Lack of parallel genetic patterns underlying the repeated ecological divergence of beach and stream spawning kokanee salmon

Recent progress in methods for detecting adaptive population divergence in situ shows promise for elucidating the conditions under which selection acts to generate intraspecific diversity. Rapid ecological diversification is common in fishes, however, the role of phenotypic plasticity and adaptation to local environments is poorly understood. It is now possible to investigate genetic patterns to make inferences regarding phenotypic traits under selection and possible mechanisms underlying ecotype divergence, particularly where similar novel phenotypes have arisen in multiple independent populations. Here, we employed a bottom-up approach to test for signatures of directional selection associated with divergence of beach- and stream-spawning kokanee, the obligate freshwater form of sockeye salmon (Oncorhynchus nerka). Beach- and stream-spawners co-exist in many post-glacial lakes and exhibit distinct reproductive behaviors, life-history traits and spawning habitat preferences. Replicate ...