Forensic characteristics and phylogenetic analysis of 23 Y-STR loci in the Miao population from Guizhou province, southwest China

Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China

BACKGROUND

Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.

OBJECTIVES

To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.

RESULTS

The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.

CONCLUSIONS

Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.

Genetic characteristics and forensic features of Xibe ethnic group revealed via extended set of Y-STRs

BACKGROUND

Xibe is the fifth largest minority population of Liaoning province. Predominately they live in Liaoning province (69.52%), followed by Xinjiang (18.06%), Heilongjiang (3.99%), Jilin (1.63%) and Inner Mongolia provinces (1.57%).

AIM

To provide an updated and precise population database on an extended set of Y STRs not available before and explore the forensic characteristics of 26 Y chromosomal STRs.

SUBJECTS & METHODS

In this study, we genotyped 406 unrelated Xibe male individuals from Liaoning province using Goldeneye® 26Y System kit and calculated the forensic parameters of these 26 Y STRs loci.

RESULTS

All haplotypes generated for 406 Xibe samples using Goldeneye^® 26Y kit were unique with a discrimination capacity (DC) of 1. On restricting the haplotypes to the Y-filer® set of 17 Y-STRs, we observed 392 haplotypes. Among them 93.53% (380) were unique with a DC of 0.9655 and haplotype diversity (HD) of 0.9998, showing high discrimination power of the extended set of markers in this population. Allelic frequencies ranged from 0.0024 to 0.7684 across 26 Y STRs loci. DYS385 showed the highest gene diversity (0.9691) among all markers.

CONCLUSION

According to pairwise R_ST genetic distances among Xibe populations from China, the Liaoning Xibe population showed the closest genetic distance (0.0035) followed by Xinjiang Xibe population (0.0218). Multidimensional scaling (MDS) analysis among Xibe and 29 other Chinese populations showed that local populations such as Manchu from Liaoning and Han from Beijing had a close affinity while Tibetans from Aba, China, were most distant from Xibe populations. Moreover, 12 individuals showed a null allele at DYS448 in Xibe population samples. We submitted Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.

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

Guizhou Province harbors extensive ethnolinguistic and cultural diversity with Sino-Tibetan-, Hmong–Mien-, and Tai–Kadai-speaking populations. However, previous genetic analyses mainly focused on the genetic admixture history of the former two linguistic groups. The admixture history of Tai–Kadai-speaking populations in Guizhou needed to be characterized further. Thus, we genotyped genome-wide SNP data from 41 Tai–Kadai-speaking Maonan people and made a comprehensive population genetic analysis to explore their genetic origin and admixture history based on the pattern of the sharing alleles and haplotypes. We found a genetic affinity among geographically different Tai–Kadai-speaking populations, especially for Guizhou Maonan people and reference Maonan from Guangxi. Furthermore, formal tests based on the f₃/f₄-statistics further identified an adjacent connection between Maonan and geographically adjacent Hmong–Mien and Sino-Tibetan people, which was consistent with their historically documented shared material culture (Zhang et al., iScience, 2020, 23, 101032). Fitted qpAdm-based two-way admixture models with ancestral sources from northern and southern East Asians demonstrated that Maonan people were an admixed population with primary ancestry related to Guangxi historical people and a minor proportion of ancestry from Northeast Asians, consistent with their linguistically supported southern China origin. Here, we presented the landscape of genetic structure and diversity of Maonan people and a simple demographic model for their evolutionary process. Further whole-genome-sequence–based projects can be presented with more detailed information about the population history and adaptative history of the Guizhou Maonan people.

Inferring the population structure and admixture history of three Hmong-Mien-speaking Miao tribes from southwest China based on Genome-wide SNP genotyping

BACKGROUND

Hmong-Mien speaking Miao, also called Hmong, is the sixthlargest ethnic group in mainland China. However, the fine-scale genetic profiles and population history of Miao populations in southwest China, especially in Guizhou province, remain uncharacterised due to a scarcity of samples of genome-wide data from different tribes.

AIM

To further investigate the population substructure and admixture history of the Guizhou Miao minority.

SUBJECTS AND METHODS

We collected 29 samples from three Miao tribes of Guizhou province in southwest China and genotyped about 700,000 genome-wide SNPs of each sample. We analysed newly generated data in together with published modern/ancient East Asian populations datasets via a series of population genetic methods, including principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm.

RESULTS

PCA and ADMIXTURE results showed that the three studied Guizhou Miao groups consistently fell on the Hmong-Mien-related genetic cline and were relatively genetically homogeneous, displayingd a genetic affinity with neighbouring Tai-Kadai speaking populations such as Dong. These results were further confirmed by the observed genetic clade in Fst, TreeMix, outgroup-f₃ -statistics, and f₄ -statistics. Furthermore, f₄ -based allele sharing patterns illustrated that compared with Hunan Miao in central China, Guizhou Miao shared more alleles with Hmong-Mien-speaking Vietnam Hmong and Tai-Kadai-speaking CoLao, Dong, while exhibiting less northeast Asian-related ancestry. Admixture-f₃ and f₄ statistics revealed the North-South admixture pattern for the studied Guizhou Miao. A qpAdm-based two-way admixture model further revealed that the studied Guizhou Miao harboured 44%∼55.4% indigenous Austronesian-speaking Atayal-related ancestry and 44.6%∼56% Late Neolithic Yellow River farmer-related ancestry.

CONCLUSIONS

The population structure within Hmong-Mien-related populations showed a geographic correlation. Hmong-Mien speaking Hunan Miao, Guizhou Miao, and Vietnam Hmong presented closer genetic relationships although they dwelt in different regions, suggesting the preservation of the original Hmong-related genetic diversity. The results based on genome-wide SNPs data generally matched the migration history for the Miao population. Our study contributes to a better knowledge of Miao populations and the population structure in southwest China.

Technical note: multi-alleles at the DYS385ab locus with high frequency in a Han Chinese population from southwestern China

Y-chromosome short tandem repeat (Y-STR) markers have been widely used in forensic applications and usually show monoallelic or diallelic genotypic patterns at certain double-copied loci. In this study, we have found 13 samples among 703 males with multi-alleles at the DYS385ab locus, including one with five mutant alleles, nine with four, and three with three. The frequency of abnormal DYS385ab genotypes was 1.85% (13/703), which is very high in the Han Chinese population. The percentage of samples with diallelic patterns at DYS385ab was higher than that of monoallelic patterns (80.23% vs. 17.92%). Additionally, the percentage of samples with tetra-allelic patterns at DYS385ab was higher than that of tri-allelic patterns (1.28% vs. 0.43%), suggesting that there are possibly two copies with duplicated events happening frequently on the Y chromosome. Interestingly, the peak height of allele 13 was two to three-folds higher than that of other alleles. The allele 18 peak height was also two-fold higher than others, which could potentially be explained by a duplication event mechanism. We also found that tri-allelic genotypes for alleles 13, 17, and 20, tetra-allelic genotypes for alleles 13, 14, 19, and 20, and tetra-allelic genotypes for alleles 12, 13, 19 and 21 were more common than others. Furthermore, all 13 samples had multi-alleles containing allele 13, implying a founder effect in this particular Chinese-specific ethnic group. Taken together, this study provides new information for this population and will be useful for paternal lineage identification, kinship analysis, and family relationship reconstruction using Y-STR forensic DNA analysis methods.

Genetic diversity, forensic feature, and phylogenetic analysis of Guizhou Tujia population via 19 X-STRs

BACKGROUND

X-chromosome short tandem repeats (X-STRs) with unique sex-linkage inheritance models play a complementary role in forensic science. Guizhou is a multiethnic province located in southwest China and some genetic evidence focusing on X-STRs for various minorities was reported. However, population data of Guizhou Tujia are scarce.

METHODS

A total of 507 Guizhou Tujia individuals were profiled using the AGCU X-19 STR kit. Allele frequencies and forensic parameters were calculated. Additionally, population genetic relationships between Guizhou Tujia and other 19 populations were explored.

RESULTS

A total of 257 alleles with the allele frequencies ranged from 0.0013 to 0.6098 were found. The combined power of discrimination in males and females and mean exclusion chances in all case scenarios were all greater than 0.99999. Population comparisons showed Guizhou Tujia had a homogeneity with all Han populations from different administrative regions, and other ethnic populations residing in Guizhou, while had obviously genetic heterogeneity with the Altaic family populations except Xibe.

CONCLUSION

Nineteen X-STRs can afford a reliable and informative database of Guizhou Tujia population for human identification and paternity testing, especially in complex biological relations. The genetic relationships of Chinese are significantly influenced by the geographic position and ethnolinguistic origin.

Phylogenic analysis and forensic genetic characterization of Guizhou Miao tribes from 58 microareas via autosomal STR

Genetic polymorphism of 17 autosomal short tandem repeat (STR) loci, included in the PowerPlex®18D amplification kit, were analyzed in Miao tribes from 58 different sampling microareas (N = 5255) of Guizhou as well as two cities (N = 151) of Hunan, China. Allele frequencies and forensic efficiency parameters were calculated. Moreover, comprehensive population genetic comparisons among 91 nationwide populations and 174 Asian populations were conducted based on raw genotype data and allele frequency data, respectively. Our results of forensic efficiency parameters showed that the panel was a robust tool in forensic individual identification and paternity cases for this population. Genetic affinities were observed among most of the Miao tribes revealed by multidimensional scaling plot, principal component analysis, and neighboring-joining tree. The genetic distance between Miao tribes and Han nationalities were varies by different geographical positions. Some of the Miao tribes were genetically closer to the Hmong-Mien populations living in southeastern contiguous regions and even the Indochina. The result coincided with the migration or reverse migration routes for Miao nationality in modern history. This study of the Miao tribes from plenty of microareas in Guizhou would be useful in reconstructing the population history and establishing a more comprehensive forensic reference database.

Population genetic data from 23 autosomal STR loci of Huaxia Platinum system in the Jining Han population

BACKGROUND

Genetic polymorphisms at 23 short tandem repeat (STR) loci were investigated in 1,215 Jining Han individuals from Jining city, Shandong province, eastern China.

METHODS

We used population genetic data of 23 autosomal STR loci included in the Huaxia Platinum system to evaluate 1,215 unrelated Chinese Han individuals in the Jining Han population. Allele frequencies and forensic parameters of the STR loci were determined and genetic relationships among the Jining Han and other Chinese populations were evaluated.

RESULTS

In total, we observed 321 alleles, with frequencies ranging from 0.00041 to 0.52222. The combined discrimination power and probability of excluding paternity were 0.99999999999999999999999999919 and 0.99999999962, respectively. No deviations from HWE were observed at any loci. Population comparisons showed that the Xinjiang groups (Uyghur and Kazakh) and the Mongolian and Tibetan groups were isolated, while the Jining Han population clustered together with other populations, except the Guizhou Han population.

CONCLUSION

This study demonstrated that 23 autosomal STR loci included in the Huaxia Platinum system are highly polymorphic and suitable for personal forensic identification and paternity testing in this population.