An evaluation of genetic distances for use with microsatellite loci.

Abstract

Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

Ghosts from the past: even comprehensive sampling of the native range may not be enough to unravel the introduction history of invasive species—the case of Acacia dealbata invasions in South Africa

“…Based on the historical information that A. dealbata was introduced to South Africa in the middle of the 19 th century (Poynton, ) and given its minimum generation time of four to five years (Stelling, ), we assumed that the invasion in South Africa is not older than 45 generations (Appendix S3). We applied a generalized stepwise mutation model for the ABC approach for which mean number of alleles, mean genetic diversity (Nei, ), mean allele size variance, mean Garza‐Williamson's M (Garza and Williamson, ; Excoffier et al., ), F ST (Weir and Cockerham, ), shared allele distance (Chakraborty and Jin, ) and (δμ) 2 genetic distance (Goldstein et al., ) were considered for the summary statistics. The posterior probabilities of the competing scenarios were compared using logistic regression on the 1% of simulated data sets closest to the observed data set (Cornuet et al., ).…”

The Number of Alleles at a Microsatellite Defines the Allele Frequency Spectrum and Facilitates Fast Accurate Estimation of

“…The moment C j = E [ i p i p i +j ], in particular, has been investigated in detail and specifies the probability that two randomly chosen alleles are separated by j steps (Ohta and Kimura 1973;Brown et al 1975;Moran 1975). Numerous studies have explored the relationship between divergence time and genetic distance at a microsatellite locus, leading to the important result that this relationship is linear for certain genetic distances (Goldstein et al 1995a(Goldstein et al ,1995bZhivotovsky and Feldman 1995;Sun et al 2009). Pritchard and Feldman (1996) investigated the divergence measure s, which is the difference in repeat number between two individuals, providing formulas for the expected value of s 2 and its variance under a variety of conditions including structured and bottlenecked populations.…”

Sampling from Natural Populations with RNAi Reveals High Outcrossing and Population Structure in Caenorhabditis elegans

“…The population mutation rate, q = 4N e u, was estimated for each locus under the assumption of a stepwise mutation model as the mean squared pairwise difference in allele sizes expressed as the number of repeat units [41]. Differences between alleles from the same individual were not included, in order to avoid the effects of nonindependence due to selfing.…”