Inverse relationship betweenF_STand microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure

Abstract

Microsatellites have proved to be useful for the detection of weak population structure in marine fishes and other species characterized by large populations and high gene flow. None the less, uncertainty remains about the net effects of the particular mutational properties of these markers, and the wide range of locus polymorphism they exhibit, on estimates of differentiation. We examined the effect of varying microsatellite polymorphism on the magnitude of observed differentiation in a population survey of walleye pollock, Theragra chalcogramma. Genetic differentiation at 14 microsatellite loci among six putative populations from across the North Pacific Ocean and Bering Sea was weak but significant on large geographical scales and conformed to an isolation-by-distance pattern. A negative relationship was found between locus variability and the magnitude of estimated population subdivision. Estimates of F(ST) declined with locus polymorphism, resulting in diminished power to discriminate among samples, and we attribute this loss to the effects of size homoplasy. This empirical result suggests that mutation rates of some microsatellite loci are sufficiently high to limit resolution of weak genetic structure typical of many marine fishes.

Mito-nuclear discordance in the degree of population differentiation in a marine goby

“…The situations where size homoplasy is most prevalent involve high mutation rates and large population sizes together with strong allele size constraints (Estoup et al, 2002). Therefore, effects of homoplasy are expected to be common for microsatellites in marine fishes (O'Reilly et al, 2004), which has implications for the identification of genetic structuring (Carreras-Carbonell et al, 2006). Microsatellites probably suffered from higher levels of homoplasy than mtDNA because of higher mutation rates and larger effective population sizes (Balloux et al, 2000).…”

A multi-locus assessment of connectivity and historical demography in the bluehead wrasse (Thalassoma bifasciatum)

“…The presence of nonamplifying alleles may affect the results of population genetic analyses (Dakin and Avise, 2004), although there is no reason to suspect that their presence would bias towards finding high-gene flow. For example, other studies that made use of microsatellite data to examine population structure in marine and freshwater organisms have uncovered significant genetic structure in the presence of heterozygosity deficiency that was possibly caused by null alleles (O'Reilly et al, 2004;Pampoulie et al, 2004;Therriault et al, 2005). In the O'Reilly et al…”

Ten new microsatellite markers in cutlassfishTrichiurus lepturusderived from an enriched genomic library

“…Brandströ m and Ellegren (2008) observed a relationship between microsatellite length and degree of polymorphism, and were able to quantify this relationship for lengths of a few to several repeat units. They concluded that most repeats are 'perfect' repeats with no interruptions; however, when interruptions were present in more than 15% of the loci, polymorphism was significantly lower compared with that associated with perfect repeats (O'Reilly et al 2004).…”