thought that Paleo-Inuit were the first people that settled the American Arctic about 5000 BP (before the present) from a migration that crossed Beringia from Northeast Asia. It is theorized that this group initially migrated to the North Slopes of Alaska and subsequently expanded eastward, eventually reaching Greenland. A second circumpolar dispersal of Neo-Inuit from the North Slopes associated with the Thule-Inuk culture has been postulated to have extended eastward around 800 BP, totally replacing the original Paleo-Inuit without admixing. Although generally accepted, this migration scenario is incompatible with previously reported indications of east to west gene flow across the American Arctic. Here we report on the Y-chromosome haplogroup and Y-STR diversity of the four circumpolar populations of the Tuva Republic (N = 24), Northeast Siberia (N = 9), Bethel, Alaska (N = 40), and Barrow, Alaska (N = 31). Four haplogroup lineages (Q-NWT01, Q-M3, Q-M346, and Q-M120) were detected, Q-NWT01 and Q-M3 being the most abundant at 11.11 and 66.67% in Northeast Siberia, 32.50 and 65.00% in Bethel, and 67.74 and 32.26% in Barrow, respectively. The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STYR loci using the AmpFlSTR Yfiler system. Age estimates and diversity values for the Q-NWT01 and Q-M3 mutations suggest extensive movement of male individuals along the entire longitudinal stretch of the American circumpolar region. Throughout the entire region, Q-M3 exhibits a west to east decreasing gradient in age and diversity while Q-NWT01 indicates the opposite with older TMRCA and higher diversity values running from east to west with the most recent estimates in Canada and Alaska. The high age and diversity values in Greenland are congruent with an origin of the Q-NWT01 mutation in the east of the circumpolar range about 2000-3000 ya. This scenario is incompatible with a complete biological replacement starting about 700 BP of Paleo-Inuit like the Dorset by the Thule-Inuit (Neo-Inuit), as is currently thought, and more parsimonious with gene flow carrying the NWT01 mutation from a pre-Thule population to the ancestors of the present-day Inuit.

Post-Austronesian migrational wave of West Polynesians to Micronesia

This study examines Y-chromosome and mtDNA markers in the population of the island of Kiritimati in the context of geographically targeted reference populations from the Pacific. Kiritimati derives its population from the atoll islands of the Gilbert Archipelago and representsa geographicaltransitional region between Micronesia, Polynesia and Melanesia that likely played a critical role during theAustronesian expansion. The large presence(84.1%)of individuals withO-M175, O2a-M324 and O2a2b-P164 sub-haplogroups, 69.9% being O2a2b-P164, the Y-STR homogeneity within O2a2b-P164 and the very recent age of the sub-haplogroup(363-548 years ago)inKiritimati suggestthe arrival ofa genetically homogenous population to the Gilberteses followed by a population expassion.The close Y-STR haplotype affinities with profiles from the Samoa and Tonga Archipelagos point to an unprecedented massive post-Austronesian expansionexodus from West Polynesia.Contrasting the abundance of AustronesianO2a2b-P164 sub-haplogroup, the most abundantMelanesian/Papuansub-haplogroup,C-M130is present at a frequency of 13.5%. Thenetwork topology suggests that C-M130 arrived to theKiribati Archipelago from West Polynesia, specifically from West Samoa, Tonga and/or Tutuila subsequent to the Austronesian expansion about 832-1408 years ago. The haplotype affinities withinO2a2b-P164 argue for anoriginal source in Taiwan and its dispersal to West Polynesia and then to Southeast Micronesia. The present investigation provides an understanding of the genetic composition and complex migration history of an understudied region of the Pacific and provides evidence for recent dispersals towards Micronesia from West Polynesia subsequent to the initial Austronesian expansion.

Genetic characterization of populations in the Marquesas Archipelago in the context of the Austronesian expansion

Our exploration of the genetic constitution of Nuku Hiva (n = 51), Hiva Oa (n = 28) and Tahuata (n = 8) of the Marquesas Archipelago based on the analyses of genome-wide autosomal markers as well as high-resolution genotyping of paternal and maternal lineages provides us with information on the origins and settlement of these islands at the fringe of the Austronesian expansion. One widespread theme that emerges from this study is the genetic uniformity and relative isolation exhibited by the Marquesas and Society populations. This genetic homogeneity within East Polynesia groups is reflected in their limited average heterozygosity, uniformity of constituents in the Structure analyses, reiteration of complete mtDNA sequences, marked separation from Asian and other Oceanic populations in the PC analyses, limited differentiation in the PCAs and large number of IBD segments in common. Both the f3 and the Outgroup f3 results provide indications of intra-East Polynesian gene flow that may have promoted the observed intra-East Polynesia genetic homogeneity while ALDER analyses indicate that East Polynesia experienced two gene flow episodes, one relatively recent from Europe that coincides roughly with the European incursion into the region and an early one that may represent the original settlement of the islands by Austronesians. Median Network analysis based on high-resolution Y-STR loci under C2a-M208 generates a star-like topology with East Polynesian groups (especially from the Society Archipelago) in central stem positions and individuals from the different populations radiating out one mutational step away while several Samoan and outlier individuals occupy peripheral positions. This arrangement of populations is congruent with dispersals of C2a-M208 Y chromosomes from East Polynesia as a migration hub signaling dispersals in various directions. The equivalent ages of the C2a-M208 lineage of the populations in the Network corroborate an east to west flow of the most abundant Polynesian Y chromosome.

The Y-chromosome of the Soliga, an ancient forest-dwelling tribe of South India

A previous autosomal STR study provided evidence of a connection between the ancient Soliga tribe at the southern tip of the Indian subcontinent and Australian aboriginal populations, possibly reflecting an eastbound coastal migration circa (15 Kya). The Soliga are considered to be among India's earliest inhabitants. In this investigation, we focus on the Y chromosomal characteristics shared between the Soliga population and other Indian tribes as well as western Eurasia and Sub-Saharan Africa groups. Some noteworthy findings of this present analysis include the following: The three most frequent haplogroups detected in the Soliga population are F*, H1 and J2. F*, the oldest (43 to 63 Kya), has a significant frequency bias in favor of Indian tribes versus castes. This observation coupled with the fact that Y-STR haplotypes shared with sub-Saharan African populations are found only in F* males of the Soliga, Irula and Kurumba may indicate a unique genetic connection between these Indian tribes and sub-Saharan Africans. In addition, our study suggests that haplogroup H is confined mostly to South Asia and immediate neighbors and the H1 network may indicate minimal sharing of Y-STR haplotypes among South Asian collections, tribal and otherwise. Also, J2, brought into India by Neolithic farmers, is present at a significantly higher frequency in caste versus tribal communities. This last observation may reflect the marginalization of Indian tribes to isolated regions not ideal for agriculture.

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Hg F*, H1 and J2 of the Soliga population chronicle the demographic history of the Indian tribal communities.

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Frequency bias for F* in Indian tribes may be a result of genetic drift due isolation and low population growth.

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Sharing of Y-STR haplotypes among tribal populations may be indicative of a common source population.

The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

This article reports on the genetic characteristics of the Ami and Yami, two aboriginal populations of Taiwan. Y-SNP and mtDNA markers as well as autosomal SNPs were utilized to investigate the phylogenetic relationships to groups from MSEA (mainland Southeast Asia), ISEA (island Southeast Asia), and Oceania. Both the Ami and Yami have limited genetic diversity, with the Yami having even less diversity than the Ami. The partitioning of populations within the PCA plots based on autosomal SNPs, the profile constitution observed in the structure analyses demonstrating similar composition among specific populations, the average IBD (identical by descent) tract length gradients, the average total length of genome share among the populations, and the outgroup f3 results all indicate genetic affinities among populations that trace a geographical arc from Taiwan south into the Philippine Archipelago, Borneo, Indonesia, and Melanesia. Conversely, a more distant kinship between the Ami/Yami and MSEA based on all the markers examined, the total mtDNA sequences as well as the admixture f3 and f4 analyses argue against strong genetic contribution from MSEA to the Austronesian dispersal. The sharing of long IBD tracts, total genome length, and the large number of segments in common between the Ami/Yami and the Society Archipelago populations East Polynesia standout considering they are located about 10,700 km apart.

The Y chromosome of autochthonous Basque populations and the Bronze Age replacement

Here we report on the Y haplogroup and Y-STR diversity of the three autochthonous Basque populations of Alava (n = 54), Guipuzcoa (n = 30) and Vizcaya (n = 61). The same samples genotyped for Y-chromosome SNPs were typed for 17 Y-STR loci (DYS19, DYS385a/b, DYS398I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4) using the AmpFlSTR Yfiler system. Six major haplogroups (R, I, E, J, G, and DE) were detected, being R-S116 (P312) haplogroup the most abundant at 75.0% in Alava, 86.7% in Guipuzcoa and 87.3% in Vizcaya. Age estimates for the R-S116 mutation in the Basque Country are 3975 ± 303, 3680 ± 345 and 4553 ± 285 years for Alava, Guipuzcoa and Vizcaya, respectively. Pairwise Rst genetic distances demonstrated close Y-chromosome affinities among the three autochthonous Basque populations and between them and the male population of Ireland and Gascony. In a MDS plot, the population of Ireland segregates within the Basque cluster and closest to the population of Guipuzcoa, which plots closer to Ireland than to any of the other Basque populations. Overall, the results support the notion that during the Bronze Age a dispersal of individuals carrying the R-S116 mutation reached the Basque Country replacing the Paleolithic/Neolithic Y chromosome of the region.

The Marquesans at the fringes of the Austronesian expansion

In the present study, 87 unrelated individuals from the Marquesas Archipelago in French Polynesia were typed using mtDNA, Y-chromosome and autosomal (STRs) markers and compared to key target populations from Island South East Asia (ISEA), Taiwan, and West and East Polynesia to investigate their genetic relationships. The Marquesas, located at the eastern-most fringes of the Austronesian expansion, offer a unique opportunity to examine the effects of a protracted population expansion wave on population structure. We explore the contribution of Melanesian, Asian and European heritage to the Marquesan islands of Nuku-Hiva, Hiva-Oa and Tahuata. Overall, the Marquesas Islands are genetically homogeneous. In the Marquesan Archipelago all of the mtDNA haplogroups are of Austronesian origin belonging to the B4a1 subhaplogroup as the region marks the end of a west to east decreasing cline of Melanesian mtDNA starting with the West Polynesian population of Tonga. Genetic discrepancies are less pronounced between the Marquesan and Society islands, and among the Marquesan islands. Interestingly, a number of Melanesian, Polynesian and European Y-chromosome haplogroups exhibit very different distribution between the Marquesan islands of Nuku Hiva and Hiva Oa, likely resulting from drift, differential migration involving various source populations and/or unique trading routes.

Cebú, Thailand and Taiwanese aboriginal populations according to Y-STR loci

Here we report for the first time the Y27-STR Yfiler plus profiles of the insular population of Cebú in the central region of the Philippine Archipelago and the general continental population of Thailand, two strategic locations of interest in connection with the Austronesian expansion. Traditionally, the peopling of Taiwan has been envisioned as a single wave of agriculturists migrating from mainland Southeast Asia. Yet, more recent data support a scenario in which a number of migrations from the continent populated the island. Genetic affinity parameters from this study indicate that certain Formosan tribes are genetically closer to geographical distant populations in the Solomon Island than to other nearby Taiwanese tribes. Furthermore, Taiwanese aboriginal populations in this study partition into three clusters, one associated with populations from the Philippines and Thailand, a second one segregating with populations of the Solomon Islands and a third grouping made up exclusively of Taiwanese aboriginal tribes. The populations within each of these three clusters exhibit different degrees of differentiation among them suggesting unique population histories. All together, these differential genetic affinities of specific Taiwanese tribes to groups from different geographical regions and to each other are compatible with multiple origins of the Austronesian expansion from Formosa as well as from mainland Southeast Asia.

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Partitioning of Taiwanese aboriginal populations into three clusters.

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The middle cluster includes the populations from Cebú and Thailand.

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A second cluster segregates with populations of the Solomon Islands.

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A third cluster is made up exclusively of Taiwanese aboriginal tribes.

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Some Formosan tribes are genetically closer to geographical distant Solomon Island populations.

Investigating the genetic diversity and affinities of historical populations of Tibet

This study elucidates Y chromosome distribution patterns in the three general provincial populations of historical Tibet, Amdo (n = 88), Dotoe (n = 109) and U-Tsang (n = 153) against the backdrop of 37 Asian reference populations. The central aim of this study is to investigate the genetic affinities of the three historical Tibetan populations among themselves and to neighboring populations. Y-SNP and Y-STR profiles were assessed in these historical populations. Correspondence analyses (CA) were generated with Y-SNP haplogroup data. Y-STR haplotypes were determined and employed to generate multidimensional scaling (MDS) plots based on Rst distances. Frequency contour maps of informative Y haplogroups were constructed to visualize the distributions of specific chromosome types. Network analyses based on Y-STR profiles of individuals under specific Y haplogroups were generated to examine the genetic heterogeneity among populations. Average gene diversity values and other parameters of population genetics interest were estimated to characterize the populations. The Y chromosomal results generated in this study indicate that using two sets of markers (Y-SNP, and Y-STR) the three Tibetan populations are genetically distinct. In addition, U-Tsang displays the highest gene diversity, followed by Amdo and Dotoe. The results of this transcontinental biogeographical investigation also indicate various degrees of paternal genetic affinities among these three Tibetan populations depending on the type of loci (Y-SNP or Y-STR) analyzed. The CA generated with Y-SNP haplogroup data demonstrates that Amdo and U-Tsang are closer to each other than to any neighboring non-Tibetan group. In contrast, the MDS plot based on Y-STR haplotypes displays Rst distances that are much shorter between U-Tsang and its geographic nearby populations of Ladakh, Punjab, Kathmandu and Newar than between it and Amdo. Moreover, although Dotoe is isolated from all other groups using both types of marker systems, it lies nearer to the other Tibetan collections in the Y-SNP CA than in the Y-STR MDS plot. High resolution and shallow evolutionary time frames engendered by Y-STR based analyses may reflect a more recent demographic history than that delineated by the more conserved Y-SNP markers.

On the Bantu expansion

Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.

Y-STR markers from Ladakh in the Himalayas

A total of 223 samples from the general population of Ladakh in Northwestern India were amplified at 17 Y-STR loci using the AmpFlSTR® Yfiler™ system. The DNA profiles generated were employed to generate allelic frequencies, gene diversity, haplotype diversity and discrimination capacity values as well as number of different haplotypes, fraction of unique haplotypes and Rst pair wise genetic distances. Multidimensional Scaling (MDS) and Correspondence Analysis (CA) were performed with the Rst values and allelic frequencies, respectively. The 17-loci discrimination capacity of Ladakh was found to be 0.8093. Eleven out of the 16 loci have diversity values greater than 0.6, and 13 loci possess values greater than 0.5. Ladakh exhibits no significant genetic difference to seven of the 15 reference forensic databases after Bonferroni correction, three of which are located in South Central Asian and four are from the Himalayan region. Rst genetic distance values before and after Bonferroni corrections illustrate the capacity of the Yfiler system to discriminate among Himalayan populations. The intermediate position of the Ladakh population in the MDS and CA plots likely reflects genetic flow and admixture with neighboring populations. In addition, the longitudinal partition of populations in the MDS and CA plots likely reflect human dispersals such as the silk road migrations.

Mayans: a Y chromosome perspective

In spite of the wealth of available cultural and archeological information as well as general interest in the Mayans, little is known about their genetics. In this study, for the first time, we attempt to alleviate this lacuna of knowledge by comprehensively investigating the Y chromosome composition of contemporary Mayan populations throughout their domain. To accomplish this, five geographically targeted and ethnically distinct Mayan populations are investigated using Y-SNP and Y-STR markers.

FINDINGS

overall, the Mayan populations as a group are highly homogeneous, basically made up of only two autochthonous haplogroups, Q1a2a1a1*-M3 and Q1a2a1*-L54. Although the Y-STR data illustrates diversity, this diversity, for the most part, is uniformly distributed among geographically distant Mayan populations. Similar haplotypes among populations, abundance of singletons and absence of population partitioning within networks among Mayan populations suggest recent population expansion and substantial gene flow within the Mayan dominion, possibly due to the development of agriculture, the establishment of interacting City-State systems and commerce.

From Arabia to Iberia: A Y chromosome perspective

At different times during recent human evolution, northern Africa has served as a conduit for migrations from the Arabian Peninsula. Although previous researchers have investigated the possibility of the Strait of Gibraltar as a pathway of migration from North Africa to Iberia, we now revisit this issue and theorize that although the Strait of Gibraltar, at the west end of this corridor, has acted as a barrier for human dispersal into Southwest Europe, it has not provided an absolute seal to gene flow. To test this hypothesis, here we use the spatial frequency distributions, STR diversity and expansion time estimates of Y chromosome haplogroups J1-P58 and E-M81 to investigate the genetic imprints left by the Arabian and Berber expansions into the Iberian Peninsula, respectively. The data generated indicate that Arabian and Berber genetic markers are detected in Iberia. We present evidence that suggest that Iberia has received gene flow from Northwest Africa during and prior to the Islamic colonization of 711A.D. It is interesting that the highest frequencies of Arabia and Berber markers are not found in southern Spain, where Islam remained the longest and was culturally most influential, but in Northwest Iberia, specifically Galicia. We propose that Moriscos' relocations to the north during the Reconquista, the migration of cryptic Muslims seeking refuge in a more lenient society and/or more geographic extensive pre-Islamic incursions may explain the higher frequencies and older time estimates of mutations in the north of the Peninsula. These scenarios are congruent with the higher diversities of some diagnostic makers observed in Northwest Iberia.

Sousse: extreme genetic heterogeneity in North Africa

The male genetic landscape of the territory currently known as Tunisia is hampered by the scarcity of data, especially from cosmopolitan areas such as the coastal city of Sousse. In order to alleviate this lacuna, 220 males from Sousse were examined, for the first time, for more than 50 Y-chromosome single-nucleotide polymorphisms (Y-SNPs) markers and compared with 3099 individuals from key geographically targeted locations in North Africa, Europe and the Near East. The paternal lineages observed belong to a common set of Y haplogroups previously described in North Africa. In addition to the prominent autochthonous North African E-M81 haplogroup which is exclusively represented by its subclade E-M183 (44.55% of Y-chromosomes), a number of Near Eastern Neolithic lineages including E-M78, J-M267 and J-M172 account for 39% of the Y-chromosomes detected. Principal component analysis based on haplogroup frequencies, multidimensional scaling based on Rst genetic distances and analyses of molecular variance using both Y-chromosome short tandem repeat haplotypes and Y-SNP haplogroup data revealed that the Tunisian and North African groups, as a whole, are intra- and inter-specific diverse with Sousse being highly heterogeneous.

At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific.

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Maputo Bantus exhibit close affinities with other West and East African Bantus.

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Traces of Khoisan and Pygmy markers persist in the Maputo Province Bantus.

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R1a1a-M17/M198 in the Maputo Province may represent back or recent migration.

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Linguistic, cultural and genetic heritages are reflected in Maputo's gene pool.

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Admixture and assimilation processes of Bantu elements were region-specific.

Extreme genetic heterogeneity among the nine major tribal Taiwanese island populations detected with a new generation Y23 STR system

The Taiwanese aborigines have been regarded as the source populations for the Austronesian expansion that populated Oceania to the east and Madagascar off Africa to the West. Although a number of genetic studies have been performed on some of these important tribes, the scope of the investigations has been limited, varying in the specific populations examined as well as the maker systems employed. This has made direct comparison among studies difficult. In an attempt to alleviate this lacuna, we investigate, for the first time, the genetic diversity of all nine major Taiwanese aboriginal tribes (Ami, Atayal, Bunun, Rukai, Paiwan, Saisat, Puyuma, Tsou and Yami) utilizing a new generation multiplex Y-STR system that allows for the genotyping of 23 loci from a single amplification reaction. This comprehensive approach examining 293 individuals from all nine main tribes with the same battery of forensic markers provides for the much-needed equivalent data essential for comparative analyses. Our results have uncovered that these nine major aboriginal populations exhibit limited intrapopulation genetic diversity and are highly heterogeneous from each other, possibly the result of endogamy, isolation, drift and/or unique ancestral populations. Specifically, genetic diversity, discrimination capacity, fraction of unique haplotypes and the most frequent haplotypes differ among the nine tribes, with the Tsou possessing the lowest values for the first three of these parameters. The phylogenetic analyses performed indicate that the genetic diversity among all nine tribes is greater than the diversity observed among the worldwide reference populations examined, indicating an extreme case of genetic heterogeneity among these tribes that have lived as close neighbors for thousands of years confined to the limited geographical area of an island.

Taiwanese aborigines: genetic heterogeneity and paternal contribution to Oceania

In the present study, for the first time, 293 Taiwanese aboriginal males from all nine major tribes (Ami, Atayal, Bunun, Rukai, Paiwan, Saisat, Puyuma, Tsou, Yami) were genotyped with 17 YSTR loci in a attend to reveal migrational patterns connected with the Austronesian expansion. We investigate the paternal genetic relationships of these Taiwanese aborigines to 42 Asia-Pacific reference populations, geographically selected to reflect various locations within the Austronesian domain. The Tsou and Puyuma tribes exhibit the lowest (0.1851) and the highest (0.5453) average total genetic diversity, respectively. Further, the fraction of unique haplotypes is also relatively high in the Puyuma (86.7%) and low in Tsou (33.3%) suggesting different demographic histories. Multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) revealed several notable findings: 1) the Taiwan indigenous populations are highly diverse. In fact, the level of inter-population heterogeneity displayed by the Taiwanese aboriginal populations is close to that exhibited among all 51 Asia-Pacific populations examined; 2) the asymmetrical contribution of the Taiwanese aborigines to the Oceanic groups. Ami, Bunun and Saisiyat tribes exhibit the strongest paternal links to the Solomon and Polynesian island communities, whereas most of the remaining Taiwanese aboriginal groups are more genetically distant to these Oceanic inhabitants; 3) the present YSTR analyses does not reveal a strong paternal affinity of the nine Taiwanese tribes to their continental Asian neighbors. Overall, our current findings suggest that, perhaps, only a few of the tribes were involved in the migration out of Taiwan.

Ascertaining the role of Taiwan as a source for the Austronesian expansion

Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the "Out of Taiwan" hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.