Contrasting levels of genetic differentiation among putative neutral microsatellite loci in Atlantic herring Clupea harengus populations and the implications for assessing stock structure

Abstract

Microsatellite DNA loci, when used in population genetic studies, are usually assumed to be neutral (unaffected by natural selection, either directly or as a result of tight linkage), but this assumption is rarely tested. Here, the assumption of neutrality is examined using established methods, principally that based on the expected relationship between F ST and heterozygosity, at 12 putative neutral microsatellite loci utilised in a study of Atlantic herring Clupea harengus in the north east Atlantic (west of Great Britain and around Ireland) and in the Baltic Sea. All but two of these loci demonstrate relationships that suggest that they may be regarded as neutral genetic markers. Of the other two loci, however, one shows a relationship suggestive of the action of directional selection and the other of balancing natural selection, though other locusspecific effects may operate. Thus, the latter two loci may provide inaccurate inference if used in phylogeographic studies and also demonstrate the danger of assuming neutrality at all microsatellite loci without explicit testing. However, such loci, particularly those affected by directional as opposed to balancing selection, may be of great use in stock discrimination studies, and selected loci in general, have considerably potential in studies of adaptation.

A rapid and cost‐effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments

“…If unavailable, they can be easily found by mining expressed sequence tag (EST) or other genomic data sets, of which many exist for model and non-model protist species. With this in mind, it is important to remember that microsatellite loci are not necessarily neutral markers, with divergence among natural populations at some loci driven by selection (Vasemagi, Nilsson & Primmer 2005;Watts et al 2008) through linkage with another locus or directly. For example, the length of the microsatellite tract affects transcription at several loci in yeast, and selection can be quite efficient in generating new alleles of different lengths (Vinces et al 2009).…”

Outlier Loci and Selection Signatures of Simple Sequence Repeats (SSRs) in Flax (Linum usitatissimum L.)

“…Several genome scan studies have been conducted in artificial and natural populations to quantify the percentage of outlier loci and their association to environmental factors. For example, gSSRs have been applied in humans (Storz et al 2004 ), sorghum (Casa et al 2005 ), and Atlantic herring (Watts et al 2008 ) reporting between 4 and 12 % outliers. SSRs identified from ESTs would have a higher probability of detecting the footprints of selection since they occur in coding regions or the sequences that flank them (Rise et al 2004 ).…”

Population and Immunocompetent Genetic Variation: A Field-Based Study

“…Microsatellites should not be under direct selection, however there are a few exceptions; for example certain loci have been shown to act as enhancer elements in gene expression, to have protein binding abilities or to have phenotypic effects on physiology and development (Kashi and Soller, 1999) . In some studies certain microsatellite loci show unusually low or high levels of genetic diversity; a factor that may be attributable to natural selection acting on a nearby locus to which the microsatellite is linked (' genetic hitch-hiking' , see Beaumont and Nichols, 1996;Maynard Smith and Haigh, 1974;Watts et al, 2008).…”