Phylogenetic analysis among 27 Chinese populations and genetic polymorphisms of 20 autosomal STR loci in a Chinese Uyghur ethnic minority group

Forensic features and genetic structure of the Hotan Uyghur inferred from 27 forensic markers

Background: The Uyghur is the fifth largest group in China and also the largest ethnic minority in Xinjiang.Aim: To explore the genetic variations of 27 forensic genetic markers included in the newly developed SureID^® PanGlobal Human DNA Identification System and analyse the genetic relationship between Xinjiang Uyghur and their neighbours.Subjects and methods: We genotyped 27 markers in 2,189 unrelated Uyghur individuals from the Hotan Prefecture in Southwest Xinjiang. Comprehensive population genetic studies among Chinese populations and worldwide populations were conducted via various statistics.Results: The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the new-generation autosomal STR amplification system in the Hotan Uyghur are 9,9999-E01 and 9,9999-E01, respectively. Population genetic studies indicate that the Hotan Uyghur show a close genetic relationship with geographically different Uyghurs and Kazakhs, while significant genetic differentiation exists between the Hotan Uyghur and some ethnicities from other non-Turkic-speaking populations. The results of population comparisons among the 52 worldwide populations demonstrate that geographically approached intercontinental populations have close genetic relationships.Conclusions: 24 autosomal STRs are highly polymorphic and informative in the Uyghur and this system is suitable for forensic personal identification and paternity testing. Our findings not only reveal that Chinese Uyghur is a homogenous population based on forensic genetic markers, but also indicate that population genetic affinity is closely related to the adjacent populations with common ethnic origin.

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.

Genetic characteristics and phylogenetic analysis of three Chinese ethnic groups using the Huaxia Platinum System

Short tandem repeats (STRs) are attractive to genetic applications like forensic, anthropological and population genetics studies. The Huaxia Platinum System was specifically developed to allow co-amplification and detection of all markers in the expanded CODIS core loci and the Chinese National Database. In this study, in continuation to our previous validation study, 568 unrelated individuals were firstly genotyped to investigate the effectiveness of this novel assay in 3 main ethnic groups of China (Han, Tibetan and Yi). The combined power of discrimination (CPD) were 0.9999999999999999999999999992, 0.999999999999999999999999992, 0.999999999999999999999999998, respectively, and the combined power of exclusion (CPE) were 0.9999999999, 0.999999995, 0.999999998, respectively. Next, genetic relationships along administrative and ethnic divisions were analyzed using pairwise genetic distances, multidimensional scaling (MDS), principal component analysis (PCA) and phylogenetic analysis. The Han ethnicity showed a high genetic homogeneity all across China, and significant genetic differences existed between Han groups and some minority groups, most prominently for the Tibetans, the Uyghurs, the Kazakhs, the Miaos, the Zhuangs and the Dais. Aforementioned results suggested that the Huaxia Platinum System is polymorphic and informative, which provides an efficient tool not only for human forensics, but also for population genetics studies.

Genetic Diversity and Phylogenetic Differentiation of Southwestern Chinese Han: a comprehensive and comparative analysis on 21 non-CODIS STRs

Short tandem repeats (STRs), with high polymorphism and complex evolution information, play a significant role in genetic association studies like population genetics, molecular anthropology and human forensics. However, human genetic diversity has only been partially sampled and available for Southwest Chinese Han population, as well as the genetic architecture of this population remains uncharacterized. In this work, 368 unrelated Han individuals from Sichuan province were firstly genotyped with 21 non-CODIS autosomal STRs, and phylogenetic relationships along administrative (Han Chinese from different regions) and ethnic divisions (minority ethnic groups) were subsequently investigated. The CMP and CPE were 6.2796 × 10-20 and 0.9999999, respectively. Analysis of molecular variance (AMOVA), principal component analysis (PCA), multidimensional scaling plots (MDS) and phylogenetic analysis consistently demonstrated that the Southwest Han population had a close genetic relationship with the geographically close population (Hunan Han) and kept a distant genetic relationship with some ethnic groups, most prominently for Gansu Yugu and Fujian She. Furthermore, no significant genetic distinction between the Northern Han and Southern Han was observed. Aforementioned results suggested that these 21 STRs are highly polymorphic and informative, which are suitable for human identification and population genetics.

Forensic features and phylogenetic analyses of Sichuan Han population via 23 autosomal STR loci included in the Huaxia Platinum System

Short tandem repeats (STRs) are DNA regions with a variable number of repeated units (2-6 bp) and attractive to genetic application like forensic, population genetics, and anthropological studies. The Huaxia Platinum System allows the multiplex amplification of 23 autosomal STR loci and two gender determination loci. In the present study, genetic polymorphisms of these 23 autosomal STR loci were first obtained from 309 Sichuan Han individuals, southwest China. No evidence of deviation from the Hardy-Weinberg equilibrium (HWE) was identified. The combined match probability (CMP), combined power of discrimination (CPD), and combined power of exclusion (CPE) are 1.087 × 10^-27, 0.999999999999999999999999999, and 0.9999999996 in the Sichuan Han Chinese population, respectively. The inter-population differentiation, PCA, MDS, and phylogenetic analysis revealed that Sichuan Han had a closer genetic relationship with neighboring Han Chinese populations. Our findings indicated that the 23 autosomal STR loci are polymorphic and informative in studied southwestern Chinese Han population and can be utilized as a powerful tool for forensic applications. In addition, population comparisons demonstrated that the genetic similarities widely existed among Han Chinese populations distributed in different administrative divisions, and genetic differences had existed between minorities (most prominently for Uyghur and Kazakh) and Han groups.

X-chromosomal STR-based genetic structure of Sichuan Tibetan minority ethnicity group and its relationships to various groups

The X-chromosomal short tandem repeats (STRs) with more informative than autosomal STRs in some complicated biological relationships identification due to its specific mode of genetic transmission can be used as a complementary tool in forensic case practices. In this study, we presented the population genetic data of 19 X-STRs, consisting of DXS10174, DXS10075, DXS10079, DXS101, DXS10101, DXS10103, DXS10134, DXS10135, DXS10148, DXS10159, DXS10162, DXS10164, DXS6789, DXS6809, DXS7132, DXS7423, DXS7424, DXS8378, and HPRTB loci, in a sample of 235 individuals of Tibetan nationality from Sichuan province, Southwest China. All 19 X-STR loci were consistent with Hardy-Weinberg equilibrium. The results showed that the combined power of discrimination in females and males are 0.999999999999999999997 and 0.9999999999997, respectively. In addition, the mean paternity exclusion chances based on the formula of MEC_Krüger, MEC_Kishida, and MEC_Desmarais as well as MEC_{Desmarais Duo} are 0.99999991, 0.9999999999924, 0.9999999999929, and 0.999999985, respectively. In summary, our findings suggested that the AGCU X19 kit can be considered to serve as a high polymorphic information tool for forensic identification and kinship testing in the Sichuan Tibetan population. Furthermore, population genetic structure investigation between Sichuan Tibetan population and other 19 populations using PCA, MDS, and phylogenetic tree illustrated that significant genetic difference was observed between the Sichuan Tibetan and Malay, as well as the Xinjiang Uyghur population.

Genetic diversity of 21 autosomal STR loci in the Han population from Sichuan province, Southwest China

Exploration of the ethnic origin and genetic differentiation of 56 Chinese officially recognized nationalities populations played a fundamental role in the research field of population genetics, forensic science, linguistics, anthropology, and archaeology. In the present study, population data of 21 autosomal STR loci (CSF1PO, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D2S441, D3S1358, D5S818, D6S1043, D7S820, D8S1179, FGA, Penta D, Penta E, TH01, TPOX, and vWA) included in the AGCU EX22 kit in 2793 Southwest Han Chinese individuals was obtained and population genetic relationships among 28 Chinese populations were investigated. Our study indicated that the twenty-one autosomal STRs are highly polymorphic in the Sichuan Han population and can be used as a powerful tool in the routine forensic usage. MDS and phylogenetic analysis suggested that the Sichuan Han population kept a close genetic relationship with the southwest populations.

Genetic polymorphisms for 19 autosomal STR loci of Chongqing Han ethnicity and phylogenetic structure exploration among 28 Chinese populations

The allele frequencies and forensic statistical parameters of 19 autosomal short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, THOl, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, D6S1043, Penta D, Penta E, and D12S391) included in the Goldeneye™ DNA ID system 20A kit were obtained in 671 Chinese Han individuals residing in Chongqing, Southwest China. All 19 STR loci were identified in agreement with the Hardy-Weinberg equilibrium. A total of 238 alleles were observed with corresponding allele frequencies that varied from 0.0007 to 0.5119. The combined power of discrimination and the combined probability of exclusion for 19 STR loci in the Chongqing Han population were 0.99999999999999999999998954 and 0.99999998387, respectively. The findings indicated that the 19 autosomal STR loci were highly polymorphic in the Chongqing Han population and can be used as a powerful tool in personal identification and parentage testing. Our genetic study enriched the Chinese local forensic reference database. Population comparisons and phylogenetic analyses revealed that genetic heterogeneity widely existed among the Chongqing Han, Xinjiang Uyghur, and Kazakh populations as well as demonstrated that genetic similarity was tightly associated with those of close geographic origin or of the same ethnic origin.