Sewall Young - Academia.edu (original) (raw)

Papers by Sewall Young

The Energy Citations Database (ECD) provides access to historical and current research (1948 to t... more The Energy Citations Database (ECD) provides access to historical and current research (1948 to the present) from the Department of Energy (DOE) and predecessor agencies.

We used pyrosequencing to characterize the transcriptome of four male Chinook salmon (Oncorhynchu... more We used pyrosequencing to characterize the transcriptome of four male Chinook salmon (Oncorhynchus tshawytscha) collected from four populations throughout Puget Sound (George Adams, Soos Creek, North Fork Stillaguamish, and Marblemount). Our goal was to use the transcriptome as a source of novel and informative single nucleotide polymorphisms (SNPs) that can discriminate between Puget Sound populations, known for their high value among recreational fishers and for their poor resolution using other genetic markers. Pyrosequencing yielded nearly 2.5 million of high-quality reads (combined for all four fish) with an average length of 378 bp, which were assembled de novo using 98% sequence similarity and 50% read overlap. De novo assembly generated 44,253 contiguous sequences (contigs) with an average length of 567 bp and an average depth of 29 reads. Contigs were annotated by running BLASTX against protein databases and by associating proteins to gene ontology (GO) terms using a relati...

Ecology and Evolution, 2011

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference a... more Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

Transactions of the American Fisheries Society, 2005

... The ge-netic structure of herring in BC reflects this stray-ing rate in a high connectivity a... more ... The ge-netic structure of herring in BC reflects this stray-ing rate in a high connectivity among BC herring spawning sites (Beacham et al. 2002). In many comparisons, temporal variation exceeded spatial variation (Beacham et al. 2002; McPherson et al. ...

Transactions of the American Fisheries Society, 2010

Abstract Spring Chinook salmon Oncorhynchus tshawytscha native to the upper Yakima River, Washing... more Abstract Spring Chinook salmon Oncorhynchus tshawytscha native to the upper Yakima River, Washington, were placed into an artificial stream to evaluate the effect of a single generation of hatchery culture on their spawning behavior and ability to produce offspring. From 2001 to 2005, seven independent test groups containing wild and hatchery fish were placed into the stream. The effects of body weight, spawning ground longevity, attack frequency, social dominance, courting frequency, and mate number on breeding success ...

Transactions of the American Fisheries Society, 2010

We describe the use of high-resolution melting (HRM), a recent enhancement to traditional DNA mel... more We describe the use of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analyses for the characterization of polymerase chain reaction products, in the identification of 11 novel single-nucleotide polymorphisms (SNPs) for distinguishing between rainbow trout Oncorhynchus mykiss and cutthroat trout O. clarkii. Single-nucleotide polymorphisms provide an important tool for species identification in studies of hybridization and introgression between these two species, but until now the time-consuming and costly nature of DNA sequencing has limited identification of new markers. The ability of HRM to accurately discern nucleotide changes in a DNA sequence make it a cost-and time-effective alternative to traditional sequencing for the detection of novel SNPs.

Transactions of the American Fisheries Society, 2000

Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered b... more Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered by the inability to assign population identity to individuals in an admixture. This knowledge is of particular concern in supportive breeding programs, in which misidentification of individuals to population may result in progeny of mixed heritage, which, in turn, results in the erosion of the genetic population structure and of the existing genetic diversity and local adaptations of the target population. We evaluated two classes of genetic markers, allozymes and microsatellites, for estimating population identity of pink salmon Oncorhynchus gorbuscha in a supportive breeding program on the Dungeness River in Washington State. Fall-run pink salmon of the Dungeness River are the target of restoration, but they presumably overlap, in terms of timing, with an earlier summer run. Both marker types revealed similarly low estimates of relative genetic differentiation ( ϭ 0.02), which suggests that there is little variation in allele frequency among populations. However, microsatellites provided a more accurate estimate of population identity. When applying a log-likelihood ratio criterion of greater than 1.3, 74.8% of individuals were correctly assigned to population using microsatellites (versus 3.1% of individuals using allozymes). The difference in assignment accuracy was best predicted by the statistic , which ␦ estimates cumulative allele frequency differences among populations. Our results suggest that genetic markers with many alleles are preferred when populations exhibit little genetic differentiation (as is the case in pink salmon), because is more likely to be large, presumably as a result ␦ of genetic drift at each allele. The use of microsatellites to select fall-run pink salmon for supportive breeding confirmed the run-timing overlap and prevented unintentional crosses between the two populations.

Molecular Ecology Resources, 2011

We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow... more We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow trout and steelhead (Oncorhynchus mykiss). We develop 22 novel single-nucleotide polymorphism markers based on new steelhead sequence data and on assays from sister taxa. Additionally, we adapt 154 previously developed markers to the TaqMan platform. At the beginning of this study, 59 SNPs with TaqMan assays were available to the scientific community. By adding 176 additional TaqMan assays to this number, we greatly expand the biological applications of TaqMan genotyping within both population genetics and quantitative genetics.

Conservation Genetics, 2000

For over a century, Washington State Department of Fish and Wildlife has implemented hatchery pro... more For over a century, Washington State Department of Fish and Wildlife has implemented hatchery programs as a means to boost salmon abundance. Concerns have developed that native populations may be replaced by hatchery strains, decreasing the genetic diversity required to respond to environmental changes. We report a comparison of microsatellite DNA variation in wild-spawning and hatchery-strain coho salmon from the Nooksack and Samish rivers in northern Puget Sound. Significant heterogeneity in genotype frequencies was detected between wild-spawning coho salmon from the upper North Fork (NF) Nooksack River and hatchery-strain coho salmon from the Nooksack River (descendants of primarily Nooksack River broodstock). Little difference in genotype frequencies was detected between wild-spawning coho salmon from the Samish River and hatchery-strain coho salmon from the Nooksack River. The 13locus suite provided high resolution: in assignment tests over 85% of wild-spawning coho salmon from the upper NF Nooksack River were assigned to source. Wild-spawning coho salmon collected below hatcheries in the Nooksack River and 50% of wild-spawning Samish River coho salmon were assigned to hatchery collections. The genetic divergence of wild-spawning coho salmon in the upper NF Nooksack River is remarkable given the extensive stocking history and proximity of a hatchery. We suggest that these upper river fish are native coho salmon and that wild spawners in the lower Nooksack and Samish River are descendants of hatchery productions. We attribute divergence to earlier run timing in upper NF Nooksack River wild spawners, availability of extensive spawning and rearing habitat upstream of a hatchery in the upper NF Nooksack River, and a longer stocking history in the Samish River.

Conservation Genetics, 2006

The lower Columbia River drainage once supported a run of over a million chum salmon. By the late... more The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.

Canadian Journal of Fisheries and Aquatic Sciences, 1994

We used starch-gel electrophoresis to examine over 13 000 adult chum salmon, Oncorhynchus keta, f... more We used starch-gel electrophoresis to examine over 13 000 adult chum salmon, Oncorhynchus keta, from 153 collections at 105 locations in Washington, Oregon, and southern British Columbia from 1985-92. We identified 39 variable loci and 36 monomorphic loci. In general, alleles that occurred at a frequency >lo% were found in all locations and were temporally stable within locations. Localized alleles usually occurred at a frequency 66%. Significant allele frequency differences were found among chum salmon Can. J. Fish. Aquat. Sci., VoH. SP(SuppL 4), 1994 6% Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only. Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only. Can. 9. Fish. Ayuat. Sci., Val. 54(Suppl. I), 4994 Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only. = Georgia Strait, FR = Fraser River, WCVI = west coast of Vancouver Island, WAC = Washington coast, ORC = Oregon coast. Can. B. Fish. A q w t . Sci., Vok. Sd(Suppl. d), 6994 75 Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only.

Canadian Journal of Fisheries and Aquatic Sciences, 2013

Performance of wild (W) and hatchery (H) spring Chinook salmon (Oncorhynchus tshawytscha) was eva... more Performance of wild (W) and hatchery (H) spring Chinook salmon (Oncorhynchus tshawytscha) was evaluated for a sixth generation hatchery program. Management techniques to minimize genetic divergence from the wild stock included regular use of wild broodstock and volitional releases of juveniles. Performance of HH, WW, and HW (hatchery female spawned with wild male) crosses was compared in hatchery and stream environments. The WW juveniles emigrated from the hatchery at two to three times the rate of HH fish in the fall (HW intermediate) and 35% more HH than WW adults returned (27% more HW than WW adults). Performance in the stream did not differ statistically between HH and WW fish, but outmigrants (38% WW, 30% HW, and 32% HH fish) during the first 39 days of the 16-month sampling period composed 74% of total outmigrants. Differences among hatchery-reared crosses were partially due to additive genetic effects, were consistent with domestication (increased fitness for the hatchery population in the hatchery program), and suggested that selection against fall emigration from the hatchery was a possible mechanism of domestication.

The Energy Citations Database (ECD) provides access to historical and current research (1948 to t... more The Energy Citations Database (ECD) provides access to historical and current research (1948 to the present) from the Department of Energy (DOE) and predecessor agencies.

We used pyrosequencing to characterize the transcriptome of four male Chinook salmon (Oncorhynchu... more We used pyrosequencing to characterize the transcriptome of four male Chinook salmon (Oncorhynchus tshawytscha) collected from four populations throughout Puget Sound (George Adams, Soos Creek, North Fork Stillaguamish, and Marblemount). Our goal was to use the transcriptome as a source of novel and informative single nucleotide polymorphisms (SNPs) that can discriminate between Puget Sound populations, known for their high value among recreational fishers and for their poor resolution using other genetic markers. Pyrosequencing yielded nearly 2.5 million of high-quality reads (combined for all four fish) with an average length of 378 bp, which were assembled de novo using 98% sequence similarity and 50% read overlap. De novo assembly generated 44,253 contiguous sequences (contigs) with an average length of 567 bp and an average depth of 29 reads. Contigs were annotated by running BLASTX against protein databases and by associating proteins to gene ontology (GO) terms using a relati...

Ecology and Evolution, 2011

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference a... more Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

Transactions of the American Fisheries Society, 2005

... The ge-netic structure of herring in BC reflects this stray-ing rate in a high connectivity a... more ... The ge-netic structure of herring in BC reflects this stray-ing rate in a high connectivity among BC herring spawning sites (Beacham et al. 2002). In many comparisons, temporal variation exceeded spatial variation (Beacham et al. 2002; McPherson et al. ...

Transactions of the American Fisheries Society, 2010

Abstract Spring Chinook salmon Oncorhynchus tshawytscha native to the upper Yakima River, Washing... more Abstract Spring Chinook salmon Oncorhynchus tshawytscha native to the upper Yakima River, Washington, were placed into an artificial stream to evaluate the effect of a single generation of hatchery culture on their spawning behavior and ability to produce offspring. From 2001 to 2005, seven independent test groups containing wild and hatchery fish were placed into the stream. The effects of body weight, spawning ground longevity, attack frequency, social dominance, courting frequency, and mate number on breeding success ...

Transactions of the American Fisheries Society, 2010

We describe the use of high-resolution melting (HRM), a recent enhancement to traditional DNA mel... more We describe the use of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analyses for the characterization of polymerase chain reaction products, in the identification of 11 novel single-nucleotide polymorphisms (SNPs) for distinguishing between rainbow trout Oncorhynchus mykiss and cutthroat trout O. clarkii. Single-nucleotide polymorphisms provide an important tool for species identification in studies of hybridization and introgression between these two species, but until now the time-consuming and costly nature of DNA sequencing has limited identification of new markers. The ability of HRM to accurately discern nucleotide changes in a DNA sequence make it a cost-and time-effective alternative to traditional sequencing for the detection of novel SNPs.

Transactions of the American Fisheries Society, 2000

Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered b... more Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered by the inability to assign population identity to individuals in an admixture. This knowledge is of particular concern in supportive breeding programs, in which misidentification of individuals to population may result in progeny of mixed heritage, which, in turn, results in the erosion of the genetic population structure and of the existing genetic diversity and local adaptations of the target population. We evaluated two classes of genetic markers, allozymes and microsatellites, for estimating population identity of pink salmon Oncorhynchus gorbuscha in a supportive breeding program on the Dungeness River in Washington State. Fall-run pink salmon of the Dungeness River are the target of restoration, but they presumably overlap, in terms of timing, with an earlier summer run. Both marker types revealed similarly low estimates of relative genetic differentiation ( ϭ 0.02), which suggests that there is little variation in allele frequency among populations. However, microsatellites provided a more accurate estimate of population identity. When applying a log-likelihood ratio criterion of greater than 1.3, 74.8% of individuals were correctly assigned to population using microsatellites (versus 3.1% of individuals using allozymes). The difference in assignment accuracy was best predicted by the statistic , which ␦ estimates cumulative allele frequency differences among populations. Our results suggest that genetic markers with many alleles are preferred when populations exhibit little genetic differentiation (as is the case in pink salmon), because is more likely to be large, presumably as a result ␦ of genetic drift at each allele. The use of microsatellites to select fall-run pink salmon for supportive breeding confirmed the run-timing overlap and prevented unintentional crosses between the two populations.

Molecular Ecology Resources, 2011

We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow... more We establish a TaqMan-based assay panel for genotyping single-nucleotide polymorphisms in rainbow trout and steelhead (Oncorhynchus mykiss). We develop 22 novel single-nucleotide polymorphism markers based on new steelhead sequence data and on assays from sister taxa. Additionally, we adapt 154 previously developed markers to the TaqMan platform. At the beginning of this study, 59 SNPs with TaqMan assays were available to the scientific community. By adding 176 additional TaqMan assays to this number, we greatly expand the biological applications of TaqMan genotyping within both population genetics and quantitative genetics.

Conservation Genetics, 2000

For over a century, Washington State Department of Fish and Wildlife has implemented hatchery pro... more For over a century, Washington State Department of Fish and Wildlife has implemented hatchery programs as a means to boost salmon abundance. Concerns have developed that native populations may be replaced by hatchery strains, decreasing the genetic diversity required to respond to environmental changes. We report a comparison of microsatellite DNA variation in wild-spawning and hatchery-strain coho salmon from the Nooksack and Samish rivers in northern Puget Sound. Significant heterogeneity in genotype frequencies was detected between wild-spawning coho salmon from the upper North Fork (NF) Nooksack River and hatchery-strain coho salmon from the Nooksack River (descendants of primarily Nooksack River broodstock). Little difference in genotype frequencies was detected between wild-spawning coho salmon from the Samish River and hatchery-strain coho salmon from the Nooksack River. The 13locus suite provided high resolution: in assignment tests over 85% of wild-spawning coho salmon from the upper NF Nooksack River were assigned to source. Wild-spawning coho salmon collected below hatcheries in the Nooksack River and 50% of wild-spawning Samish River coho salmon were assigned to hatchery collections. The genetic divergence of wild-spawning coho salmon in the upper NF Nooksack River is remarkable given the extensive stocking history and proximity of a hatchery. We suggest that these upper river fish are native coho salmon and that wild spawners in the lower Nooksack and Samish River are descendants of hatchery productions. We attribute divergence to earlier run timing in upper NF Nooksack River wild spawners, availability of extensive spawning and rearing habitat upstream of a hatchery in the upper NF Nooksack River, and a longer stocking history in the Samish River.

Conservation Genetics, 2006

The lower Columbia River drainage once supported a run of over a million chum salmon. By the late... more The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.

Canadian Journal of Fisheries and Aquatic Sciences, 1994

We used starch-gel electrophoresis to examine over 13 000 adult chum salmon, Oncorhynchus keta, f... more We used starch-gel electrophoresis to examine over 13 000 adult chum salmon, Oncorhynchus keta, from 153 collections at 105 locations in Washington, Oregon, and southern British Columbia from 1985-92. We identified 39 variable loci and 36 monomorphic loci. In general, alleles that occurred at a frequency >lo% were found in all locations and were temporally stable within locations. Localized alleles usually occurred at a frequency 66%. Significant allele frequency differences were found among chum salmon Can. J. Fish. Aquat. Sci., VoH. SP(SuppL 4), 1994 6% Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only. Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only. Can. 9. Fish. Ayuat. Sci., Val. 54(Suppl. I), 4994 Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only. = Georgia Strait, FR = Fraser River, WCVI = west coast of Vancouver Island, WAC = Washington coast, ORC = Oregon coast. Can. B. Fish. A q w t . Sci., Vok. Sd(Suppl. d), 6994 75 Can. J. Fish. Aquat. Sci. Downloaded from www.nrcresearchpress.com by 74.121.191.133 on 06/07/13 For personal use only.

Canadian Journal of Fisheries and Aquatic Sciences, 2013

Performance of wild (W) and hatchery (H) spring Chinook salmon (Oncorhynchus tshawytscha) was eva... more Performance of wild (W) and hatchery (H) spring Chinook salmon (Oncorhynchus tshawytscha) was evaluated for a sixth generation hatchery program. Management techniques to minimize genetic divergence from the wild stock included regular use of wild broodstock and volitional releases of juveniles. Performance of HH, WW, and HW (hatchery female spawned with wild male) crosses was compared in hatchery and stream environments. The WW juveniles emigrated from the hatchery at two to three times the rate of HH fish in the fall (HW intermediate) and 35% more HH than WW adults returned (27% more HW than WW adults). Performance in the stream did not differ statistically between HH and WW fish, but outmigrants (38% WW, 30% HW, and 32% HH fish) during the first 39 days of the 16-month sampling period composed 74% of total outmigrants. Differences among hatchery-reared crosses were partially due to additive genetic effects, were consistent with domestication (increased fitness for the hatchery population in the hatchery program), and suggested that selection against fall emigration from the hatchery was a possible mechanism of domestication.