Invasion genomics: genotyping-by-sequencing approach reveals regional genetic structure and signatures of temporal selection in an introduced mud crab

Introduced species can cause large impacts on communities and ecosystems. To prevent invasions and the impacts of invasions, a better understanding of species-specific invasion routes, establishment processes, demographic histories and range expansions is needed. Such valuable biological information can be obtained using population genomics approaches that allow fast and simultaneous screening of thousands of loci and SNP markers without prior knowledge of the genome of studied species. As a result, invasion genomics has the potential to reveal previously undetected population relationships, invasion routes and evolutionary patterns. Here, we characterized the genetic diversity, structure, temporal stability and putative footprints of selection in introduced Baltic Sea populations of the mud crab Rhithropanopeus harrisii using restriction-site associated DNA (RAD) sequencing. Similar to earlier mtDNA reports, analysis of 1013 SNPs revealed strong differentiation between the native and introduced populations. At a regional scale, clear evidence of population structuring was detected between Finnish and Estonian samples indicating that R. harrisii does not form a single panmictic population in the Baltic Sea. Clustering of samples according to the age groups (juvenile and adult) instead of geographical location within the Archipelago Sea revealed the presence of significant temporal variation at small spatial scale. Finally, we identified a number of outlier loci under temporal divergent selection between cohorts suggesting that contemporary selection in newly established areas may be stronger than selection associated with spatial heterogeneity within the Baltic Sea. These results demonstrate the utility of next-generation sequencing to increase understanding of the population diversity and structuring, and highlight the importance of temporal genetic analysis when dissecting fine-scale genetic structure for introduced marine species with high reproductive potential.