Molecular Genetics and Genomics

, Volume 290, Issue 1, pp 141–150

Inferring population structure and demographic history using Y-STR data from worldwide populations

  • Hongyang Xu
  • Chuan-Chao Wang
  • Rukesh Shrestha
  • Ling-Xiang Wang
  • Manfei Zhang
  • Yungang He
  • Judith R. Kidd
  • Kenneth K. Kidd
  • Li Jin
  • Hui Li
Original Paper

DOI: 10.1007/s00438-014-0903-8

Cite this article as:
Xu, H., Wang, CC., Shrestha, R. et al. Mol Genet Genomics (2015) 290: 141. doi:10.1007/s00438-014-0903-8

Abstract

The Y chromosome is one of the best genetic materials to explore the evolutionary history of human populations. Global analyses of Y chromosomal short tandem repeats (STRs) data can reveal very interesting world population structures and histories. However, previous Y-STR works tended to focus on small geographical ranges or only included limited sample sizes. In this study, we have investigated population structure and demographic history using 17 Y chromosomal STRs data of 979 males from 44 worldwide populations. The largest genetic distances have been observed between pairs of African and non-African populations. American populations with the lowest genetic diversities also showed large genetic distances and coancestry coefficients with other populations, whereas Eurasian populations displayed close genetic affinities. African populations tend to have the oldest time to the most recent common ancestors (TMRCAs), the largest effective population sizes and the earliest expansion times, whereas the American, Siberian, Melanesian, and isolated Atayal populations have the most recent TMRCAs and expansion times, and the smallest effective population sizes. This clear geographic pattern is well consistent with serial founder model for the origin of populations outside Africa. The Y-STR dataset presented here provides the most detailed view of worldwide population structure and human male demographic history, and additionally will be of great benefit to future forensic applications and population genetic studies.

Keywords

Y chromosome STR Population structure Demographic history 

Supplementary material

438_2014_903_MOESM1_ESM.docx (255 kb)
Supporting doc1. Average gene diversity over loci, allele size range and number of alleles at different loci, and expected heterozygosity. (DOCX 255 kb)
438_2014_903_MOESM2_ESM.docx (806 kb)
Supporting doc2. Plots of matrix of pairwise FST, Slatkins linearized FST, average number of pairwise differences, and matrix of coancestry coefficients at continental level. (DOCX 806 kb)
438_2014_903_MOESM3_ESM.xlsx (11 kb)
Table S1. Population size, residency, ancestry and YHRD accession number of population samples. (XLSX 11 kb)
438_2014_903_MOESM4_ESM.xls (235 kb)
Table S2. The 979 haplotypes analyzed in this study. (XLS 235 kb)
438_2014_903_MOESM5_ESM.xls (126 kb)
Table S3. Pairwise genetic distance values and corresponding p-values between all populations at both the continental and population level. (XLS 125 kb)
438_2014_903_MOESM6_ESM.xls (39 kb)
Table S4. Coancestry coefficient at both the continental and population level. (XLS 39 kb)
438_2014_903_MOESM7_ESM.xls (54 kb)
Table S5. Locus by locus AMOVA (XLS 54 kb)
438_2014_903_MOESM8_ESM.xls (151 kb)
Table S6. TMRCA, expansion time, effective population size, and population growth rate for 44 worldwide populations estimated in Batwing. (XLS 151 kb)
438_2014_903_MOESM9_ESM.xls (222 kb)
Table S7. Y chromosome haplogroup prediction and demographic history inference of 25 Y chromosome predicted haplogroups. (XLS 222 kb)

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Hongyang Xu
    • 1
  • Chuan-Chao Wang
    • 2
  • Rukesh Shrestha
    • 2
  • Ling-Xiang Wang
    • 2
  • Manfei Zhang
    • 2
  • Yungang He
    • 1
  • Judith R. Kidd
    • 3
  • Kenneth K. Kidd
    • 3
  • Li Jin
    • 1
    • 2
  • Hui Li
    • 2
    • 3
  1. 1.CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
  2. 2.State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
  3. 3.Department of Genetics, School of MedicineYale UniversityNew HavenUSA

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