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Population genetics, diversity and forensic characteristics of Tai–Kadai-speaking Bouyei revealed by insertion/deletions markers

  • Guanglin He
  • Zheng Ren
  • Jianxin Guo
  • Fan Zhang
  • Xing Zou
  • Hongling Zhang
  • Qiyan Wang
  • Jingyan Ji
  • Meiqing Yang
  • Ziqian Zhang
  • Jing Zhang
  • Yilizhati Nabijiang
  • Jiang HuangEmail author
  • Chuan-Chao WangEmail author
Original Article
  • 67 Downloads

Abstract

China, inhabited by over 1.3 billion people and known for its genetic, cultural and linguistic diversity, is considered to be indispensable for understanding the association between language families and genetic diversity. In order to get a better understanding of the genetic diversity and forensic characteristics of Tai–Kadai-speaking populations in Southwest China, we genotyped 30 insertion/deletion (InDel) markers and amelogenin in 205 individuals from Tai–Kadai-speaking Bouyei people using the Qiagen Investigator DIPplex amplification kit. We carried out a comprehensive population genetic relationship investigation among 14,303 individuals from 84 worldwide populations based on allele frequency correlation and 4907 genotypes of 30 InDels from 36 populations distributed in all continental or major subregions and seven linguistic phyla in China. Forensic parameters observed show highly polymorphic and informative features for Asians, although the DIPplex kit was developed focusing on Europeans, and indicate that this amplification system is appropriate to forensic personal identification and parentage testing. Patterns of InDel variations revealed by principal components analysis, multidimensional scaling plots, phylogenetic relationship exploration, model-based clustering as well as four pairwise genetic distances (Fst, Nei, Cavalli-Sforza and Reynolds) demonstrate significant genetic differentiation at the continental scale and genetic uniformity in Asia except for Tibeto-Burman and Turkic-speaking populations. Additionally, Tai–Kadai speakers, including Bouyei, Zhuang and Dong, share more genetic ancestry components than with other language speakers, and in general they are genetically very similar to Hmong–Mien-speaking populations. The dataset of Bouyei people generated in the present study is valuable for forensic identification and parentage tests in China.

Keywords

InDels Population structure Tai–Kadai Forensic genetics Population genetics Linguistic family 

Notes

Author contributions

GH wrote the manuscripts. CCW revised the manuscript. HZ, ZR surveyed and collected the samples. HZ, ZR performed extraction of the genomic DNA. GH, JG, FZ, XZ, HZ, QW, JJ, MY, ZZ, JZ and YN performed the analysis of population diversity and genetic structure. CCW, JH initiated and supervised the project.

Funding

The work was funded by the National Natural Science Foundation of China (81601650, 31801040), Guizhou Province Engineering Technology Research Center Project (Qian High-Tech of Development and Reform Commission No. [2016]1345), Nanqiang Outstanding Young Talents Program of Xiamen University (X2123302), and Fundamental Research Funds for the Central Universities (ZK1144).

Compliance with ethical standards

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Ethics statement

We followed the recommendations of the “Medical Ethics Committee of Guizhou Medical University, China” in this study. All DNA samples are collected from unrelated donors with written informed consent. The protocol has been approved by the “Medical Ethics Committee of Guizhou Medical University” and in accordance with the Declaration of Helsinki.

Supplementary material

438_2019_1584_MOESM1_ESM.tif (3.6 mb)
Supplementary Fig. S1. Allele frequency differences among 36 populations based on the Insertion allele
438_2019_1584_MOESM2_ESM.tif (346 kb)
Supplementary Fig. S2. The delta K results under the ‘independent allele frequencies’ and ‘LOCPRIOR’ models
438_2019_1584_MOESM3_ESM.tif (1.2 mb)
Supplementary Fig. S3. Genetic relationship among 84 reference populations revealed by allele frequency distribution. (A), PCA results of the two-dimensional plots of the second and third components; (B), Patterns of population genetic relationship inferred from the first and third components
438_2019_1584_MOESM4_ESM.tif (3.6 mb)
Supplementary Fig. S4. A heatmap of the pairwise Nei’s genetic distances among 84 worldwide populations
438_2019_1584_MOESM5_ESM.tif (3.7 mb)
Supplementary Fig. S5. A heatmap of the pairwise Reynolds’s genetic distances among 84 worldwide populations
438_2019_1584_MOESM6_ESM.tif (1.2 mb)
Supplementary Fig. S6. Multidimensional scaling plots between Guizhou Bouyei and 83 worldwide reference populations revealed the corresponding genetic affinity and differences on the basis of the pairwise Nei’s genetic distance
438_2019_1584_MOESM7_ESM.tif (2.6 mb)
Supplementary Fig. S7. Multidimensional scaling plots between Guizhou Bouyei and 83 worldwide reference populations revealed the corresponding genetic relationships based on the pairwise Reynolds genetic distances
438_2019_1584_MOESM8_ESM.tif (1.9 mb)
Supplementary Fig. S8. Neighbor-joining tree reconstructed on the pairwise Nei’s genetic distances
438_2019_1584_MOESM9_ESM.xlsx (59 kb)
Supplementary Table S1. The raw genotype data of 30 InDels included in the Investigator DIPplex amplification system in Guizhou Bouyei population
438_2019_1584_MOESM10_ESM.xlsx (15 kb)
Supplementary Table S2. The p values of Linkage Disequilibrium among 30 InDels included in the Investigator DIPplex amplification system in Guizhou Bouyei ethnic group
438_2019_1584_MOESM11_ESM.xlsx (19 kb)
Supplementary Table S3. The pairwise Fst genetic distances between the Guizhou Bouyei and 35 worldwide populations on the basis of the raw data of 30 InDels included in the Investigator DIPplex amplification system
438_2019_1584_MOESM12_ESM.xlsx (57 kb)
Supplementary Table S4. The Nei’s genetic distances between the Guizhou Bouyei and 83 worldwide populations on the basis of genetic variations of 30 InDels included in the Investigator DIPplex amplification system
438_2019_1584_MOESM13_ESM.xlsx (52 kb)
Supplementary Table S5. The Cavalli-Sforza chord measures between the Guizhou Bouyei and 83 worldwide populations on the basis of genetic variations of 30 InDels included in the Investigator DIPplex amplification system
438_2019_1584_MOESM14_ESM.xlsx (41 kb)
Supplementary Table S6. The Reynolds’s genetic distances between the Guizhou Bouyei and 83 worldwide populations on the basis of genetic variations of 30 InDels included in the Investigator DIPplex amplification system

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Copyright information

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

Authors and Affiliations

  • Guanglin He
    • 1
    • 2
  • Zheng Ren
    • 3
  • Jianxin Guo
    • 2
  • Fan Zhang
    • 3
  • Xing Zou
    • 1
  • Hongling Zhang
    • 3
  • Qiyan Wang
    • 3
  • Jingyan Ji
    • 3
  • Meiqing Yang
    • 3
  • Ziqian Zhang
    • 2
  • Jing Zhang
    • 2
  • Yilizhati Nabijiang
    • 2
  • Jiang Huang
    • 3
    Email author
  • Chuan-Chao Wang
    • 2
    Email author
  1. 1.Institute of Forensic Medicine, West China School of Basic Science and Forensic MedicineSichuan UniversityChengduChina
  2. 2.Department of Anthropology and Ethnology, Institute of AnthropologyXiamen UniversityXiamenChina
  3. 3.Department of Forensic MedicineGuizhou Medical UniversityGuiyangChina

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