A Comparison of Biallelic Markers and Microsatellites for the Estimation of Population and Conservation Genetic Parameters in Atlantic Salmon (Salmo salar)

Abstract

Biallelic markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms have become increasingly popular markers for various population genetics applications. However, the effort required to develop biallelic markers in nonmodel organisms is still substantial. In this study, we compared the estimation of various population genetic parameters (genetic divergence and structuring, isolation-by-distance, genetic diversity) using a limited number of biallelic markers (in total 7 loci) to those estimated with 14 microsatellite loci in 21 Atlantic salmon (Salmo salar) populations from northern Europe. Pairwise F ST values were significantly correlated between biallelic loci and microsatellite datasets, as was overall heterozygosity when both anadromous and nonanadromous populations were analyzed together. However, when the anadromous and nonanadromous samples were analyzed separately, only genetic divergence correlations remained significant. Biallelic markers alone were not sufficient for reliable neighbor-joining clustering of populations but gave highly similar isolation-by-distance signals when compared with microsatellites. Finally, although several population prioritization measures for conservation exhibited significant correlation between different marker types, the specific populations highlighted as being most valuable for conservation purposes varied depending on the marker type and conservation criteria applied. This study demonstrates that a relatively small set of biallelic markers can be sufficient for obtaining concordant results in most of the analyses compared with microsatellites, although estimates of genetic distance are generally more concordant than estimates of genetic diversity. This suggests that a relatively small number of biallelic markers can provide useful information for various population genetic applications. However, we emphasize that the use of much higher number of loci is preferable, especially when the genetic differences between populations are subtle or individual multilocus genotype-based analyses are to be performed.

Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

“…Standardized F ST was usually several times higher than unstandardized F ST for microsatellite loci (e.g., Criscione et al 2007;Jordan and Snell 2008;González-Pérez et al 2009). Standardizing of F ST became now a required procedure when different markers are compared or combined for analysis (e.g., Langergraber et al 2007;Ryynänen et al 2007). Therefore, our study as well as other published studies confirmed a necessity of using a standardized measure of genetic differentiation when measures are based on different genetic markers.…”

“…They are independent of the amount of genetic variation and therefore suitable for comparisons between studies that employ different genetic markers. Although these measures are relatively new, they were already used in a few recently published studies that, together with our study, validated their use (e.g., Criscione et al 2007;Kettle et al 2007;Langergraber et al 2007;Ryynänen et al 2007;Leinonen et al 2008). Standardized F ST was usually several times higher than unstandardized F ST for microsatellite loci (e.g., Criscione et al 2007;Jordan and Snell 2008;González-Pérez et al 2009).…”

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

“…SNP markers, adaptive variation, and balancing selection SNPs offer the advantages of abundance, a simpler and better understood mutational mechanism than microsatellites, and relatively low rates of genotyping error, and because they are more often gene-linked, they will be particularly useful for studies of adaptive variation and selection processes (Ryyanen et al 2007). The confluence of massively parallel sequencing technologies and whole-genome or transcriptome sequences has given rise to the field of population genomics, where genome-wide scans of populations are undertaken to find genes underlying adaptive differentiation (GonzalezMartinez et al 2006;Luikart et al 2003).…”

New evidence for habitat-specific selection in Wadden Sea Zostera marina populations revealed by genome scanning using SNP and microsatellite markers

“…Such sites occur in very high numbers in genomes of higher organisms. Recently, they have been regarded as the new genetic marker of choice, due to high frequencies, simple mutation mechanism and low error rates (Ryynanen et al 2007). Information concerning the utility of SNPs for population genetic and evolutionary studies in nonmodel organisms is scarce, in particular in genome scans (but see Rengmark et al 2006).…”