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

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.

An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia

“…Additionally, pairwise F ST values were verified for Cham and Khmer (as Khmer Loeu had only eight samples) over all samples, showing a Weir and Cockerham mean F ST estimate of 0.0027702, confirming the high homogeneity between the two groups. The populations with the lowest F ST values compared to our 264 Cambodian samples were the 1,234 samples from Thailand and Laos (Kutanan et al 2017 10 , F ST = 0.0102) and the 609 Vietnamese samples (Duong et al 14 , F ST = 0.016).…”

“…( B ) Schematic representation of data sets analysed, letters A–H representing publications with the colour denoting the completeness of the mtDNA sequences (yellow = complete, red = control region (CR) sequences). A = Summerer et al (327 CR, 44 full) 18 , B = Bodner et al 16 (214 CR), C = Zhang et al (1,054 CR, 98 full) 2 , D = Kutanan et al (1,234 full) 10 , E = Kutanan et al (560 full) 12 , F = Kutanan et al (415 full) 11 , H = Duong et al (609 full) 14 , G = 1000 Genome samples from Vietnam (KHV. 99 full).…”

“…East Asia is reported individually as Vietnam (KHV = Kinh in Ho Chi Minh City, Vietnam), China (CDX = Chinese Dai in Xishuangbanna, CHB = Han Chinese in Beijing, CHS = Southern Han Chinese) and Japan (JPT = Japanese in Tokyo). ( B ) Haplogroup distribution by publication, Bodner et al 16 (Laos), Duong et al 14 (mostly Vietnam), Kutanan et al 10 – 12 (mostly Thailand), Summerer et al 18 (Myanmar), Zhang et al 2 (Cambodia). “This study” indicates the present work’s data set.…”

“…Genetic studies of complete mitochondrial DNA (mtDNA) have been conducted previously in populations from Southeast Asia (SEA) 5 – 9 , mostly in Thailand 10 – 12 and Vietnam 13 , 14 , with very limited samples from Cambodia 2 . Besides various control region sequencing projects in populations from Southeast Asia (for example, populations from Thailand 15 , Laos 16 , Vietnam 17 , Burma 18 , and other Southeast Asian countries 19 – 22 ), only one publication sequenced the mtDNA HVS-I (range 16,038–16,462) and HVS-II (range 65–417) from 1,054 unrelated Cambodians 2 .…”

New insights from the combined discrimination of modern/ancient genome-wide shared alleles and haplotypes: Differentiated demographic history reconstruction of Tai-Kadai and Sinitic people in South China

“…Over the past hundreds of years, the TK people gradually migrated southward, driven by various cultural, political, economic, environmental and other relevant factors, and became the majority inhabitants of Southeast Asia [8,13,14]. In light of the complex population history of TK-speaking groups and the important role played in the peopling of East and Southeast Asia, the analyses of genetic variations in TK-speaking populations have been conducted in several studies using different sets of autosomal [15][16][17], X-chromosomal [18,19], Y-chromosomal [20,21], mitochondrial [13,14,[21][22][23] and genome-wide [7,24] markers. Previous studies showed that the Proto-languages of TK and AN might be related [25], and TK people from Thailand are related to AN speakers based on mitogenome sequences [14].…”