Abstract
The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.
Highlights
Studies that characterize the genetic structure of natural populations can provide important insights into the processes of gene flow, genetic drift and selection [1]
A number of significant deviations from Hardy–Weinberg equilibrium (HWE) were found after table-wide false discovery rate (FDR) correction, but most of the microsatellites deviated from HWE in fewer than two populations
We are only aware of a single empirical study that directly compared the strength and pattern of population structure resolved by microsatellites and restriction site-associated DNA (RAD) sequencing, and this was over an intercontinental scale [16]
Summary
Studies that characterize the genetic structure of natural populations can provide important insights into the processes of gene flow, genetic drift and selection [1]. Markers like amplified fragment length polymorphisms have sometimes been used because they do not require prior genomic information, microsatellites have long been the marker of choice as they are co-dominant, tend to have high allelic diversity and are relatively straightforward to genotype. They are time-consuming to develop and impractical to genotype in large numbers, limiting most studies to the use of around 10–20 markers. SNPs are individually less informative than microsatellites, simulations suggest that thousands of SNPs should outperform tens of microsatellites for uncovering population structure [13] This is supported by recent empirical studies showing that RAD sequencing is capable of resolving fine-scale population structure They found that the population structure of yellow fever mosquitoes (Aedes aegypti) sampled from three different continents was better resolved with 18 147 SNPs than eight microsatellites
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