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.

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Identifying and understanding temporal genetic changes within fish populations is important for the management of these populations, especially those of conservation concern. Such changes are often the result of genetic drift, which can be exacerbated when the size of a population decreases. Using molecular‐genetics techniques, we monitored nine populations of Chinook salmon Oncorhynchus tshawytscha in the Salmon River, Idaho, to determine how the genetic characteristics within and among these populations have changed over time. We found no evidence of change in the level of heterozygosity or allelic richness over three to four generations in eight of the populations. This is probably due to the fact that the populations all maintained a sufficiently large effective size, even though a few of the populations did show a decline in effective size. Also, the genetic structure among the populations did not change appreciably over time. Populations that had been supplemented with hatchery‐reared fish showed genetic similarity to the within‐basin hatchery source population, presumably because of the extensive use of native fish for hatchery brood stocks and minimal out‐of‐basin stock transfers. The lack of a detectable decline in these populations’ levels of genetic diversity is encouraging, given the species’ threatened status under the U.S. Endangered Species Act.Received September 22, 2010; accepted December 8, 2010

Conservation efforts aimed at Pacific salmon (Oncorhynchus spp.) populations have frequently utilized artificial propagation in an attempt to increase fish abundance. However, this approach carries the risk of unwanted changes in the genetic characteristics of the target population and perhaps others that might incidentally be affected. We used genetic monitoring techniques to estimate the amount of introgression that has occurred from nonnative hatchery stocks into native populations and to determine the extent of genetic changes that have occurred in association with supplementation efforts over the past 20–50 years in Snake River Chinook Salmon O. tshawytscha populations from northeastern Oregon. A total of 4,178 fish from 13 populations were genotyped for 12 microsatellite DNA loci. Expected heterozygosity values for each sample ranged from 0.707 to 0.868. Estimates of the effective number of breeders per year in the naturally spawning populations ranged from 20.6 to 459.1, whereas in the hatchery populations they ranged from 33.8 to 1,118.8. We found that introgression from the Rapid River Hatchery stock was particularly noticeable in the early 1990s but that it appears to have had a substantial effect on only two of the native populations (Lookingglass Creek and the upper Grande Ronde River) despite the ample opportunities for introgression to occur. All seven of the native populations sampled have maintained their levels of within‐population genetic diversity throughout the sampling period. Overall, this region's supplementation efforts appear to have had a minimal effect on the genetic diversity of its Chinook Salmon populations.Received October 9, 2012; accepted March 25, 2013

The need to rebuild Pacific ocean perch, Sebastes alutus, populations on the west coast of the United States has precipitated a need to better understand the life history characteristics of this rockfish species. One such characteristic is mating behavior, which has the potential to influence the amount of genetic diversity in a population. We documented and examined the frequency of multiple mating in Pacific ocean perch collected off the Oregon coast using five microsatellite loci. We found that 47 of 66 (71.2%) females examined had broods sired by multiple males.The mean number of sires per brood was 1.92 (SD= 0.76) and ranged from 1-4. Polyandrous females were significantly larger and had an older average age than monogamous females. Our results suggest that polyandrous behavior among female Pacific ocean perch off the coast of Oregon is prevalent, is related to female size and age, and should be preserved by maintaining a natural age structure in this population.

Captive propagation is widely used for the conservation of imperiled populations. There have been concerns about the genetic effects of such propagation, but few studies have measured this directly at a genomic level. Here, we use moderate-coverage (10X) genome sequences from 80 individuals to evaluate the genomic distribution of variation of several paired groups of Chinook salmon (Oncorhynchus tshawytscha). These include 1) captive and natural-origin sh separated by at least one generation, 2) sh within the same generation having high tness in captivity compared to those with high tness in the wild, and 3) sh listed as different Evolutionarily Signi cant Units (ESUs) under the US Endangered Species Act. The distribution of variation between high tness captive and high tness natural sh was nearly identical to that expected from random sampling, indicated that differential selection in the two environments did not create large allele frequency differences within a single generation. In contrast, the samples from distinct ESUs were clearly more divergent than expected by chance, including a peak of divergence near the GREB1L gene on chromosome 28, a gene previously associated with variation in time of return to fresh water. Comparison of hatchery and natural-origin sh within a population fell between these extremes, but the maximum value of F ST was similar to the maximum between ESUs, including a peak of divergence on chromosome 8 near the slc7a2 and pdgfrl genes. These results suggest that efforts at limiting genetic divergence between captive and natural sh in these populations have successfully kept the average divergence low across the genome, but at a small portion of their genomes, hatchery and natural salmon were as distinct as individuals from different ESUs.