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opencc-zeroFeb 2022View details →

Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

opencc-zeroMar 2022View details →

Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: genetic drift and environmental factors

Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations of Chinook salmon (Oncorhynchus tshawytscha) and assayed DNA methylation at 23 genes involved in development, immune function, stress response, and metabolism using a gene-targeted PCR-based assay for next-generation sequencing. Evidence for population differences in methylation was found at eight out of 23 gene loci after controlling for developmental timing in each individual. However, we found no correlation between freshwater environmental parameters and methylation variation among populations at those eight genes. A weak correlation was identified between pairwise DNA methylation dissimilarity among populations and pairwise FST based on 15 microsatellite loci, indicating weak effects of genetic drift or geographic distance on methylation. The weak correlation was primarily driven by two genes, GTIIBS and Nkef. However, single-gene Mantel tests comparing methylation and pairwise FST were not significant after Bonferroni correction. Thus, population differences in DNA methylation are more likely related to unmeasured oceanic environmental conditions, local adaptation, and/or genetic drift. DNA methylation is an additional mechanism that contributes to among population variation, with potential influences on organism phenotype, adaptive potential, and population resilience.

opencc-zeroSep 2022View details →

Data from: Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)

Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography and life history of native biota, while disrupting the behaviour of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (Oncorhynchus nerka), with the last records of migrants occurring in the 1930's. Since that time, O. nerka persisted as a resident population in Alouette Reservoir until experimental water releases beginning in 2005 created conditions for migration; two years later, returning migrants were observed for the first time in ~70 years, raising important basic and applied questions regarding life history variation and population structure in this system. Here, we investigated the genetic distinctiveness and population history of Alouette Reservoir O. nerka using genome-wide SNP data (n=7,709 loci) collected for resident and migrant individuals, as well as for neighbouring anadromous sockeye salmon and resident kokanee populations within the Fraser River drainage (n=312 individuals). Bayesian clustering and principal components analyses based on neutral loci revealed five distinct clusters, largely associated with geography, and clearly demonstrated that Alouette Reservoir resident and migrant individuals are genetically distinct from other O. nerka populations in the Fraser River drainage. At a finer-level, there was no clear evidence for differentiation between Alouette Reservoir residents and migrants; although we detected eight high-confidence outlier loci, they all mapped to sex chromosomes suggesting that differences were likely due to uneven sex ratios rather than life history. Taken together, these data suggest that contemporary Alouette Reservoir O. nerka represents a landlocked sockeye salmon population, constituting the first reported instance of deep-water spawning behaviour associated with this life history form. This finding punctuates the need for re-assessment of conservation status and supports on-going fisheries management activities in Alouette Reservoir.

opencc-zeroDec 2015View details →

Data from: Broodstock history strongly influences natural spawning success in hatchery steelhead (Oncorhynchus mykiss)

We used genetic parentage analysis of 6200 potential parents and 5497 juvenile offspring to evaluate the relative reproductive success of hatchery and natural steelhead (Onchorhynchus mykiss) when spawning in the wild between 2008 and 2011 in the Wenatchee River, Washington. Hatchery fish originating from two prior generation hatchery parents had <20% of the reproductive success of natural origin spawners. In contrast, hatchery females originating from a cross between two natural origin parents of the prior generation had equivalent or better reproductive success than natural origin females. Males originating from such a cross had reproductive success of 26–93% that of natural males. The reproductive success of hatchery females and males from crosses consisting of one natural origin fish and one hatchery origin fish was 24–54% that of natural fish. The strong influence of hatchery broodstock origin on reproductive success confirms similar results from a previous study of a different population of the same species and suggests a genetic basis for the low reproductive success of hatchery steelhead, although environmental factors cannot be entirely ruled out. In addition to broodstock origin, fish size, return time, age, and spawning location were significant predictors of reproductive success. Our results indicate that incorporating natural fish into hatchery broodstock is clearly beneficial for improving subsequent natural spawning success, even in a population that has a decades-long history of hatchery releases, as is the case in the Wenatchee River.

opencc-zeroDec 2020View details →

Data from: Genome-wide investigation of the multiple origins hypothesis for deep-spawning kokanee salmon (Oncorhynchus nerka) across its pan-Pacific distribution

Salmonids have emerged as important study systems for investigating molecular processes underlying parallel evolution given their tremendous life history variation. Kokanee, the resident form of anadromous sockeye salmon (Oncorhynchus nerka), have evolved multiple times across the species' pan-Pacific distribution, exhibiting multiple reproductive ecotypes including those that spawn in streams, on lake-shores, and at lake depths >50 meters. The latter has only been detected in five locations in Japan and British Columbia, Canada. Here, we investigated the multiple origins hypothesis for deep-spawning kokanee, using 9,721 SNPs distributed across the genome analyzed for the vast majority of known populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East Barrière Lakes) relative to stream-spawning populations in both regions. We detected 397 outlier loci, none of which were robustly identified in paired-ecotype comparisons in Japan and Canada independently. Bayesian clustering and principal components analyses based on neutral loci revealed six distinct clusters, largely associated with geography or translocation history, rather than ecotype. Moreover, a high level of divergence between Canadian and Japanese populations, and between deep- and stream-spawning populations regionally, suggest the deep-spawning ecotype independently evolved on the two continents. On a finer level, Japanese kokanee populations exhibited low estimates of heterozygosity, significant levels of inbreeding, and reduced effective population sizes relative to Canadian populations, likely associated with transplantation history. Along with preliminary evidence for hybridization between deep-spawning and stream-spawning ecotypes in Saiko Lake, these findings should be considered within the context of on-going kokanee fisheries management in Japan.

FIGURE 7 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 7. Phylogenetic network of individuals examined in this study produced by the neighbor net algorithm. Tips are labeled by individual codes described in Table 1. Each subspecies of Rainbow Trout (Oncorhynchus mykiss) is indicated. McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento River Redband Trout (O. m. stonei) are show in bold. The outgroup species, Lahontan Cutthroat Trout (O. clarkii henshawi) is indicated.

FIGURE 3 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 3. Admixture plots from the population genetics data set. Number of genetic clusters (K) presented for K = 2–6 from all samples (n = 318) analyzed in a population genetics framework. Admixture analysis was conducted in NGSAdmix with an optimal K = 3. Labeling of x-axis is according to Group as in Table 1: CAGT, California Golden Trout; KRRT, Kern River Rainbow Trout; LKGT, Little Kern Golden Trout; CRT, Coastal Rainbow Trout; EGLK, Eagle Lake Rainbow Trout; HRNB, Hatchery Rainbow Trout; MRRB, McCloud River Redband Trout; REDB, all other Redband Trout.

FIGURE 6 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 6. Species tree produced by SVDQuartets. The species tree branch lengths are equal and bootstrap support was maximal for all nodes and not shown. Each subspecies of Rainbow Trout (Oncorhynchus mykiss) is indicated with McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) in bold text. For Rainbow Trout subspecies, sampling locations are labeled with a four-letter code corresponding to Figure 1 and Table 1. The two samples of Lahontan Cutthroat Trout (O. clarkii henshawi) are labeled as LCT.

FIGURE 2 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 2. Principal Component Analyses. The first two Principal Components (PCs) are presented for all samples (n = 318) in the population genetics analysis in A and Redband Trout samples (n = 204) in B. Genotype likelihoods were generated separately for the PCs presented in each panel. In A points are color coded by Group corresponding broadly to lineage, and further condensed into a Major Group by consolidating the California Golden Trout Complex and represented by shape (Table 1). In B, points are colored by watershed and the same shape applied to the Major Group (MRRB and REDB). Abbreviations for Major Group are explained in the text.

FIGURE 1 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 1. Map of key features and distributions of key lineages in this study. The distribution of Coastal Rainbow Trout (Oncorhynchus mykiss irideus) is shown in grey shading. Other lineages are labeled in different colors. Distributions were retrieved from the PISCES database (pisces.ucdavis.edu, "Historic Range—Expert Opinion") except for Warner Lakes Redband Trout (O. m. ssp.), which is represented by a polygon of hydrologic unit code (HUC) 17120007. Sampling locations used in phylogenetic analyses are indicated with a four-letter code that corresponds to Table 1 and Supplemental Table S1. Samples of O. m. gairdnerii from Idaho are not shown.

FIGURE 5 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 5. Maximum Likelihood (ML) tree (A) and ML consensus tree (B). In both panels subspecies of Rainbow Trout (Oncorhynchus mykiss) are indicated along with members of the Golden Trout Complex. McCloud River Redband Trout (O. m. calisulat, ssp. nov.) and Sacramento Redband Trout (O. m. stonei) are indicated with bold text. Individual sample names are provided at tips and further described in Table 1. In 5A, nodes receiving Shimodaira-Hasegawa approximate Likelihood Ratio Test scores> 80 and bootstrap support (BS)> 95% are indicated with a diamond. In 5B, two spans of bootstrap support are presented, with 100%> BS> 95% as solid black circles and 95%> BS> 90% as grey circles at nodes.

FIGURE 8 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 8. McCloud River Redband Trout, Onchorhynchus mykiss calisulat, ssp. nov., Sheepheaven Creek. A. WFB 5020, holotype, 120 mm SL. B. same specimen as in A, radiograph. C. TCWC 28772.01, paratype, 144 mm SL. D. Illustration of O. m. calisulat, ssp. nov., showing life colors, © J. Tomelleri, used with permission.

FIGURE 4 in Molecular Systematics of Redband Trout from Genome-Wide DNA Sequencing Substantiates the Description of a New Taxon (Salmonidae: Oncorhynchus mykiss calisulat) from the McCloud River

FIGURE 4. Admixture plots from McCloud river trout and other Redband Trout in population genetics dataset. Admixture results from NGSAdmix for genetic clusters (K) from 2-4 with the subset of samples collected as Redband Trout. Sample size of 204, optimal K = 2. The x-axis labels are labeled according to watershed.

opencc-zeroApr 2023View details →

Data for: Effects of domestication and captive breeding on reaction to moving objects: Implications for avoidance behaviors of obstacles and predators by masu salmon Oncorhynchus masou

Domestication and captive breeding can compromise obstacle- and predator-avoidance of animals in the wild. Whereas previous studies only examined these effects in combination, here we examine them individually by comparing the abilities of wild, F1 (offspring of wild parents), and captive-bred (approx. F15) masu salmon (Oncorhynchus masou) to avoid a falling object under experimental conditions. Rates of avoidance failure were low (wild, 12.5%; F1, 10.7%; captive-bred, 8%) under light conditions but increased under dark conditions (wild, 11.1%; F1, 32.1%; captive-bred, 60.0%). We attribute the elevated avoidance-failure rate among F1 fish to the lack of learning opportunities in hatchery environments, and the further elevation of avoidance-failure rate among captive-bred fish to the degradation of sensory organ function. These results imply reduced survival rates for F1 and captive-bred fish in the wild and are consistent with the low stocking efficiencies reported for captive-bred masu salmon.

opennotspecifiedJul 2021View details →

FIG. 3 in Few Impacts of Introduced Cutthroat Trout (Oncorhynchus clarki) on Aquatic Stages of Boreal Toads (Anaxyrus boreas boreas)

FIG. 3. Estimated relationships between Cutthroat Trout habitat use and water depth (a), vegetation density (b), and temperature (c) by using the most parsimonious occupancy model, Ψ(size + depth + veg + temp), p(.), during the embryo stage of Boreal Toad development. Relationships with each covariate is plotted using the average values of other covariates. The dashed line designates the relationship for small Cutthroat Trout, and the solid line represents the relationships for large Cutthroat Trout. Shaded areas represent 95% confidence intervals. In (a) and (b), the circles indicate the vegetation density and predicted use at the three egg mass locations. In (c), the squares indicate the average morning temperatures and predicted use at the three egg mass locations. The triangles represent the same for the average evening temperatures.

opennotspecifiedJul 2021View details →

FIG. 1 in Few Impacts of Introduced Cutthroat Trout (Oncorhynchus clarki) on Aquatic Stages of Boreal Toads (Anaxyrus boreas boreas)

FIG. 1. Map of Rocky Mountain National Park and its major water bodies. The two study sites, Spruce Lake and Fay Lakes, are denoted by black triangles.

opennotspecifiedJul 2021View details →

FIG. 2 in Few Impacts of Introduced Cutthroat Trout (Oncorhynchus clarki) on Aquatic Stages of Boreal Toads (Anaxyrus boreas boreas)

FIG. 2. Photograph of two caged Boreal Toad egg mass halves at Spruce Lake. The paired exposed egg mass halves are not visible, but located directly adjacent to each cage.

publicApr 2021View details →

Data for: Sex-specific differences in swimming, aerobic metabolism, and recovery from exercise in adult coho salmon (Oncorhynchus kisutch) across ecologically relevant temperatures

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publicOct 2015View details →

Data from: Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

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