Jeffrey B. Olsen

Evidence of partial anadromy and resident-form dispersal bias on a fine scalein populations of Oncorhynchus mykiss

We examine sympatric anadromous (steelhead) and nonanadromous (resident) rainbow trout (Oncorhynchus mykiss) from neighboring locations to test three hypotheses: (1) the sympatric life history types are not genetically different; (2) fine-scale dispersal is the same for both sexes, and (3) fine-scale dispersal is the same for steelhead and resident individuals. Data from 13 microsatellite loci reveal no genetic difference between sympatric steelhead and resident O. mykiss but moderate population structure (FST=0.019–0.028) between adjacent samples, regardless of life history type. Our results provide further evidence of partial anadromy and suggest that geographic proximity and genetic history, more than migratory type, should be considered when identifying populations for use in restoration of local genetic diversity. We find evidence of resident-form dispersal bias on a fine spatial scale, however, we find no evidence that fine-scale dispersal varies by gender. Conservation strategies should aim to maintain resident and anadromous forms when they occur in sympatry, as they may be important in facilitating gene flow on small and large spatial scales, respectively.

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

We agree with Shafer et al. [1] that there is a need for well-documented case studies of the application of genomics in conservation and management as well as increased communication between academics and natural resource managers. However, we challenge Shafer et al.’s [1] relatively pessimistic assertion that ‘conservation genomics is far from seeing regular application’. Here we illustrate by examples that conservation practitioners utilize more genomic research than is often apparent. In addition, we highlight the work of nonacademic laboratories [government and nongovernmental organizations (NGOs)], some of which are not always well represented in peer-reviewed literature.

The Application of Microsatellites for Stock Identification of Yukon River Chinook Salmon

Abstract In a cooperative project among three agencies, variation at 30 microsatellite loci was surveyed for 19 populations of Chinook salmon Oncorhynchus tshawytscha from the Yukon River. The observed number of alleles per locus ranged from 2 to 63. Loci with a greater number of alleles displayed lower genetic differentiation index (FST) values, but loci with lower FST values also tended to provide more-accurate estimates of stock composition. The observed number of alleles was related to the power of the locus for providing accurate estimates of stock composition of simulated single-population samples. Mean estimated stock compositions for these mixtures ranged from 38.9% for simulations of single loci with fewer than 10 alleles to 85.5% for simulated loci with more than 60 alleles. Reliable population-specific estimation of stock composition was obtained with a minimum of five loci. Comparison of microsatellite stock identification power with an existing nine-locus single-nucleotide polymorphism (SNP) ...

Genetic and Phenotypic Evidence of Reproductive Isolation between Seasonal Runs of Sockeye Salmon in Bear Lake, Alaska

Abstract The effective conservation of salmonids requires the recognition and preservation of populations that are diverse in genetic composition and life history. The management of sockeye salmon Oncorhynchus nerka in Bear Lake, Alaska, is based on the presumption that there are two, genetically isolated seasonal runs that exhibit a bimodal escapement pattern. We investigated the genetic composition and life history of the putative early and late runs in two consecutive years. Significant allele frequency differences at six microsatellite loci demonstrate restricted gene flow between the early and late runs (F ST = 0.017). There were also significant, and presumably adaptive, differences between the runs with respect to body weight, somatic weight, ovary weight, and egg size among females after correction to equal body sizes. Further, scale pattern analysis revealed highly significant differences in the growth-at-age patterns of these runs. These results demonstrate that there are significant genetic dif...

The influence of hydrographic structure and seasonal run timing on genetic diversity and isolation-by-distance in chum salmon (Oncorhynchus keta)

We used 20 microsatellite loci to compare genetic diversity and patterns of isolation-by-distance among three groups of chum salmon (Oncorhynchus keta) from two physically distinct watersheds in western Alaska, USA. The results were consistent with the hypothesis that gene flow decreases as the complexity of the hydrographic system increases. Specifically, higher gene flow was inferred among 11 populations from a nonhierarchical collection of short coastal rivers in Norton Sound compared with 29 populations from a complex hierarchical network of inland tributaries of the Yukon River. Within the Yukon River, inferred gene flow was highest among 15 summer-run populations that spawn in the lower drainage, compared with 14 fall-run populations that spawn in the upper drainage. The results suggest that the complexity of the hydrographic system may influence population connectivity and hence the level of genetic diversity of western Alaska chum salmon. Finally, evidence of isolation-by-time, when controlling fo...

The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.

DNA Barcoding of Eight North American Coregonine Species

Coregonine fishes have a circumpolar distribution in the Arctic and sub‐Arctic Northern Hemisphere. This subfamily of Salmonidae consists of three genera: Prosopium, Stenodus and Coregonus, including over 30 species. Many species overlap spatially and are difficult to distinguish based on morphological characteristics, especially as larvae or juveniles. Here we present a method for rapid and cost‐effective species identification for representatives of the three genera based on sequence variation at the mitochondrial cytochrome c oxidase subunit I gene (COI). We examined eight species common to North America with distributional overlap in Alaska. Mean pairwise sequence divergence for all eight species was 7.04% and ranged from 0.46% to 14.23%. This sequence variation was used to develop a genetic assay based on restriction fragment length polymorphism. In a blind test, this assay provided correct species assignment for 48 of 49 individuals representing all eight species. The single incorrect assignment may reflect hybridization between two closely related species. This DNA barcode‐based assay promises to aid fishery managers and researchers by providing a cost‐effective alternative to large‐scale sequence analysis for identification of North American coregonine fishes.

Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study.

Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling after an eradication event. This complication is a large concern for fish eradication efforts in lakes since killed fish can sink to the bottom and slowly decay. DNA released from these carcasses may remain detectable for long periods. Here, we evaluated the efficacy of eDNA sampling to detect invasive Northern pike (Esox lucius) following piscicide eradication efforts in southcentral Alaskan lakes. We used field observations and experiments to test the sensitivity of our Northern pike eDNA assay and to evaluate the persistence of detectable DNA emitted from Northern pike carcasses. We then used eDNA sampling and traditional sampling (i.e., gillnets) to test for presence of Northern pike in four lakes subjected to a piscicide-treatment designed to eradicate this species. We found that our assay could detect an abundant, free-roaming population of Northern pike and could also detect low-densities of Northern pike held in cages. For these caged Northern pike, probability of detection decreased with distance from the cage. We then stocked three lakes with Northern pike carcasses and collected eDNA samples 7, 35 and 70 days post-stocking. We detected DNA at 7 and 35 days, but not at 70 days. Finally, we collected eDNA samples ~ 230 days after four lakes were subjected to piscicide-treatments and detected Northern pike DNA in 3 of 179 samples, with a single detection at each of three lakes, though we did not catch any Northern pike in gillnets. Taken together, we found that eDNA can help to inform eradication efforts if used in conjunction with multiple lines of inquiry and sampling is delayed long enough to allow full degradation of DNA in the water.

Variation in the Population Structure of Yukon River Chum and Coho Salmon: Evaluating the Potential Impact of Localized Habitat Degradation

Abstract We used microsatellite and mitochondri-al DNA–restriction fragment length polymorphism (mtDNA–RFLP) analyses to test the hypothesis that chum salmon Oncorhynchus keta and coho salmon O. kisutch in the Yukon River, Alaska, exhibit population structure at differing spatial scales. If the hypothesis is true, then the risk of losing genetic diversity because of habitat degradation from a gold mine near a Yukon River tributary could differ between the two species. For each species, collections were made from two tributaries in both the Innoko and Tanana rivers, which are tributaries to the lower and middle Yukon River. The results revealed a large difference in the degree and spatial distribution of population structure between the two species. For chum salmon, the microsatellite loci (F-statistic (F ST) = 0.021) and mtDNA (F ST = −0.008) revealed a low degree of interpopulation genetic diversity on a relatively large geographic scale. This large-scale population structure should minimize, although no...

Introduction to a Special Section: Genetic Adaptation of Natural Salmonid Populations

Introduction to a Special Section: Genetic Adaptation of Natural Salmonid Populations David J. Teela; Shawn R. Narumb; Jeffrey B. Olsenc; Fred M. Utterd a Northwest Fisheries Science Center, Manchester Research Laboratory, Manchester, Washington, USA b Columbia River Inter-Tribal Fish Commission, Hagerman Fish Culture Experiment Station, Hagerman, Idaho, USA c U.S. Fish and Wildlife Service, Alaska Region, Conservation Genetics Laboratory, Anchorage, Alaska, USA d School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA