Standardizing for microsatellite length in comparisons of genetic diversity

Abstract

Mutation rates at microsatellites tend to increase with the number of repeats of the motif, leading to higher levels of polymorphism at long microsatellites. To standardize levels of diversity when microsatellites differ in size, we investigate the relationship between tract length and variation and provide a formula to adjust allelic richness to a fixed mean number of repeats in the specific case of chloroplast microsatellites. A comparison between 39 loci from eight species of conifers (where chloroplast DNA is paternally inherited) and 64 loci from 12 species of angiosperms (where chloroplast DNA is generally predominantly maternally inherited) indicates that the greater allelic richness found in conifers remains significant after controlling for number of repeats. The approach stresses the advantage of reporting variation in number of repeats instead of relative fragment sizes.

Rampant Gene Exchange Across a Strong Reproductive Barrier Between the Annual Sunflowers,Helianthus annuusandH. petiolaris

“…Diversity is significantly greater for anonymous than for EST-associated microsatellites, as has been reported in previous studies of Helianthus (Pashley et al 2006) and other organisms (Cho et al 2000;Cherdsak et al 2004;Woodhead et al 2005). Levels of genetic diversity are significantly affected by the number of microsatellite repeats (anonymous loci, mean number of repeats ¼ 11.91; ESTassociated loci, mean ¼ 5.83; P , 0.001, one-tailed t-test), which are known to correlate strongly with mutation rate (Petit et al 2005), but not by the length of repeat motifs. However, EST-associated microsatellites are seemingly more likely to have experienced significant selection in the recent past (see below), which might also have contributed to the reduced diversity.…”

Origin, evolution and genome distribution of microsatellites

“…Another important point regarding the use of microsatellites for genetic analysis of populations has been raised by Petit et al (2005) who suggested that microsatellite loci with more repeats generally show higher mutation rates (probably because DNA slippage increases in proportion to the number of repeats). In addition, if genetic diversity depends on mutation rate and mutation rate itself depends on the number of repeats subsequently there should be a relationship between microsatellite genetic diversity and the mean number of repeats (MNR).…”

“…In addition, if genetic diversity depends on mutation rate and mutation rate itself depends on the number of repeats subsequently there should be a relationship between microsatellite genetic diversity and the mean number of repeats (MNR). Petit et al (2005) proposed using allele size and the polymorphism rate of chloroplast microsatellite loci to standardize the level of diversity when microsatellites differ in size and investigated the relationship between the MNR and genetic variation as a prerequisite to comparative studies of genetic diversity. Their findings suggested that the greater allelic richness 300 Microsatellites, a review found in some species remains significant after controlling for the number of repeats.…”

What sampling is needed for reliable estimations of genetic diversity in Fraxinus excelsior L. (Oleaceae)?

“…Bias was estimated separately with reference to: a) the sampled array population (480 seeds); and b) to the standardized value of the adult population at n = 400 and n = 480. For this last standardized value we used the results from the first simulations, as resampling without replacement for different sizes produce the same results as rarefaction techniques (Petit et al, 2005), but with the advantage of providing standard errors for the estimations (Fernández-Manjarrés, unpublished results). To further investigate the effect of tree vs. family sampling efforts, we genotyped a subset of 10 of the original 24 families with the most variable molecular marker M2-30 for 40 seeds per tree (n = 40).…”