Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia

Nguyen Thuy Duong,Nguyen Thi Xuan,Nguyen Van Phong,Le Thi Thu Hien,Nong Van Hai,Brigitte Pakendorf,Leonardo Arias,Mark Stoneking,Kim Thi Phuong Oanh,Huynh Thi Thu Hue,Vo Thi Bich Thuy,Nguyen Huy Hoang,Enrico Macholdt,Nguyen Hai Ha,Roland Schröder,Nguyen Dang Ton

doi:10.1038/s41598-018-29989-0

Abstract

Vietnam is an important crossroads within Mainland Southeast Asia (MSEA) and a gateway to Island Southeast Asia, and as such exhibits high levels of ethnolinguistic diversity. However, comparatively few studies have been undertaken of the genetic diversity of Vietnamese populations. In order to gain comprehensive insights into MSEA mtDNA phylogeography, we sequenced 609 complete mtDNA genomes from individuals belonging to five language families (Austroasiatic, Tai-Kadai, Hmong-Mien, Sino-Tibetan and Austronesian) and analyzed them in comparison with sequences from other MSEA countries and Taiwan. Within Vietnam, we identified 399 haplotypes belonging to 135 haplogroups; among the five language families, the sequences from Austronesian groups differ the most from the other groups. Phylogenetic analysis revealed 111 novel Vietnamese mtDNA lineages. Bayesian estimates of coalescence times and associated 95% HPD for these show a peak of mtDNA diversification around 2.5–3 kya, which coincides with the Dong Son culture, and thus may be associated with the agriculturally-driven expansion of this culture. Networks of major MSEA haplogroups emphasize the overall distinctiveness of sequences from Taiwan, in keeping with previous studies that suggested at most a minor impact of the Austronesian expansion from Taiwan on MSEA. We also see evidence for population expansions across MSEA geographic regions and language families.

Highlights

Mainland Southeast Asia (MSEA) consists of a number of very long river valleys, including the Chao Phraya, the Irrawaddy, the Mekong, the Red, and the Salween; most of these have their source in the eastern fringes of the Himalayas and follow a generally north-south direction[3]
Since we provide the first complete mitochondrial DNA (mtDNA) genome sequences for HM populations in MSEA, the HM haplogroup distributions are identical for Vietnam (Figure S2a, Online Resource 2) and MSEA (Figure S2b, Online Resource 2)
For Vietnam, the most striking feature is the difference between AN groups and the other four language families: A and B4 are lacking in AN groups but comprise 1.12–33.58% of the haplogroups in the other language families, while M71 is at much higher frequency in AN groups (37.04%) than in the other language families (0–19.32%) (Table S3 in Online Resource 1)

Summary

Introduction

MSEA consists of a number of very long river valleys, including the Chao Phraya, the Irrawaddy, the Mekong, the Red, and the Salween; most of these have their source in the eastern fringes of the Himalayas and follow a generally north-south direction[3]. New advances in next-generation sequencing have made it feasible to sequence and analyze large numbers of complete mtDNA genomes[9,10,11], and we have used these methods to obtain complete mitochondrial genomes from 609 unrelated Vietnamese subjects that encompass all five language families (Figure S1, Online Resource 2). This is the first comprehensive study of complete mtDNA sequences of Vietnamese populations, with the goal of investigating the matrilineal ancestry of Vietnamese populations. We analyze the phylogeography of mtDNA haplogroups in MSEA, with an emphasis on the additional insights arising from this large sample of Vietnamese sequences; insights into the genetic history of specific Vietnamese populations will be described elsewhere

Methods

Results

Conclusion