To what extent do microsatellite markers reflect genome‐wide genetic diversity in natural populations?

Abstract

Microsatellite variability is widely used to infer levels of genetic diversity in natural populations. However, the ascertainment bias caused by typically selecting only the most polymorphic markers in the genome may lead to reduced sensitivity for judging genome-wide levels of genetic diversity. To test this potential limitation of microsatellite-based approaches, we assessed the degree of nucleotide diversity in noncoding regions of eight different carnivore populations, including inbred as well as outbred populations, by sequencing 10 introns (5.4-5.7 kb) in 20 individuals of each population (wolves, coyotes, wolverines and lynxes). Estimates of nucleotide diversity varied 30-fold (7.1 x 10(-5 )-2.1 x 10(-3)), with densities of one single nucleotide polymorphism every 112-5446 bp. Microsatellite genotyping (10-27 markers) of the same animals revealed mean multilocus heterozygosities of 0.54-0.78, a 1.4-fold difference among populations. There was a positive yet not perfect (r(2) = 0.70) correlation between microsatellite marker heterozygosity and nucleotide diversity at the population level. For example, point estimates of nucleotide diversity varied in some cases with an order of magnitude despite very similar levels of microsatellite marker heterozygosity. Moreover, at the individual level, no significant correlation was found. Our results imply that variability at microsatellite marker sets typically used in population studies may not accurately reflect the underlying genomic diversity. This suggests that researchers should consider using resequencing-based approaches for assessing genetic diversity when accurate inference is critical, as in many conservation and management contexts.

Estimating genome-wide heterozygosity: effects of demographic history and marker type

“…Although significant correlations were seen in both populations, it was much tighter in NBR (Figure 3). In contrast, Väli et al (2008) found no significant correlation between individual heterozygosity at SNPs and microsatellites at the level of the individual in four populations of wolves (Canis lupus) and one of coyotes (C. latrans). However, both of these species have high dispersal rates and large effective population sizes (Pilot et al, 2006), which may not allow for such correlations to develop.…”

“…However, both of these species have high dispersal rates and large effective population sizes (Pilot et al, 2006), which may not allow for such correlations to develop. In addition, Väli et al (2008) used only 10-17 microsatellites and 25-51 SNPs in 10 introns, which our results suggest may not have had the power to detect an association in a population with low g 2 (for example, 0.001-0.005). The contrasting effect of demographic history is equally apparent when trying to estimate genome-wide heterozygosity from a subset of markers (Figure 4).…”

“…However, as the demographic history of a population will heavily influence correlations in marker heterozygosity within individuals (Ljungqvist et al, 2010;Szulkin et al, 2010), such modest numbers of markers may sometimes be insufficient (Balloux et al, 2004;Väli et al, 2008;Ljungqvist et al, 2010;Forstmeier et al, 2012). For example, Väli et al (2008) looked at the correlation between heterozygosity at 10-17 microsatellites and allelic diversity in 10 introns across eight populations of carnivores. They found a positive correlation between average heterozygosity and allelic diversity among populations but not between individual heterozygosity at SNPs and microsatellites.…”

What keeps ‘living dead’ alive: demography of a small and isolated population of Maculinea (= Phengaris) alcon

“…A potential manifestation of the above principle could be the very low female fecundity that we recorded in the present study, although we do not have any direct evidence for its genetic basis. Moreover, the correlation between variation in neutral markers, such as microsatellites, and fitness components remains hotly debated issue (Väli et al 2008;Ljungqvist et al 2010;Szulkin et al 2010). Nonetheless, most previous studies estimated the number of eggs laid per an average female of M. alcon at 80-100 (WallisDeVries 2004; Maes et al 2004;Radchuk et al 2012), whereas our reported value is about three-fold lower.…”

A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data

“…A number of articles discuss these potential issues (for example, Selkoe and Toonen 2006;Väli et al 2008;Guichoux et al 2011;Putman and Carbone 2014) and should be reviewed by any potential microsatellite users. Users of the pipeline described here are also encouraged to consult the articles cited for each of the programs utilised, as well as the user manual for the pipeline (see https://palfinder.ls.…”