These so-called ‘pedigree’ rates have turned out to be an order of magnitude higher than the ‘evolutionary’ rate estimate of 2.6×10−4 per generation for the same STR loci, obtained in a study based on counting the number of mutations on the branches of a haplotype network .
This discrepancy might be explained by the fact that a large share of STR variation derived within a haplogroup is being effectively removed by genetic drift, rendering mutation rate estimates based on evolutionary considerations 3 or more times lower than those based on pedigree studies .The effective mutation rate (based on evolutionary considerations) has been estimated as 1.52×10−3 per generation for an average autosomal dinucleotide STR locus and as 0.85−0.93×10−3 per generation for tri- and tetranucleotide loci ; the mutation rate for an average Y chromosome tri- or tetranucleotide STR locus has been estimated as 6.9×10−4 per 25 years .
PLoS ONE 4(9): e7276. doi:10.1371/journal.pone.0007276
Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit
Mari Järve et al.
Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.
In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.
Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.