Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta)

Abstract

A comparative study between microsatellite and allozyme markers was conducted on natural populations of resident brown trout (Salmo trutta) sampled over a reduced geographical scale and on hatchery strains. The higher level of polymorphism observed at microsatellite loci resulted in higher power of statistical tests for differentiation among population samples and for genotypic linkage disequilibrium. Genetic distances of Cavalli-Sforza and Edwards were on average two times larger for microsatellites than for allozymes but multilocus FST estimates computed over the entire set of populations were not significantly different for both categories of markers. Assignment tests of individual fish to the set of sampled populations demonstrated a much higher efficiency of microsatellites compared to allozymes. Pairwise multilocus FST estimates were significantly correlated to waterway distances and there was a significant tendency for the incorrectly classified individuals to be assigned to one of the nearest populations, indicating that isolation-by-distance acted significantly on brown trout populations. This increase of differentiation with distance was higher for allozymes than for microsatellites. Traditional measures of genetic differentiation (Cavalli-Sforza and Edwards' chord distance and FST) were compared for microsatellites to recently proposed statistics taking into account allele size differences (Goldstein's distance and PST). Using Goldstein's distance for neighbour-joining analysis did not improve the tree structure resolution. Multilocus estimates of PST and FST were not significantly different when computed over the entire set of populations but no significant correlation was detected between matrices of pairwise multilocus PST estimates and waterway distances.

Extensive population subdivision of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda) around the Iberian Peninsula indicated by microsatellite DNA variation

“…Finally, allozymes also show less geographically concordant relationships among samples: unrooted NJ trees based on D and D chord gave different topologies [(((GalW,FFoz),RMar),(SBar,VGel))] and less bootstrap support for nodes (72-89%) than NJ trees obtained using microsatellites. These results may indicate that, as found previously in studies of brown trout (Estoup et al, 1998) and squid (Shaw et al, 1999a), microsatellites have greater power than allozymes for resolving genetic relationships among closely related sub-populations of aquatic species with a facility for gene flow on a small geographical scale, and could be more suitable for resolving historical relationships at the intraspecific level.…”

“…As loci Sof3 and Sof5 both display allelic arrays that suggest a non-SMM (Shaw and Pérez-Losada, 1999), non-SMMbased methods (F ST , D chord and Nei's D) were used preferentially in the following analyses. Nevertheless, because the performance of statistics based on one or another mutation model is still a matter of argument (Estoup et al, 1995;Takezaki and Nei, 1996;Goodman, 1997;Estoup et al, 1998) and for comparative purposes, SMM statistics were also included [R ST and (␦ ) 2 ]. F ST was estimated by ˆ ( Weir and Cockerham, 1984) using f-stat, and unbiased R ST using the rst-calc programme (Goodman, 1997), which adjusts for differences in sample size and allele size variances among loci.…”

“…Microsatellite markers have shown considerable utility for genetic studies of population structure, particularly in organisms exhibiting low variability detectable by other methods (Hughes and Queller, 1993;Estoup et al, 1998). Several recent studies of widespread and abundant marine species (eg, squid, Shaw et al, 1999a;and herring, Shaw et al, 1999b) have indicated the greater capacity of microsatellite vs allozyme markers to detect fine population structure in such species.…”

Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples

“…1993), Ssa 85 , Ssa 197 (O'Reilly et al . 1996, SsOSL 417 (Slettan, Olsaker & Lie 1995), SsOSL 438 (Slettan, Olsaker & Lie 1996) and T3-13 (Estoup et al . 1998).…”

Genetic structure of the high dispersal Atlanto-Mediterreanean sea star Astropecten aranciacus revealed by mitochondrial DNA sequences and microsatellite loci

“…In this study, we sequenced the complete control region of the mitochondrial DNA, a region that has the highest rate of evolutionary change of any mtDNA region (Aquadro and Greenberg 1983;Parsons et al 1997). As nuclear markers, we used four polymorphic microsatellite loci, which are believed to be neutral and have been shown to be more variable compared to e.g., allozyme data (Shaw et al 1999;Estoup et al 1998;Perez-Losada et al 2002).…”