Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia

Abstract

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 to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned.

Results: We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South.

Conclusion: The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.

Figure 1

Geographic map showing the locations of the samples of Fujian, Taiwan, the Philippines and Indonesia genotyped in this study. Group numbers identifying sampling locations are described in Table 1, and color codes are : Black squares = Mainland Han, Dark blue squares = Taiwan Han, Sky blue circles = Taiwan Plain tribes, Red circles = Taiwan Mountain tribe Aborigines, Orange triangles = Philippines, Green stars = Indonesia, Yellow hexagons = Indochina (Indochina). The Wallace’s line (black dotted line) separates Eastern ISEA from Western ISEA. Locations without a number indicate groups obtained from additional literature (Additional file 1: Table S1), namely: Brown circle = Yueh/Daic/Hainan in south China, Grey = Madagascar, White = Solomon island, Pink = Japan and Korea, and Black with red frame = North China.

Figure 2

Phylogenetic tree of 47 Y-chromosome haplogroups seen in this study (shown in boldface) and hierarchically defined using 81 slowly evolving binary markers (68 in the Figure). The marker names are shown along the branches, and haplogroup names are shown on the right side according to ISOGG Y-DNA Haplogroup Tree 2011. Potentially paraphyletic undefined subgroups are distinguished from recognized haplogroups by the asterisk symbol. Haplogroups tested for but not seen in this study are shown in (italic). See Additional file 1: Table S2 for a more detailed frequency table.

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]. Arrows symbolize dispersals and gene flow, and stages (B, C and D) are according to Karafet et al. [26] (see Discussion section). The age at the beginning of arrows represents the likely time of origin of the haplogroup as estimated from its STR diversity (Table 2 and Additional file 1: Table S3), and arrow colors represent time of dispersal (red for Paleolithic, blue for Neolithic/Austronesian expansion and yellow for contemporary historical times).

Figure 4

Median joining Networks for the whole dataset and published East Asian Y haplogroup lineages based on seven Y-STR loci [7,8,12,29,30,41]. Sizes of circles are proportional to Y-STR haplotype frequency; lines between circles (links) represent mutation differences. Green links in O1a2 and O2a1a represent ancestry sharing between Solomon and Madagascar (note that only TwMtA O1a2 is included in this pathway. Colors within circles indicate populations.

Figure 5

Multidimensional scaling plot of Reynolds pairwise population genetic distances using high definition Y-SNP genotypic data. The stress value is 0.111.