Data From: Polygenic basis and the role of genome duplication in adaptation to similar selective environments

Genetic changes underlying adaptation vary greatly in terms of complexity
and, within the same species, genetic responses to similar selective
pressures may or may not be the same. We examine both complex (supergene)
and simple (SNP) genetic variants occurring in populations of rainbow
trout (Oncorhynchus mykiss) independently isolated from ocean access and
compared them to each other and to an anadromous below-barrier population
representing their ancestral source to search for signatures of both
parallel and non-parallel adaptation. All landlocked populations displayed
an increased frequency of a large inversion on chromosome Omy05, while
three of the four populations exhibited elevated frequencies of another
inversion located on chromosome Omy20. In addition, we identified numerous
regions outside these two inversions that also show significant shifts in
allele frequencies consistent with adaptive evolution. However, there was
little concordance among above-barrier populations in these specific
genomic regions under selection. In part, the lack of concordance appears
to arise from ancestral autopolyploidy in rainbow trout that provides
duplicate genomic regions of similar functional composition for selection
to act upon. Thus, while selection acting on landlocked populations
universally favors the resident ecotype, outside of the major chromosomal
inversions, the resulting genetic changes are largely distinct among
populations. Our results indicate that selection on standing genetic
variation is likely the primary mode of rapid adaptation, and that both
supergene complexes and individual loci contribute to adaptive evolution,
further highlighting the diversity of adaptive genomic variation involved
in complex phenotypic evolution.