Genetic evidence for ecological divergence in kokanee salmon

The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of non-model organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines), however outside of the spawning season the two ecotypes co-occur in many lakes and lack diagnostic morphological characteristics. We used restriction site associated DNA (RAD) sequencing to identify 6,145 SNPs and genotype kokanee from multiple spawning sites in Okanagan Lake (British Columbia, Canada). Outlier tests revealed 18 loci putatively under divergent selection between ecotypes, all of which exhibited temporally stable allele frequencies within ecotypes. Six ...