Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand

Abstract

The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non-recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely-related group.

Contrasting paternal and maternal genetic histories of Thai and Lao populations

“…Genomic DNA was extracted from blood, buccal swab or saliva of 914 males belonging to 57 populations that were classified into 26 ethnolinguistic groups, as described previously Kutanan et al 2018a) (Figure 1; Table S5). Ethical approval for this study was provided by Khon Kaen University, Naruesuan University, and the Ethics Commission of the University of Leipzig Medical Faculty.…”

“…This study thus includes 928 MSY sequences from 59 populations and 28 ethnolinguistic groups of Thailand and Laos. To compare with the MSY data, we selected 1,434 mtDNA sequences from the same populations from our previous studies Kutanan et al 2018a; (Table S5). We used Arlequin 3.5.1.3 (Excoffier and Lischer 2010) for the following analyses: summary statistics of genetic diversity within populations, the matrix of genetic distances (Φst), Analyses of Molecular Variance (AMOVA), and Mantel tests of the correlation between genetic and geographic distances.…”

“…We have previously carried out comprehensive studies of the maternal genetic history of the Thai/Lao region, based on 1,823 complete mtDNA genome sequences Kutanan et al 2018a;. In order to investigate the paternal genetic variation and demographic history, here, we investigate ~2.3 mB of MSY sequence in a subset of the above individuals, comprising 928 sequences from 59 populations.…”

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

“…Indexed libraries produced previously 9 were enriched for 2.3 Mb of target NRY as previously described 17 . Paired-end sequencing data of 100+7 bp length were generated on the Illumina HiSeq 2500 platform and standard Illumina base-calling was performed using Bustard.…”

“…We trimmed Illumina adapters and merged completely overlapping paired sequences using leeHOM 18 , and de-multiplexed the pooled sequencing data using deML 19 . The sequencing data were aligned to the human reference genome hg19 and SNPs were identified following 17 . Y chromosome haplogroups were determined using yhaplo 20 , with two modifications: i) the SNP defining B2b1 was corrected according to a recent ISOGG update (August 6th, 2017); and ii) since the mutation commonly used to identify haplogroup E1b1a1a1c1a1 was not typed in this study (P252/U174), we based our E1b1a1a1c1a1 assignment on the presence of mutation V1245/M4671, previously identified on E1b1a1a1c1a1 branches 21,22 .…”