Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations

Abstract

Ancestry informative markers (AIMs), which are distributed throughout the human genome, harbor significant allele frequency differences among diverse ethnic groups. The use of sets of AIMs to reconstruct population history and genetic relationships is attracting interest in the forensic community, because biogeographic ancestry information for a casework sample can potentially be predicted and used to guide the investigative process. However, subpopulation ancestry inference within East Asia remains in its infancy due to a lack of population reference data collection and incomplete validation work on newly developed or commercial AIM sets. In the present study, 316 Chinese persons, including 85Sinitic-speaking Haikou Han, 120 Qiongzhong Hlai and 111 Daozhen Gelao individuals belonging to Tai-Kadai-speaking populations, were analyzed using the Precision ID Ancestry Panel (165 AISNPs).Combined with our previous 165-AISNP data (375 individuals from 6 populations), the 1000 Genomes Project and forensic literature, comprehensive population genetic comparisons and ancestry inference were further performed via ADMIXTURE, TreeMix, PCA, f-statistics and N-J tree. Although several nonpolymorphic loci were identified in the three southern Chinese populations, the forensic parameters of this ancestry inference panel were better than those for the 23 STR-based Huaxia Platinum System, which is suitable for use as a robust tool in forensic individual identification and parentage testing. The results based on the ancestry assignment and admixture proportion evaluation revealed that this panel could be used successfully to assign individuals at a continental scale but also possessed obvious limitations in discriminatory power in intercontinental individuals, especially for European-Asian admixed Uyghurs or in populations lacking reference databases. Population genetic analyses further revealed five continental population clusters and three East Asian-focused population subgroups, which is consistent with linguistic affiliations. Ancestry composition and multiple phylogenetic analysis further demonstrated that the geographically isolated Qiongzhong Hlai harbored a close phylogenetic relationship with Austronesian speakers and possessed a homogenous Tai-Kadai-dominant ancestry, which could be used as the ancestral source proxy in population history reconstruction of Tai-Kadaispeaking populations and as one of the representatives for forensic database establishment. In summary, more population-specific AIM sets focused on East Asian subpopulations, comprehensive algorithms and high-coverage population reference data should be developed and validated in the next step.

Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages

“…Southwestern East Asia is one of the most ethnolinguistically diverse regions around the world. Genetic origin, subsequent migration, isolation, plausible admixture, and local adaptation history of ethnolinguistic southern Chinese populations were widely discussed via different genetic markers, mainly including autosomal short tandem repeats (STRs), single nucleotide polymorphism (SNPs), and copy number variations (CNVs) (Chen et al, 2019;Zhang C. et al, 2019;He et al, 2021;Liu et al, 2021a). However, most of these studies focused on the genetic variations and forensic features of low-density genetic markers in the Han Chinese populations.…”

“…There are also important studies focused on the genetic relationships between central Hans and their neighbors (e.g., Han, Manchu, Mongolian, and Tujia). However, all of these studies mainly focused on the patterns from the shared alleles and sample frequency spectrum of independent SNPs (Chen et al, 2021;He et al, 2021) and lacked evidence from a fine-scale genetic structure based on the shared haplotype chunks (successive linked SNP fragments) and uniparental haplogroup lineages.…”

Fine-Scale Population Admixture Landscape of Tai–Kadai-Speaking Maonan in Southwest China Inferred From Genome-Wide SNP Data

“…From the perspective of uniparentally inherited Y chromosome haplogroup and mitochondrial haplogroup, Chen et al made a preliminary exploration focused on the forensic parameters and genetic structure of the Tai–Kadai-speaking populations in Guizhou and the population genetic relationship based on the short tandem repeat (STR) on the autosome and X/Y-chromosomes ( Chen et al, 2018c ). Further genetic studies had focused on the population admixture history and genetic diversity of Tai–Kadai-speaking Gelao and Bouyei by insertion/deletion polymorphisms (InDels) and ancestry-informative single-nucleotide polymorphism (AISNPs) ( He et al, 2019a ; He et al, 2019b ; He et al, 2021b ). The obtained research results showed a significant genetic interaction between Tai–Kadai- and Hmong–Mien-speaking populations ( He et al, 2019a ; He et al, 2019b ; He et al, 2021b ).…”

“…Further genetic studies had focused on the population admixture history and genetic diversity of Tai–Kadai-speaking Gelao and Bouyei by insertion/deletion polymorphisms (InDels) and ancestry-informative single-nucleotide polymorphism (AISNPs) ( He et al, 2019a ; He et al, 2019b ; He et al, 2021b ). The obtained research results showed a significant genetic interaction between Tai–Kadai- and Hmong–Mien-speaking populations ( He et al, 2019a ; He et al, 2019b ; He et al, 2021b ). However, these studies were conducted based on low-density genetic markers and were mainly focused on exploring forensic characteristics.…”

“…However, their fine-scale population history and their genetic relationship with the surrounding Hmong–Mien- and Sino-Tibetan-speaking populations have not been fully characterized, which are especially focused on the sharing of genome-wide haplotype data. Genetic studies of populations from the Yunnan–Guizhou Plateau regions have found enriched genetic diversity and complex mixed population genetic history ( He et al, 2019a ; He et al, 2019b ; Zhang et al, 2019 ; Liu et al, 2021a ; He et al, 2021b ; Liu et al, 2021b ; Chen et al, 2021 ). The detailed relationship between Maonan and modern and ancient neighboring populations needs to be characterized further.…”