Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations

Abstract

Genetic affinities between aboriginal Taiwanese and populations from Oceania and Southeast Asia have previously been explored through analyses of mitochondrial DNA (mtDNA), Y chromosomal DNA, and human leukocyte antigen loci. Recent genetic studies have supported the "slow boat" and "entangled bank" models according to which the Polynesian migration can be seen as an expansion from Melanesia without any major direct genetic thread leading back to its initiation from Taiwan. We assessed mtDNA variation in 640 individuals from nine tribes of the central mountain ranges and east coast regions of Taiwan. In contrast to the Han populations, the tribes showed a low frequency of haplogroups D4 and G, and an absence of haplogroups A, C, Z, M9, and M10. Also, more than 85% of the maternal lineages were nested within haplogroups B4, B5a, F1a, F3b, E, and M7. Although indicating a common origin of the populations of insular Southeast Asia and Oceania, most mtDNA lineages in Taiwanese aboriginal populations are grouped separately from those found in China and the Taiwan general (Han) population, suggesting a prevalence in the Taiwanese aboriginal gene pool of its initial late Pleistocene settlers. Interestingly, from complete mtDNA sequencing information, most B4a lineages were associated with three coding region substitutions, defining a new subclade, B4a1a, that endorses the origin of Polynesian migration from Taiwan. Coalescence times of B4a1a were 13.2 +/- 3.8 thousand years (or 9.3 +/- 2.5 thousand years in Papuans and Polynesians). Considering the lack of a common specific Y chromosomal element shared by the Taiwanese aboriginals and Polynesians, the mtDNA evidence provided here is also consistent with the suggestion that the proto-Oceanic societies would have been mainly matrilocal.

Figure 1. Geographic Distribution of Nine Indigenous Tribes of Taiwan

Figure 2. Tree Drawn from a Median-Joining Network of 96 mtDNA Haplotypes Observed in Nine Indigenous Taiwanese Populations

The tree is based on sequences of HVS-I (16024–16390) and a coding region segment covering 9,793 to 10,899 bps. Haplogroup defining HVS-II mutations were manually added after the generation of the network. Additional coding region mutations, ascertained through complete mtDNA sequencing of an individual of each subclade of the haplogroup defined by the mutation, were used to generate the network and are shown in blue. All nps are numbered according to reference sequence [71]. Mutations in italic indicate back conversions. Nucleotide change is specified only for transversions. Node areas are proportional to haplotype frequencies of the pooled nine tribes. The population codes are as follows: A, Atayal; B, Bunun; M, Amis; P, Paiwan; R, Rukai; S, Saisiat; U, Puyuma; T, Tsou; and Y, Yami. CRS = Cambridge reference sequence [70].

Figure 3. Principal Components Analysis

Principal components map obtained from a matrix of haplogroup frequencies in nine Taiwan indigenous tribes (Table 1), northern and southern Chinese [34], Taiwan urban population (Minnan and Hakka) [29], Japan [73], Korea [33], Luzon [12], Moluccas [14], Indonesia, Ryukyu [42] Malaysia, South Vietnam, the Philippines [20], and Thai [45,46]. Austronesian-speaking populations are represented by circles, non–Austronesian-speaking populations by stars.

Figure 4. Phylogenetic Tree Relating Haplogroup B4a1 Complete Sequences

Base pair exchange is specified only for transversions. Recurrent mutations are underlined. Coalescence times are shown beside nodes.