Revisiting the genetic background and phylogenetic structure of five Sino-Tibetan-speaking populations: insights from autosomal InDels

Forensic features and phylogenetic structure survey of four populations from southwest China via the autosomal insertion/deletion markers

Insertion/Deletion (InDel) polymorphisms, characterized by their smaller amplicons, reduced mutation rates, and compatibility with the prevalent capillary electrophoresis (CE) platforms in forensic laboratories, significantly contribute to the advancement and application of genetic analysis. Guizhou province in China serves as an important region for investigating the genetic structure, ethnic group origins, and human evolution. However, DNA data and the sampling of present-day populations are lacking, especially about the InDel markers. Here, we reported data on 47 autosomal InDels from 592 individuals from four populations in Guizhou (Han, Dong, Yi, and Chuanqing). Genotyping was performed with the AGCU InDel 50 kit to evaluate their utility for forensic purposes and to explore the population genetic structure. Our findings showed no significant deviations from Hardy-Weinberg and linkage equilibriums. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) for each population demonstrated that the kit could be applied to forensic individual identification and was an effective supplement for parentage testing. Genetic structure analyses, including principal component analysis, multidimensional scaling, genetic distance calculation, STRUCTURE, and phylogenetic analysis, highlighted that the genetic proximity of the studied populations correlates with linguistic, geographical, and cultural factors. The observed genetic variances within four research populations were less pronounced than those discerned between populations across different regions. Notably, the Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi. These results underscore the potential of InDel markers in forensic science and provide insights into the genetic landscape and human evolution in multi-ethnic regions like Guizhou.

Key points

InDel markers show promise for forensic individual identification and parentage testing via the AGCU InDel 50 kit.Genetic analysis of Guizhou populations reveals correlations with linguistic, geographical, and cultural factors.Guizhou Han, Dong, and Chuanqing populations showed closer genetic affiliations with linguistically similar groups than the Guizhou Yi.

Development and validation of a forensic multiplex InDel assay: The AGCU InDel 60 kit

Marker sets based on insertion/deletion polymorphisms (InDels) combine the characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms and have served as effective complementary or stand-alone systems for human identification in forensics. We developed a novel multiplex amplification detection system, designated the AGCU InDel 60 kit, containing 57 autosomal InDels, 2 Y-chromosomal InDels, and the amelogenin locus and validated the kit in a series of studies, which included tests of the PCR conditions; tests for sensitivity, species specificity, reproducibility, stability, and mock case samples; degradation studies; and a population study. The results indicated that the AGCU InDel 60 kit was accurate, specific, reproducible, stable, and robust. Complete DNA profiles were obtained even with 125 pg of human DNA. In tests of artificially degraded samples, we found that the number of alleles detected by the validated kit was considerably greater than that detected by the STR-based AGCU 21+1 kit, even as the degree of degradation increased. Additionally, 564 unrelated individuals from three Han groups were investigated using this novel system, and the values of combined power of discrimination and combined power of exclusion were not less than 1-4.9026 × 10^-24 and 1-3.1123 × 10^-5 , respectively. Thus, the results indicated that the novel kit was more powerful than the previous version of the InDel kit (the AGCU InDel 50 kit). Our results suggest that the AGCU InDel 60 kit can serve as an efficient tool for human forensics and a supplementary kit for population genetics research.

Forensic Efficiency Estimation of a Homemade Six-Color Fluorescence Multiplex Panel and In-Depth Anatomy of the Population Genetic Architecture in Two Tibetan Groups

The genetic information of the Chinese Tibetan group has been a long-standing research hotspot among population geneticists and archaeologists. Herein, 309 unrelated individuals from two Tibetan groups living in Qinghai Province, China (CTQ), and Tibet Autonomous Region, China (CTT), were successfully genotyped using a new homemade six-color fluorescence multiplex panel, which contained 59 autosomal deletion/insertion polymorphisms (au-DIPs), two mini short tandem repeats (miniSTRs), two Y-chromosomal DIPs, and one Amelogenin. The cumulative probability of matching and combined power of exclusion values for this new panel in CTQ and CTT groups were 1.9253E-27 and 0.99999729, as well as 1.5061E-26 and 0.99999895, respectively. Subsequently, comprehensive population genetic analyses of Tibetan groups and reference populations were carried out based on the 59 au-DIPs. The multitudinous statistical analysis results supported that Tibetan groups have close genetic affinities with East Asian populations. These findings showed that this homemade system would be a powerful tool for forensic individual identification and paternity testing in Chinese Tibetan groups and give us an important insight for further perfecting the genetic landscape of Tibetan groups.

Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci

The utilization of the ancestry informative markers to disclose the ancestral composition of a certain population and explore the genetic affinities between diverse populations is beneficial to inferring the biogeographic ancestry of unknown individuals and assisting in case detection, as well as avoiding the impacts of population stratification during genome-wide association analysis studies. In the present study, we applied an in-house ancestry informative deletion/insertion polymorphic multiplex amplification system to investigate the ancestral compositions of the Beijing Han population and analyze the genetic relationships between the Beijing Han population and 31 global reference populations. The results demonstrated that 32 loci of this self-developed panel containing 39 loci significantly contributed to the inference of genetic information for the Beijing Han population. The results of multiple population genetics statistical analyses indicated that the ancestral component and genetic architecture of the Beijing Han population were analogous to the reference East Asian populations, and that the Beijing Han population was genetically close to the reference East Asian populations.

An interpretation of the genetic polymorphism and population genetic background of Ankang Han population via a novel InDel panel

In this research, genotyping data of 43 InDel loci in 311 Han individuals in Ankang City, Shaanxi Province, China were detected using a self-developed five-dye multiplex amplification panel. The allelic frequencies and forensic parameters of all InDel loci were calculated. The combined power of discrimination and probability of exclusion values were 0.999 999 999 999 999 998 827 39 and 0.999 887 424, respectively, which demonstrated that this 43-InDel panel was powerful for individual identifications in Ankang Han population. Moreover, genetic distances, pairwise F_ST values, principal component analyses, phylogenetic trees and STRUCTURE analyses were performed to investigate the genetic affinities between Ankang Han and reference groups. Population genetic investigations indicated that Ankang Han population had a close genetic relationship with Southern Han population compared with other reference groups.

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.

Molecular genetic survey and forensic characterization of Chinese Mongolians via the 47 autosomal insertion/deletion marker

The Mongolians are mainly distributed in the modern state of Mongolia, China, Russia, and other countries. While the historic and archaeological records of the rise and fall of the Mongol Empire are well documented, little has been known about the genetic legacy of modern Mongolian populations. Here, 611 Mongolian individuals from Hohhot, Hulunbuir, and Ordos of China were genotyped via the 47 Insertion/Deletion markers. Forensically statistical parameters indicated that this InDel system could be applied to forensic investigation in Mongolian populations. The comprehensive population comparisons indicated that targeted Mongolian populations are a homogeneous population, which kept close genetic proximity with geographically northern East Asians. The findings of the model-based clustering analysis revealed a southern East Asian-specific ancestral component, which was maximized in Hainan Li, and Mongolian populations harbored relatively less Hainan Li-related ancestry and more northern East Asian-related ancestry compared with reference Tai-Kadai, Austroasiatic and Sinitic people.