An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations

Abstract

The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were.86-.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, phi(ST) statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure.

Figure 1

Approximate geographic locations of 20 study populations. The color codings differentiate the eight groups of populations used for AMOVA analyses.

Figure 2

Allele-frequency distributions of the seven Y-STR loci, among all 986 male individuals combined. For each locus, the allelic designation (in number of repeats) is indicated on the X-axis, and the observed frequency (in %) is shown on the Y-axis.

Figure 3

Estimated genetic variances for each the seven Y-STR loci, and the average across the seven loci, within each of the 20 different population samples.

Figure 4

Unrooted NJ tree, based on linearized Φ_ST distances derived from AMOVA connecting all 20 population samples.

Figure 5

Genetic map based on multidimensional-scaling analysis and a matrix of the pairwise linearized Φ_ST distances derived from AMOVA.

Figure 6

Unrooted NJ tree connecting all 598 distinct seven-locus Y-STR haplotypes. The complex topology of the tree was reduced by delineation of 17 major clusters of related haplotypes. The relative contribution of haplotypes of each of the eight population groups is indicated for each cluster; that is, cluster 1 contains 7.7% of the haplotypes observed among Europeans, 17% of all Asian haplotypes, 15.9% of all New Guinean haplotypes, 4.3% of all the NSA haplotypes, no haplotypes from the Arctic (i.e., the INU) and African (i.e., the CAP) populations, 7.4% of all the SUR haplotypes, and 10% of all the WSA haplotypes. For each of the eight groups of populations, the total sum of haplotypes is 100%; thus, cluster 1 contains 62.3% of 800% (i.e., 7.8%) of all haplotypes. The color codes correspond to the eight groups of populations used for AMOVA and are the same as those used in figures 1 and 7.

Figure 7

Modified reduced median network based only on haplotypes observed in at least five male individuals (0.5%). The diameter of each circle corresponds to a categorical absolute frequency (n=5–9, n=10–14, and n>14). Multicolored pies charts denote haplotypes found in different population groups.