An evaluation of genetic distances for use with microsatellite loci.

TLDR

Microsatellite allele mutations produce alleles with similar repeat scores, so the difference in repeat count reflects the time since a common ancestor, a signal ignored by infinite‑alleles genetic distances. The study develops a genetic distance based on the stepwise mutation model that incorporates allelic repeat scores. By analytically extending stepwise‑mutation theory and validating with computer simulations, the authors show the distance’s expectation is linear in time and compare its performance to allele sharing and Nei’s distance. The results indicate that no single distance is universally best, but the new stepwise‑mutation distance outperforms others for phylogenetic reconstruction of sufficiently diverged taxa.

Abstract

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.