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

  • Atif AdnanEmail author
  • Guanglin He
  • Allah Rakha
  • Kaidirina Kasimu
  • Jianxin Guo
  • Sibt E. Hassan
  • Sibte Hadi
  • Chuan-Chao WangEmail author
  • Jin-feng XuanEmail author
Original Article

Abstract

The Xinjiang Uyghur Autonomous Region of China (XUARC) with 47 ethnic groups is a very colorful ethnic region of China, harboring abundant genetic and cultural diversity. 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 ten Y-STRs in 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 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 in these ten 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) of 0.0015. The results of population genetic analysis based on both autosomal and Y-chromosome STRs demonstrated that the genetic affinity among populations is generally consistent with ethnic, linguistic, and continental geographical classifications.

Keywords

Kazakh Xinjiang Uyghur Autonomous Region Expressmarker 16 + 10Y STR Kit Forensic genetics 

Notes

Acknowledgements

This study was financially supported by the National Natural Science Foundation of China (31801040), Nanqiang Outstanding Young Talents Program of Xiamen University (X2123302), and Fundamental Research Funds for the Central Universities (ZK1144).

Author contributions

JF, CW, and AA designed this study, AA wrote the manuscript, AA, KK, JG, and GH, conducted the experiment, AA, GH, KK, AR, SH, SHJF, and CW analyzed the results, AA, and CW modified the manuscript. All authors reviewed the manuscript.

Funding

The authors declare no competing financial interests.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the China Medical University, Shenyang, Liaoning Province, People’s Republic of China and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

438_2019_1617_MOESM1_ESM.jpg (114 kb)
Figure S1: Genetic homology between Ili Kazakhs and 7 other populations from China revealed by NJ phylogenetic tree based on Fst values (JPEG 113 kb)
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Figure S2: Neighbor-joining phylogenetic tree based on Nei’s genetic distance between Ili Kazakhs and other 70 reference populations across China (JPEG 871 kb)
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Figure S3: A heat map of Nei’s genetic distance values between Ili Kazakhs and other 70 reference populations across China (JPEG 908 kb)
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Figure S4: Interactivity test based on allelic frequencies of overlapping 15 autosomal STRs between Ili Kazakhs and other 70 reference populations across China (JPEG 178 kb)
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Figure S5: Principal component analysis based on the frequency of overlapping 15 autosomal STRs between Ili Kazakh population of Xinjiang and already published 32 worldwide populations (JPEG 59 kb)
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Figure S6: Neighbor-joining phylogenetic tree based on Nei’s genetic distance between Ili Kazakh population of Xinjiang and already published 32 worldwide populations (JPEG 578 kb)
438_2019_1617_MOESM7_ESM.jpg (129 kb)
Figure S7: Interactivity test based on allelic frequencies of overlapping 15 autosomal STRs between Ili Kazakhs population of Xinjiang and already published 32 worldwide populations (JPEG 128 kb)
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Figure S8: A two-dimensional multidimensional scaling plot of Ili Kazakh population of Xinjiang and other regional populations based on pairwise Rst values (JPEG 196 kb)
438_2019_1617_MOESM9_ESM.jpg (130 kb)
Figure S9: Interactivity test based on allelic frequencies of overlapping 10 Y-STRs between Ili Kazakhs population of Xinjiang and already published 47 worldwide populations (JPEG 129 kb)
438_2019_1617_MOESM10_ESM.xlsx (190 kb)
Table S1: The haplotypes of 25 STR loci in Ili Kazakhs from Xinjiang using AGCU Expressmarker 16 and 10Y-STR Kit (EX16 + 10Y) (n = 889) (XLSX 190 kb)
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Table S2: Sequential Bonferroni corrections for p values from exact tests for HWE of 15 autosomal STRs in Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang (n = 889) (XLSX 10 kb)
438_2019_1617_MOESM12_ESM.xlsx (30 kb)
Table S3:p values from exact tests for linkage equilibrium (LE) employing pairwise combinations of 15 autosomal STRs in Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang (n = 889) (XLSX 29 kb)
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Table S4: Pairwise Fst genetic distances between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and 7 Chinese reference populations on the basis of raw genotype data of 15 STRs (XLSX 9 kb)
438_2019_1617_MOESM14_ESM.xlsx (23 kb)
Table S5: Genetic distance (Fst) and associated p values for population differentiation between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and other published populations (XLSX 23 kb)
438_2019_1617_MOESM15_ESM.xlsx (62 kb)
Table S6: Nei’s pairwise genetic distance between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and other published populations (XLSX 62 kb)
438_2019_1617_MOESM16_ESM.xlsx (12 kb)
Table S7: Interactivity test between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and other published populations (XLSX 12 kb)
438_2019_1617_MOESM17_ESM.xlsx (24 kb)
Table S8: Nei’s pairwise genetic distance between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and other Worldwide published 32 populations (XLSX 23 kb)
438_2019_1617_MOESM18_ESM.xlsx (11 kb)
Table S9: Interactivity test between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and other 32 Worldwide published populations (XLSX 10 kb)
438_2019_1617_MOESM19_ESM.xlsx (14 kb)
Table S10: Allelic distribution of 10 Y-STRs in Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang (XLSX 13 kb)
438_2019_1617_MOESM20_ESM.xlsx (21 kb)
Table S11: Pairwise Rst genetic distance between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and other published populations (XLSX 20 kb)
438_2019_1617_MOESM21_ESM.xlsx (23 kb)
Table S12: Renoyld distance between Kazakh population from Ili Kazak Autonomous Prefecture from Xinjiang and other published populations (XLSX 22 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Human Anatomy, School of Basic MedicineChina Medical UniversityShenyangChina
  2. 2.Department of Forensic Genetics and Biology, School of Forensic MedicineChina Medical UniversityShenyangChina
  3. 3.Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and MedicineXiamen UniversityXiamenChina
  4. 4.Department of Forensic SciencesUniversity of Health SciencesLahorePakistan
  5. 5.School of Forensic and Investigative SciencesUniversity of Central LancashirePrestonUK
  6. 6.West China School of Basic Science and Forensic MedicineSichuan UniversityChengduChina

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