In the past decade, much of the research in the field of evolutionary genetics has been
focused on identifying connections between genotype and phenotype. The next frontier
in evolutionary biology is to connect specific genotypes and phenotypes to the survival
of organisms in the wild. An ideal experimental approach would track survival (or
fitness), all possible phenotypes and genotypes on a genome-wide scale, but this has
not yet been done in any system. Threespine stickleback (Gasterosteus aculeatus) fish
provide a remarkable opportunity to connect genotype, phenotype, and fitness. Here,
we propose an ambitious and novel study using the lake-stream stickleback pairs,
which have evolved repeatedly and independently in different watersheds, providing a
striking example of parallel evolution. We will examine natural selection in action in an
archetypal lake-stream pair, the Misty Lake system by following phenotypes and
genotypes in fish that have survived in a stream environment using a large collection of
marked (starting) and recaptured (surviving) fish. Next, we will measure phenotypes on
all of the starting and surviving fish, and also genotype these fish at markers
distributed across the genome using RAD-tag genotyping. With these genotype data,
we will: (1) identify the genetic loci that show changes in allele frequency between
starting and surviving fish; and (2) determine whether the loci that appear to be targets
of selection are also associated with phenotypic differences between the starting and
surviving populations. Our data will further allow us to address a major question in
evolutionary biology: does ecological divergence result from multifarious selection
across a number of traits or from strong selection on one or a few traits? Identifying
the distribution of loci that are under selection across the genome and associating
these loci with the phenotypes under selection will provide important and novel
insights into this question, and into the connections between genotype, phenotype and
fitness.