A comprehensive survey of human Y-chromosomal microsatellites

Abstract

We have screened the nearly complete DNA sequence of the human Y chromosome for microsatellites (short tandem repeats) that meet the criteria of having a repeat-unit size of > or = 3 and a repeat count of > or = 8 and thus are likely to be easy to genotype accurately and to be polymorphic. Candidate loci were tested in silico for novelty and for probable Y specificity, and then they were tested experimentally to identify Y-specific loci and to assess their polymorphism. This yielded 166 useful new Y-chromosomal microsatellites, 139 of which were polymorphic, in a sample of eight diverse Y chromosomes representing eight Y-SNP haplogroups. This large sample of microsatellites, together with 28 previously known markers analyzed here--all sharing a common evolutionary history--allowed us to investigate the factors influencing their variation. For simple microsatellites, the average repeat count accounted for the highest proportion of repeat variance (approximately 34%). For complex microsatellites, the largest proportion of the variance (again, approximately 34%) was explained by the average repeat count of the longest homogeneous array, which normally is variable. In these complex microsatellites, the additional repeats outside the longest homogeneous array significantly increased the variance, but this was lower than the variance of a simple microsatellite with the same total repeat count. As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations.

Figure 1

Unit-size distribution of 53 previously known and 166 new human Y-chromosomal microsatellites.

Figure 2

Localization of the 219 currently known microsatellites on the euchromatic part of the human Y chromosome

Figure 3

Relative frequencies of retroposon-associated Y-chromosomal microsatellites with different complexities.

Figure 4

Variance characteristics of Y-chromosomal microsatellites with different repeat-unit lengths.

Figure 5

A, Relationship between average repeat count and repeat variance for 65 completely simple Y-chromosomal microsatellites (R=0.595; P<.001). B, Relationship between average repeat count of the longest homogeneous array (which normally is variable) and repeat variance for 104 complex Y-chromosomal microsatellites (R=0.591; P<.001).

Figure 6

A, Comparison between simple and complex microsatellites, grouped according to average total repeat count, and complex microsatellites with the same average repeat count in the longest homogeneous array. B, Comparison between simple microsatellites, grouped according to average total repeat count, and complex microsatellites with the same average total repeat count. For repeat count <7, the average repeat variance was 0 for both simple and complex microsatellites.