Next-generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. The use of these two approaches in parallel is especially attractive in nonmodel organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a nonmodel fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and nonmigratory ecotypes and to further our understanding about the genetic basis of migration. Restriction site-associated DNA (RAD) tag sequencing was used to identify single-nucleotide polymorphisms (SNPs) in migrant and resident O. mykiss from two systems, one in Alaska and the other in Oregon. A total of 7920 and 6755 SNPs met filtering criteria in the Alaska and Oregon data sets, respectively. Population genetic tests determined that 1423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Previous linkage mapping studies that used RAD DNA tag SNPs were available to determine the position of 1990 markers. Several significant SNPs are located in genome regions that contain quantitative trait loci for migratory-related traits, reinforcing the importance of these regions in the genetic basis of migration/residency. Annotation of genome regions linked to significant SNPs revealed genes involved in processes known to be important in migration (such as osmoregulatory function). This study adds to our growing knowledge on adaptive divergence between migratory and nonmigratory ecotypes of this species; across studies, this complex trait appears to be controlled by many loci of small effect, with some in common, but many loci not shared between populations studied.

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Hatchery supplementation programs are designed to enhance natural production and maintain the fitness of the target population; however, it can be difficult to evaluate the success of these programs. Key to the success of such programs is a relatively high reproductive success of hatchery fish. This study investigated the relative reproductive success (RRS) of steelhead Oncorhynchus mykiss (anadromous rainbow trout) by creating pedigrees for hatchery and natural spawning steelhead. We genotyped adult steelhead that returned to a weir and were released upstream to spawn in Little Sheep Creek, a tributary to the Imnaha River in eastern Oregon. The broodstock for this supplementation program were originally chosen from natural‐origin steelhead returning to the weir and in subsequent years consisted of both natural‐ and hatchery‐origin individuals. Microsatellite analyses showed the broodstock to be genetically similar to the natural population across years. We also genotyped adult resident rainbow trout from multiple locations upstream of the weir and determined the parentage of progeny collected at various life history stages, including returning adults in subsequent years. Analysis of progeny sampled at both the juvenile and adult life stages suggested that the RRS of hatchery‐origin fish was 30–60% that of their natural‐origin counterparts. Using generalized linear models to address the importance of various factors associated with reduced reproductive success, we found that the greatest effects on RRS were origin (natural versus hatchery), length, return date, and the number of same‐sex competitors. Natural parents were less negatively affected by same‐sex competitors. Differential survival of juveniles and the behavior of offspring and/or spawning adults may all contribute to diminished fitness in hatchery‐reared salmon, although it could not be determined to what extent these effects were of a persistent, heritable nature as distinct from an environmental effect associated with hatchery rearing and release strategies.