Search

Genetic stock identification (GSI) estimates the contribution of each population to a mixture and these analyses are usually conducted regionally using genetic baselines specific to the stocks expected in that region. Often these regional baselines cannot be combined to produce broader geographical baselines. In cases where the mixture contains stocks spanning across a wide area a broad-scale baseline is created, but these baselines often are unable to resolve among regional stocks. Here, we introduce a new GSI method to harness the resolution capabilities of baselines developed for regional applications in the analyses of mixtures containing fish from a broad geographic range. This multistage process allows for disparate baselines to be used in a single integrated process that estimates the propagated errors from each stage. The baselines used by this model do not require any overlap in markers or in populations representing the broad-scale or regional baselines. The integrated multistage framework allows GSI of a wide geographic area without first developing a large scale, high resolution genetic baseline, or dividing a mixture sample into smaller regions beforehand. This approach is more cost-effective than updating range-wide baselines with all critical regionally important markers.

The five most common species of Pacific salmon, Rainbow Trout (steelhead) Oncorhynchus spp., and Atlantic Salmon Salmo salar intermingle in the North Pacific Ocean and its freshwater tributaries. Efficient morphological methods for distinguishing among these species are sometimes limited by condition of the specimen (degraded or missing morphology), life history stage, or training of the observer. Researchers have successfully applied various genetic methods to distinguish among these species when morphological analyses are not possible, but they cannot easily incorporate these methods into standard fish and wildlife population monitoring analysis workflows. Here we test five 5′–3′ exonuclease (TaqMan) assays developed from mitochondrial genes and provide novel methods that take advantage of TaqMan output to distinguish among these species. We found that combinations of as few as two of the five assays were adequate to distinguish all species. TaqMan chemistry is designed to interrogate a single nucleotide locus. We also explore the basis for the variation in the observed scatter plot distributions (variation in florescent signals) and show that this variation is due to nucleotide diversity in and near the probe site. Because the SNPs underlying the assays developed here are all physically close to one another along the mitochondrial genome, the potential exists to develop a single DNA sequence-based assay to discriminate among salmon species. This single assay can be added to a genotyping-by-sequencing panel to identify and exclude nontarget species from analyses.

Previous studies generally report that hatchery-origin Pacific Salmon (

The supplementation of natural populations of Pacific salmon Oncorhynchus spp. with hatchery fish poses unique management challenges. Two such challenges addressed in this study are limiting the number of hatchery fish spawning with natural-origin fish and maximizing the number of natural-origin fish in the supplementation broodstock. In this study, we focus on stock enhancement of Sockeye Salmon O. nerka in Hidden Lake, Alaska, where the Trail Lakes Hatchery supplements the natural population with hatchery-raised fry. Production in Hidden Lake is limited by the availability of spawning habitat and not by juvenile rearing capacity. The hatchery collects broodstock from the lake and releases fry with thermally marked otoliths at one of two primary natural spawning sites in Hidden Lake each year. During this study, an average of 58% of the fish returning to the lake through a weir on the outlet stream were of hatchery origin. However, an average of 88% of the fish at the release site were hatchery-...

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nbwere bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.

We estimate patterns of nearshore migration in the eastern Bering Sea for out-migrating Bristol Bay sockeye salmon Oncorhynchus nerka in their first year at sea. Over 3,000 juveniles were collected during the late summer of 2005–2007 as part of the Bering–Aleutian Salmon International Survey and tested with a regional genetic baseline of 45 single-nucleotide polymorphisms. Population-specific and westward migrations from natal rivers were evident. Populations from Wood River and northwestward predominated in the northern latitudes of Bristol Bay and the eastern Bering Sea and populations from the Egegik River and southwestward in the southern latitudes, while the populations spawning at the head of Bristol Bay had the highest proportions in the middle latitudes. These patterns were stable across years, apparently unaffected by marine productivity and temperature. This continuum of marine migratory patterns most likely reflects stable and population-specific adaptations to buffer the distribution ...

The strict homing of sockeye salmon Oncorhynchus nerka results in reproductively isolated populations that often spawn in close proximity and share rearing habitat. High spawning fidelity enables these populations to adapt to local conditions, resulting in a wide range of life history characteristics and genetic variation within individual watersheds. The Wood River system in southwestern Alaska provides a pristine, well-studied system in which to examine fine-scale population structure and its influences on juvenile life histories. Adult sockeye salmon spawn in lake beaches, rivers, and small tributaries throughout this watershed, and juveniles rear in five nursery lakes. We genotyped 30 spawning populations and 6,066 migrating smolts at 45 single nucleotide polymorphism loci, two of which are candidates for positive selection in the study system. We show that there is significant genetic structure (F ST = 0.032) in the Wood River lakes and that divergence is generally related to spawning rather...

Genetic markers are increasingly being used to ascertain the population of origin of individuals or mixtures of individuals in complex aggregations of Pacific salmon Oncorhynchus spp. Multilocus genotype data from single-nucleotide polymorphisms (SNPs) are especially useful for admixture analyses. Single-nucleotide polymorphisms can be discovered in nonmodel organisms with relative ease and can be characterized in the coding and regulatory regions of the genome influenced by selection. Those influenced by diversifying selection may show atypically high levels of differentiation among populations and thus be particularly valuable for genetic stock identification in cases where neutral loci show little difference among populations of interest. We identified four SNP loci from a panel of 42 as candidates for diversifying selection (referred to here as nonneutral SNPs) in sockeye salmon O. nerka from the Copper River and adjacent coastal drainages in south-central Alaska. We evaluated the information...

Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.

We report stock composition estimates for immature (ocean-age .1 and .2) sockeye salmon Oncorhynchus nerka distributed across the Bering Sea in late summer and fall. We establish a baseline data set composed of single-nucleotide polymorphism markers that can achieve very high accuracies in identifying sockeye salmon stocks from throughout their range in Asia and North America. We demonstrate the capabilities of this data set to address high-seas salmon issues by analyzing samples collected by researchers from Russia, Japan, and the United States during late summer and fall 2002–2004 as part of the Bering–Aleutian Salmon International Survey. According to our findings, (1) Gulf of Alaska (GOA) stocks formed a significant portion of the immature sockeye salmon migrating in the eastern and central Bering Sea in summer and fall, and western GOA stocks had a broader distribution in the Bering Sea than eastern GOA stocks; (2) Asian stocks migrated as far east as the western Aleutian Islands and the Don...

We examined the population genetic diversity and structure of sockeye salmon Oncorhynchus nerka spawning in tributaries of Bristol Bay, Alaska, a region that supports the largest commercial fisheries for sockeye salmon in the world. Genetic variation among the sockeye salmon populations, as revealed by microsatellite data, was shallower than that found in other areas of comparable size around the Pacific Rim. This finding was driven by similarity among populations rearing in the four largest lake systems located on the southeastern side of the bay (upper and lower Ugashik, Becharof, Naknek–Grosvenor–Coville, and Iliamna lakes). Sockeye salmon in lakes located above known obstacles to migration on the southeastern side and in tributaries on the northwestern side showed variation and structure that were more typical of the species. Management of these important fisheries assumes knowledge of the composition of stock mixtures captured in each fishery. We investigated the potential of microsatellite ...

– Allozyme and mitochondrial DNA (mtDNA) data were obtained from pink salmon throughout Prince William Sound, Alaska, from two hatchery, five upstream, and 20 tidal locations distributed among five management regions collected during 1994. Screening for allozymes included 66 loci for 92 to 100 fish per sample. Thirty-four loci had variant allele frequencies

Previous studies demonstrated reduced survivorship of pink salmon embryos from populations in Prince William Sound, Alaska, USA, that were exposed to Exxon Valdez–released oil compared with populations from matched nonoiled streams. Survivorship was also significantly decreased in embyros from lineages that were oiled in Prince William Sound and reared in clean water under controlled hatchery conditions compared with the descendants of nonoiled lineages. This suggests that the effect of oiling on pink salmon populations was persistent and could be transmitted intergenerationally. However, the ability of environmentally released oil to cause DNA sequence alterations in natural populations has yet to be demonstrated. We used polymerase chain reaction analysis to screen for alterations in the K-ras oncogene in DNA from pink salmon embryos that were exposed under controlled laboratory conditions to weathered Prudhoe Bay crude oil. Polymerase chain reaction and direct DNA sequence analyses were used to identify mutational hotspots within exons 1 and 2 of K-ras, and 3′ primer mismatch analysis was used to determine the frequency of mutations in the 40 offspring of two families of pink salmon that were experimentally exposed to oiled or clean gravel. Mutations were only observed at codons 12, 13, and 61 of K-ras, sites that are frequently mutated in animal and human tumors. All mutations resulted in deduced amino acid substitutions. As expected, in all individuals exhibiting mutations, the copy number of the normal allele exceeded that of the mutated allele. The frequencies of mutations in oiled embryos at K-ras exons 1 and 2 were 68 and 41%, respectively. K-ras mutations were not observed in siblings that were exposed to clean gravel or in the parents of the two experimental matings. These results indicate that exposure of pink salmon embryos to weathered Prudhoe Bay crude oil under controlled laboratory conditions can elicit somatic cell mutations in high frequency at mutational hotspots in genes such as K-ras. However, the frequency of these events in oiled natural populations of pink salmon and other vulnerable species in Prince William Sound and the heritability of these mutations within oiled lineages have yet to be evaluated.

Coded wire tags (CWTs) are routinely injected into the snouts of Pacific salmon Oncorhynchus spp. as fry to estimate contributions of tagged populations to spawning escapements and near-shore fisheries and to assess straying. Because not all fish are tagged, tag recoveries are extrapolated to include contributions of nontagged fish released at the same time and location. A key assumption in the extrapolations is that CWTs do not affect homing ability and therefore migratory pathways. We studied tag position within the heads of homing and straying adult pink salmon O. gorbuscha returning to Prince William Sound, Alaska, to test the hypothesis that poor tag position induces straying. Heads from straying and homing tagged adults were recovered in 1992 and 1994 and X-rayed. Tag locations were categorized into critical and noncritical areas, based on tag position relative to olfactory organs and nerves. In 1992, the 37 analyzed pink salmon that strayed were more likely to have tags in critical positio...

The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960's for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964-1982) with frequencies in contemporary samples (2008-2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations.

Sterile hybrid and triploid fish may provide hatchery programs with a tool to reduce the risk of genetic contamination of wild stocks, provided these fish have acceptable performance characteristics. We examined growth, survival, and deformities in diploid and triploid families of coho salmon (Oncorhynchus kisutch) and hybrids between coho salmon females × chinook salmon (O. tshawytscha) males. Data were collected from the half-sibling families through day 387. A reparameterized Gompertz growth model showed that conspecific coho salmon grew faster than hybrids, regardless of ploidy. No difference in growth rates was found between diploids and triploids. Abnormalities were significantly associated with the male parent but not with ploidy component, in contrast to previous observations of reduced deformity occurrence in triploid hybrids. Food conversion was better for conspecifics than hybrids during initial feeding, but not different during the second half of the experiment. No ploidy or cross × ploidy interaction effects on food conversion efficiency were observed. Finally, conspecifics had better posthatching survival than hybrids, regardless of ploidy. Of the treatments studied, conspecific triploid coho salmon may be the most viable alternative for sterile fish production: they performed as well as the conspecific diploids and better than either diploid or triploid hybrids.

We successfully spawned white bass Morone chrysops that had been habituated to captivity in indoor tanks for over 1 year and whose cycles were entrained by simulated temperature and light regimes. In summer (1990) 300 white bass (300–600 g) of an approximately even sex ratio were distributed into three 10,000-L water-recycle systems. One system was maintained under an ambient photoperiod and temperature regime, one was maintained under a regime that simulated a 9-month (compressed) annual cycle of changing photoperiod and temperature, and one was held at a temperature range at or above spawning temperature (15–25°C) and constant photoperiod (14 h light: 10 h darkness). By human chorionic gonadotropin (hCG) injections (1,100 IU/kg for female fish; 275 IU/kg for males), we induced the compressed-cycle fish to spawn in March 1991 and the ambient-cycle and constant-cycle fish to spawn in May 1991. Constant-cycle fish injected with hCG in March 1991 failed to spawn. Male white bass continuously held a...

Incorporating historical tissues into the study of ecological, conservation and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for pre-existing DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for pre-existing DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect pre-existing DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Pre-existing contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The advantages of automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.

We tested signals of historical reductions in effective population size within populations of sockeye salmon Oncorhynchus nerka returning to Bristol Bay, Alaska, to examine the roles that ecotype, migration obstacles, and drainage might play in the highly variable production of the Kvichak River drainage. We collected data for eight microsatellite loci from ∼100 fish at each of 16 locations within the Kvichak River drainage and five locations within the more productively stable Naknek River drainage. Pair-wise exact tests were used to group similar collections within ecotype, within drainage, and above and below migration obstacles. After grouping, collections represented independent populations for further analyses. We examined the number of alleles per locus, mean ratio of the number of alleles to the range in allele size, heterozygosity excess, and gametic disequilibrium as measures of reduction-in-population-size events. Number of alleles per locus revealed the largest number of significant differences. Tributary populations showed a stronger signal consistent with reduced effective population size than did beach populations within the Kvichak River drainage. Kvichak River drainage populations showed a stronger signal consistent with reduced effective population size than did the Naknek River drainage populations. Populations above migration obstacles showed signals consistent with reduction in historical population sizes in multiple measures indicating some of these reductions may be severe enough to qualify as demographic bottlenecks.

Background Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci. Results For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. Conclusions First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.