Comparative Performance of Single Nucleotide Polymorphism and Microsatellite Markers for Population Genetic Analysis

Abstract

Microsatellite loci are standard genetic markers for population genetic analysis, whereas single nucleotide polymorphisms (SNPs) are more recent tools that require assessment of neutrality and appropriate use in population genetics. Twelve SNP markers were used to describe the genetic structure of Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae) in the United States of America and revealed a high mean observed heterozygosity (0.40 +/- 0.059) and low global F(ST) (0.029). Pairwise F(ST) estimates ranged from 0.007 to 0.045, and all but 2 populations showed significant levels of genetic differentiation (P < or = 0.008). Population parameters and conclusions based on SNP markers were analogous to that obtained by use of microsatellite markers from the identical population samples. SNP-based F(ST) estimates were 3-fold higher than corresponding estimates from microsatellites, wherein lower microsatellite F(ST) estimates likely resulted from an overestimate of migration rates between subpopulations due to convergence of allele size (homoplasy). No significant difference was observed in the proportion of SNP or microsatellite markers loci that were nonneutral within populations. SNP markers provided estimates of population genetic parameters consistent with those from microsatellite data, and their low back mutation rates may result in reduced propensity for error in estimation of population parameters.

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

“…Limited X-linked SNPs were evaluated in this study and, because of its transmission pattern, X-linked genes are good candidates for selection during domestication and deserve further investigation. SNPs have already demonstrated the potential to equal or even outperform microsatellites for specific questions such as individual ancestry (Lao et al, 2008), population assignment (for example, Seddon et al, 2005;Narum et al, 2008;Smith and Seeb, 2008;Coates et al, 2009) and pedigree studies (Santure et al, 2010;Hauser et al, 2011), and proved to have large allele frequency differences among populations (Freamo et al, 2011). The inclusion of SNPs associated with specific known domestic cat phenotypes, particularly recessive traits such as melanism, hair types and gloving (for review see Lyons, 2010;2012,) would likely increase the power for domestic cat introgression into wildcats.…”

Empirical comparison of single nucleotide polymorphisms and microsatellites for population and demographic analyses of bowhead whales

“…Subsequent studies have indicated that fewer SNPs are needed, based on either simulated data (Morin et al 2009c) or empirical data (e.g. Ryynänen et al 2007, Narum et al 2008, Smith & Seeb 2008, Coates et al 2009). In all of these latter cases, a given number of SNPs were compared with a set of microsatellites to determine whether SNPs performed similarly to microsatellites for one or more analyses (e.g.…”

“…Berlin et al 2008, Narum et al 2008, Hefti-Gautschi et al 2009, Amend et al 2010, Keller et al 2010, Mims et al 2010, Quintela et al 2010, Freamo et al 2011, Mesnick et al 2011. For non-model organisms, there are still few empirical studies that directly compare the utility or power of SNPs relative to microsatellites for detecting population structure (Narum et al 2008, Smith & Seeb 2008, Coates et al 2009, Glover et al 2010, Hess et al 2011. Previous comparisons of SNPs and microsatellites have typically been limited to 1 or 2 types of analysis (e.g.…”

Variabilidad genética en seis SNPs de los genes CAPN1, CAST y LEP de toros brahman en ganaderías del trópico bajo colombiano

“…Aunque los SNPs son marcadores moleculares son poco polimórficos, son codominantes y presentan tasas de mutación bajas, lo que disminuye la posibilidad de cometer errores en la estimación de los parámetros poblacionales y aumenta la reproducibilidad de los resultados (Coates et al, 2009). …”