Genomic changes underlying repeated niche shifts in an adaptive radiation

In adaptive radiations, single lineages rapidly diversify by adapting to
many new niches. Little is known yet about the genomic mechanisms
involved, i.e. the source of genetic variation or genomic architecture
facilitating or constraining adaptive radiation. Here, we investigate
genomic changes associated with repeated invasion of many different
freshwater niches by threespine stickleback in the Haida Gwaii
archipelago, Canada, by re-sequencing single genomes from one marine and
28 freshwater populations. We find 89 likely targets of parallel selection
in the genome that are enriched for old standing genetic variation. In
contrast to theoretical expectations, their genomic architecture is highly
dispersed with little clustering. Candidate genes and genotype-environment
correlations match the three major environmental axes predation regime,
light environment and ecosystem size. In a niche space with these three
dimensions, we find that the more divergent a new niche from the ancestral
marine habitat, the more loci show signatures of parallel selection. Our
findings suggest that the genomic architecture of parallel adaptation in
adaptive radiation depends on the steepness of ecological gradients and
the dimensionality of the niche space.