Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

TL;DR

This study uses simulations to assess how homoplasy impacts the accuracy of chloroplast microsatellite markers in measuring genetic diversity, revealing that some diversity estimates are more affected than others.

Contribution

It provides a coalescent-based simulation approach to evaluate homoplasy effects on chloroplast microsatellite diversity measures, highlighting their limitations.

Findings

Homoplasy has little effect on Nei's haplotype diversity (H(E)).

Goldstein's genetic distance (D2sh) is significantly affected by homoplasy.

Number of loci influences the accuracy of diversity assessments.

Abstract

Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed.