Discovery of Genes Under Selection in Marine Species: Impact on Estimates of Connectivity and Local Adaptation

The ability to analyze population variation at thousands of loci ushers in a new era in which it is possible to search for a small number of genes that may be under selection in a sea of genes affected most strongly by drift and dispersal. For purple sea urchins, an array-based method reveals polymorphism at over 12,000 protein coding loci. The vast majority of these loci show low differentiation along the coast, but a few classes of loci, especially those with immune-system function, or those that respond to cellular stress, show strong population level differences. These patterns are visible through outlier analysis, but a more powerful tool is the association of genetic differences with gene function indices. For reef building coral of the genus Acropora, RNASeq analysis delivers information on 37,000 SNPs from thousands of genes. Analysis of genetic patterns across a few short but steep ecological gradients shows marked change in genetic structure over 100s of meters. Such genetic shifts in corals or sea urchins might signal a high degree of local selection, or alternatively may suggest the selective filtering of these long lived animals by local environmental conditions. In neither of these cases do standard views of population structure with a few typical loci show anything but genetic homogeneity. Understanding the difference between local adaptation, where local populations produce locally adapted young that remain in the population, and generation of locus-specific patterns of differentiation every generation after long distance dispersal may require longitudinal sampling of larvae and recruits over space and time.