Phylogenetic relationship and genetic history of Central Asian Kazakhs inferred from Y-chromosome and autosomal variations

Abstract

The Xinjiang Uyghur Autonomous Region of China (XUARC) with 47 ethnic groups is a most colourful ethnic region of China, harboring abundant genetic and cultural diversity, which harbors 47 ethnic groups. The Kazakhs are the third largest ethnic group (7.02%) after Uyghur (46.42%) and Han (38.99%) in Xinjiang, but their genetic diversity and forensic characterization are poorly understood. In the current study, we genotyped 15 autosomal short tandem repeat (STR) loci and 10 Y-STRs on 889 individuals (659 male and 230 female) collected from Kazak population of the Ili Kazak Autonomous Prefecture using AGCU Expressmarker 16 and 10Y-STR Kit (EX16+10Y). For autosomal STRs, we observed a total of 174 different alleles ranging from 6 and to 34.2 repeat units and FGA showed the greatest power of discrimination (20 alleles) in Ili Kazakh population. We have not observed departures from Hardy-Weinberg equilibrium (HWE) after sequential Bonferroni correction and only found a minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The combined power of exclusion (CPE) was 0.99999998395 and combined power of discrimination (CPD) was 99.999999999999999798%. For Y-STRs, we observed a total of 496 different haplotypes on these 10 Y-STR loci. The gene diversities ranged from 0.5023 (DYS391) to 0.8357 (DYS385a/b). The overall haplotype diversity (GD) was 0.9985 with random matching probability (RMP) 0.0015. The results of population genetic analysies based on both autosomal and Y-chromosome STRs demonstrated that the genetic affinity among populations are generally consistent with exists along the ethnic, linguistic, and continental geographical classificationsboundary.

Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand-line revealed by Y chromosomal STRs

“…For the Afghan Hazara population, the Afghan population (0.0009) from Afghanistan showed the closest genetic distance and for the Pakistani Hazara group, the Afghan population (0.0381) from Afghanistan showed the closest genetic distance To investigate the paternal relationship among these three and other reference populations, we have generated the MDS plot (figure 1) based on pairwise Rst matrix from supplementary table 3. In the MDS plot, we have seen that the Hazara population from Afghanistan is located closer to the Afghan population from Afghanistan and the Pathan population from northern Afghanistan which is similar to the results of another study 32 , while Pakistani Hazara lined closer to Kazakh and Mongolian population which is similar to our previous study’s results 27,33 .…”

Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand line revealed by Y-chromosomal STRs

“…Fst is a standardized variance of haplotype frequency and assumes genetic drift as being the agent that differentiates pairwise Rst matrix from supplementary table 3. In the MDS plot, we have seen that the Hazara population from Afghanistan is located closer to the Afghan population from Afghanistan and the Pathan population from northern Afghanistan which is similar to the results of another study 32 , while Pakistani Hazara lined closer to Kazakh and Mongolian population which is similar to our previous study's results 27,33 .…”

“…These types of features are usually inferred as past male-lineage expansions 35 . Star-like features of haplotypes comprising haplogroup M217 (C2) have been reported previously in Hazara, Mongol, and Kazakh populations 27,33,36 . An explanation about its origin in Mongolia was about ∼1,000 years ago 36 .…”

Genetic admixture of Chinese Tajik people inferred from genome‐wide array genotyping and mitochondrial genome sequencing

“…Many previous studies have suggested extensive genetic admixture between East and West Eurasians in northwest China (Ning et al, 2019; Wang et al, 2019, 2021; Adnan et al, 2020, 2021; Wen et al, 2020; Zhao et al, 2020; He et al, 2021; Ma et al, 2021; Yang et al, 2021; Yao et al, 2021; Zhang et al, 2021), but a few focus on Tajiks. A 2018 paper by Min‐Sheng Peng et al used mitochondrial genome analysis to understand the maternal origin of multiple ethnic groups on the Pamir Plateau.…”