Abstract
BackgroundThe threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In particular, differential adaptation to freshwater and marine environments has led to high differentiation between freshwater and marine stickleback populations at the phenotypic trait of lateral plate morphology and the underlying candidate gene Ectodysplacin (EDA). Many studies have focused on this trait and candidate gene, although other genes involved in marine-freshwater adaptation may be equally important. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background.ResultsRAD (Restriction site Associated DNA) sequencing of sixty individuals representing two freshwater and one marine population led to the identification of 33,993 SNP markers. Ninety-six of these were chosen for the low-density SNP array, among which 70 represented SNPs under putatively directional selection in freshwater vs. marine environments, whereas 26 SNPs were assumed to be neutral. Annotation of these regions revealed several genes that are candidates for affecting stickleback phenotypic variation, some of which have been observed in previous studies whereas others are new.ConclusionsWe have developed a cost-efficient low-density SNP array that allows for rapid screening of polymorphisms in threespine stickleback. The array provides a valuable tool for analyzing adaptive divergence between freshwater and marine stickleback populations beyond the well-established candidate gene Ectodysplacin (EDA).Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-867) contains supplementary material, which is available to authorized users.
Highlights
The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution
Hess et al [34] conducted a population genomics study of Pacific lampreys using Restriction site associated DNA (RAD) sequencing, and subsequently used RAD data to construct a 96 Single nucleotide polymorphism (SNP) chip including markers that could be used for species identification, for general studies of genetic population structure and for screening loci previously suggested to be under directional selection [35]
We have constructed a low density SNP array that encompasses both neutral SNPs for background and SNPs representing genomic regions that exhibit differentiation compatible with diversifying selection in freshwater and marine environments
Summary
The threespine stickleback (Gasterosteus aculeatus) has become an important model species for studying both contemporary and parallel evolution. In order to develop a resource for rapid and cost efficient analysis of genetic divergence between freshwater and marine sticklebacks, we generated a low-density SNP (Single Nucleotide Polymorphism) array encompassing markers of chromosome regions under putative directional selection, along with neutral markers for background. Notably Northern Europe, the patterns of divergence between marine and freshwater populations of threespine sticklebacks appear less distinct than in other regions, possibly reflecting gene flow overcoming selection [18,19] This has mainly been studied with specific focus on EDA and/or lateral plate morphology. We aimed at generating a low-density SNP array encompassing markers of chromosomal regions under differential freshwater-marine selection along with neutral markers for background, providing a resource for extensive studies of parallel evolution and marine-freshwater hybrid zone dynamics
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