Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. Dataset.... more
Suggested citation: "Banks, Michael A. (2013): Molecular genetic characterization of Chinook salmon (Oncorhynchus tschawytscha) runs for California’s Central Valley. Oregon State University Libraries. Dataset. doi:10.7267/N9KW5CXX"
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Suggested citation: "Blouin, Michael S.; Banks, Michael A.; Moyer, Gregory R.; Theriault, Veronique; Whitcomb, Amelia; Loomis, David; Jackson, Laura S. (2013): Umpqua Coho Salmon Genetic Pedigree. Oregon State University Libraries.... more
Suggested citation: "Blouin, Michael S.; Banks, Michael A.; Moyer, Gregory R.; Theriault, Veronique; Whitcomb, Amelia; Loomis, David; Jackson, Laura S. (2013): Umpqua Coho Salmon Genetic Pedigree. Oregon State University Libraries. Dataset. doi:10.7267/N9H41PB9."
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Article history: Accepted 30 May 2011 Available online 25 June 2011 Received by A.J. van Wijnen
Pelagic dispersal of most benthic marine organisms is a fundamental driver of population distribution and persistence and is thought to lead to highly mixed populations. However, the mechanisms driving dispersal pathways of larvae along... more
Pelagic dispersal of most benthic marine organisms is a fundamental driver of population distribution and persistence and is thought to lead to highly mixed populations. However, the mechanisms driving dispersal pathways of larvae along open coastlines are largely unknown. To examine the degree to which early stages can remain spatially coherent during dispersal, we measured genetic relatedness within a large pulse of newly recruited splitnose rockfish (Sebastes diploproa), a live-bearing fish whose offspring settle along the US Pacific Northwest coast after spending up to a year in the pelagic environment. A total of 11.6% of the recruits in a single recruitment pulse were siblings, providing the first evidence for persistent aggregation throughout a long dispersal period. Such protracted aggregation has profound implications for our understanding of larval dispersal, population connectivity, and gene flow within demersal marine populations.
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Mitochondrial DNA sequence variation was characterized for the large subunit rRNA-coding gene (16SrDNA) in two closely related Pacific oyster species (Crassostrea gigas and C. sikamea) and an out group, the Olympia oyster (Ostrea lurida).... more
Mitochondrial DNA sequence variation was characterized for the large subunit rRNA-coding gene (16SrDNA) in two closely related Pacific oyster species (Crassostrea gigas and C. sikamea) and an out group, the Olympia oyster (Ostrea lurida). Although each species was shown to have a single, fixed haplotype for the DNA sequence under study, 7 nucleotide differences were found between C. gigas and C. sikamea, and these two species differed from the O. lurida haplotype at 62 and 60 nucleotide sites, respectively. Nucleotide differences for the two Crassostrea species showed a notable transition bias (85.7%) in contrast to the marginal transversion bias (54.5%) in nucleotide differences between Crassostrea haplotypes and the more distantly related O. lurida. Conservation of primary sequence in all three oyster species as well as other published 16SrDNA sequences was noted for regions with apparent functional significance. We developed DNA sequence-specific discrimination techniques and employed sequence-specific PCR primers, dot-blot hybridization, and restriction digests as alternate techniques for rapid diagnosis of Crassostrea oyster larvae.
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Spring Chinook salmon in the upper Willamette River, Oregon are listed as threatened under the endangered species act. In this system spring Chinook are being reintroduced above several high-head dams in an effort to contribute to their... more
Spring Chinook salmon in the upper Willamette River, Oregon are listed as threatened under the endangered species act. In this system spring Chinook are being reintroduced above several high-head dams in an effort to contribute to their recovery. In the South Fork McKenzie River, a Willamette River tributary, we have genetically monitored the spring Chinook reintroduction since 2007 using molecular parentage methods. Genetic pedigrees have been constructed with adults (n=3738) and outmigrating fry sampled above the dam (n= 8644) from 2008-2011. We found the average proportion offspring missing at least one parent each year was 22%; despite sampling 99.8% of all anadromous adults reintroduced; our use of 11 highly polymorphic microsatellites (average number of alleles = 33.8) when determining parent-offspring relationships; and low genotyping error (2%). Interestingly, the average proportion of offspring missing mothers (13.2%) was nearly double that of those missing fathers (7%), wh...
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Construction of large dams in the upper Willamette River Basin of Oregon in the 1950s and 1960s blocked passage to adult spring Chinook and resulted in the loss of almost half of the most highly productive spawning and rearing habitat in... more
Construction of large dams in the upper Willamette River Basin of Oregon in the 1950s and 1960s blocked passage to adult spring Chinook and resulted in the loss of almost half of the most highly productive spawning and rearing habitat in the basin. In the McKenzie River basin, construction of Cougar Dam on the South Fork McKenzie River in 1963 blocked access to 40 km of the high quality habitat. Efforts to reintroduce spring Chinook into areas upstream of dams increased after adoption of the Willamette Biological Opinion in 2008. Initial reintroductions in the South Fork McKenzie began with hatchery Chinook, but a fish trap at Cougar Dam competed in 2010 now allows naturally produced Chinook to be passed upstream. A genetic pedigree study was initiated to evaluate the reproductive success and total lifetime fitness of reintroduced Chinook, to determine the parentage of natural origin returns to the Cougar Dam fish trap, and to evaluate the relative success of alternative reintroduct...
Dams have contributed to the decline of migratory fishes by blocking access to historical habitat. The active transport (trap and haul) of migratory fish species above existing dams can sometimes support population recovery when the use... more
Dams have contributed to the decline of migratory fishes by blocking access to historical habitat. The active transport (trap and haul) of migratory fish species above existing dams can sometimes support population recovery when the use of fish ladders or dam removal is infeasible. However, little is known about the efficacy of trap and haul conservation strategies. Here we used genetic parentage assignments to evaluate the efficacy of reintroducing adult Chinook salmon (Oncorhynchus tshawytscha) above Cougar Dam on the South Fork McKenzie River, Oregon, USA, from 2008 to 2011. We found that mean reproductive success (RS) declined as adults were released later in the spawning season in 2009 and 2010; however, release location did not affect RS. In 2010 and 2011, we tested for RS differences between hatchery and natural origin (HOR and NOR, respectively) adults. HOR males were consistently less fit than NOR males, but little evidence for fitness differences was apparent between HOR a...
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It has been shown that hatchery fish have lower reproductive success (RS) than wild fish when breeding in the wild and that there is a carry-over effect from hatchery bred fish to subsequent generations of wild populations. One causal... more
It has been shown that hatchery fish have lower reproductive success (RS) than wild fish when breeding in the wild and that there is a carry-over effect from hatchery bred fish to subsequent generations of wild populations. One causal mechanism that has been suggested to result in reproductive differences between wild and hatchery fish and also among individuals of each type is mate choice. A pedigree study conducted on coho salmon from the Umpqua River, Oregon, offers a valuable opportunity to evaluate this mechanism. Mate choice can be examined in fish populations by assessing allelic variation in the Major Histocompatibility Complex (MHC) and other immune-relevant gene-linked markers. Because immune-relevant genes play a significant role in combating pathogens, they are under strong selective pressure. As a result, identifying patterns of genetic variation among mate pairs in these gene-linked markers can be used as an approach to assess mate choice. By examining pedigree data of...
Contemporary demands on fishery managers and the seafood industry require innovative approaches for supplying resource and product information. Project CROOS (Collaborative Research on Oregon Ocean Salmon) is an industry-science... more
Contemporary demands on fishery managers and the seafood industry require innovative approaches for supplying resource and product information. Project CROOS (Collaborative Research on Oregon Ocean Salmon) is an industry-science partnership designed to address the recent closures of the West Coast salmon fishery while sharing information in near real time. The project produces genetic, oceanographic, and fishery information to reduce harvests of weak salmon stocks while improving economic performance of the industry. A fundamental feature of the project is the use of barcodes to track harvested fish and related information. A website -- PacificFishTrax.com -- maps, analyzes, tracks, and communicates information for scientists, resource managers, fishermen, processors, retailers, consumers, and the public. This presentation summarizes the results of a pilot test using the PacificFishTrax concept to market local seafood. Computer-based kiosks were designed that allowed customers to sc...
Contemporary demands on public resource managers and the private seafood industry require new approaches for supplying resource and product information consistent with a future in which the stock and flow of information is effectively... more
Contemporary demands on public resource managers and the private seafood industry require new approaches for supplying resource and product information consistent with a future in which the stock and flow of information is effectively shared among scientist, producer, and marketer. This will support sustainability, improve profitability and efficiency, and also build a community of common interest ranging from resource manager to seafood consumer. ProjectCROOS (Collaborative Research on Oregon Ocean Salmon) is an industry and science partnership designed to address the recent closures of the West Coast salmon fishery. The project uses near real-time genetic, oceanographic, and fishery information to reduce harvests of weak salmon stocks, avoid major closures, and improve economic performance of the industry. A fundamental feature is the use of barcodes to track harvested fish and related near real-time information. A website -- PacificFishTrax.com -- maps, analyzes, tracks, and comm...
Many fish species have been negatively affected by the construction of high head dams because they alter temperature and flow regimes, as well as, impede fish migration. In recent years, managers have begun to reintroduce salmonids above... more
Many fish species have been negatively affected by the construction of high head dams because they alter temperature and flow regimes, as well as, impede fish migration. In recent years, managers have begun to reintroduce salmonids above dams in an effort to mitigate these effects. This strategy has been adopted on the South Fork McKenzie River, Oregon. We investigated what factors explained reproductive success (RS) of adult spring Chinook salmon reintroduced from 2008-2011 using genetic parentage methods. We estimated RS by counting the number of outmigrating fry that assigned to an adult reintroduced in the previous year. Our analysis identified a small negative relationship (p<0.001) between Reintroduction Date and RS for males; however, Release Location was not associated with RS. We also investigated hatchery origin (HOR) and natural origin (NOR) RS differences in 2010-2011, and found that the interaction between Sex and Origin was significant (p<0.001). An interaction p...
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Publisher Summary Fisheries, water diversions, and other environmental shifts have the potential to result in significant loss of specific fish stocks, necessitating careful management wherever possible. Impacts often affect complex... more
Publisher Summary Fisheries, water diversions, and other environmental shifts have the potential to result in significant loss of specific fish stocks, necessitating careful management wherever possible. Impacts often affect complex mixtures of different stocks, however, making effective management critically dependent on precise methods for stock identification. This is particularly important in contexts involving threatened and endangered species because conservation measures require focused targeting in order to achieve and monitor rebuilding goals. As a result, the application of genetic and statistical methods toward stock identification has continued to develop and improve in the past few decades, largely in response to a number of new challenges. These fall into three primary areas: continued interest in sustaining harvest and economic yield despite extreme variability and changes in habitat availability, ocean productivity, stock strengths, and effectiveness of fishing technologies; increasing interaction between farmed and hatchery-reared fish with their counterparts from wild populations;the increasing number of endangered or threatened species cases needing special attention for protection and rebuilding. Cases are selected to span major regions around the Northern Pacific Rim but also for their unique contributions to the field of genetic stock identification (GSI).
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ABSTRACT Expected daily FL ranges (length at date) of juvenile Chinook Salmon Oncorhynchus tshawytscha have been used throughout California&#39;s Central Valley to identify federally listed winter-run and spring-run juveniles in a... more
ABSTRACT Expected daily FL ranges (length at date) of juvenile Chinook Salmon Oncorhynchus tshawytscha have been used throughout California&#39;s Central Valley to identify federally listed winter-run and spring-run juveniles in a mixed four-race stock. Accurate race identification is critical both to species recovery and to management of the water supply for 25 million people and a multibillion-dollar agricultural industry. We used genetic race assignment of 11,609 juveniles sampled over 6 years to characterize the accuracy of the length-at-date approach, specifically by testing two of its central assumptions: (1) juvenile FL distributions do not overlap between races on a daily basis; and (2) the growth rates that are used to project FL at date are accurate. We found that 49% of FLs for genetically identified juveniles occurred outside the expected length-at-date ranges for their respective races, and we observed a high degree of overlap in FL ranges among the four races. In addition, empirical growth rates were well below those from which length-at-date criteria were derived. Given the high degree of FL overlap between races, we conclude that modification of the length-at-date method will not substantially reduce identification error. Thus, we recommend that genetic assignment be used at least as a supplemental approach to improve Central Valley Chinook Salmon race identification, research, and management.Received January 7, 2014; accepted July 22, 2014
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ABSTRACT Highly magnetic receptor cells of trout that contain biogenic crystals of magnetite are hypothesized to transduce geomagnetic information into neural signals utilized by fish as orientation cues during migration. However, because... more
ABSTRACT Highly magnetic receptor cells of trout that contain biogenic crystals of magnetite are hypothesized to transduce geomagnetic information into neural signals utilized by fish as orientation cues during migration. However, because these cells are extremely difficult to find and study, whether these cells are capable of magnetic signal transduction is not yet confirmed. Moreover, virtually nothing is known about the genetic underpinnings of magnetite crystal formation in eukaryotes. Here, from Chinook salmon olfactory epithelium tissue, magnetic and non-magnetic cell mRNA transcripts were isolated and sequenced using RNA-Seq. Approximately 500 genes were differentially expressed in the magnetic-cell sample, with annotation of the full olfactory rosette transcriptome in-progress. The genes most plausibly involved in magnetic sensory transduction are being developed into fluorescent probes and tested for hybridization to target cells. If successful, a probe can then be used for rapid and efficient cell location to conduct in situ tests of response to magnetic field treatments. Findings have relevance to resolving if salmon and other marine organisms imprint on magnetic fields and contributing to our understanding of how magnetic sense, genetic programming, and memory are involved in migratory distributions.
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Coho salmon (Oncorhynchus kisutch) utilize olfactory cues to recognize and home to natal streams during spawning migrations. Chemically distinct river systems may promote directional selection for appropriately tuned olfactory receptor... more
Coho salmon (Oncorhynchus kisutch) utilize olfactory cues to recognize and home to natal streams during spawning migrations. Chemically distinct river systems may promote directional selection for appropriately tuned olfactory receptor repertoires among Coho populations. Here, we use F(ST) outlier methods to test for a signal of selection over olfactory receptor gene-linked markers, characterized in Coho populations from four geographically proximate, but ecologically distinct rivers. We report evidence for directional selection over one such marker, OkiOR3001, and document substantially higher levels of genetic structure among Coho populations from Oregon coastal lakes than previously observed with putatively neutral microsatellites.
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Research Interests: Genetics, Genetic Drift, Biotechnology, Biology, Genetic Diversity, and 14 moreMicrosatellites, Genetic Population Structure, DNA markers, Fisheries Sciences, Pacific Salmon, Genetic Differentiation, Local adaptation, Washington State, Genetic Markers, Allele Frequency, Cumulant, log likelihood ratio, alleles, and progeny
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A critical seasonal event for anadromous Chinook salmon ( Oncorhynchus tshawytscha ) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation at the circadian rhythm genes,... more
A critical seasonal event for anadromous Chinook salmon ( Oncorhynchus tshawytscha ) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation at the circadian rhythm genes, OtsClock1a and OtsClock1b , underlies genetic control of migration timing among 42 populations in North America. We identified eight length variants of the functionally important polyglutamine repeat motif (PolyQ) of OtsClock1b while OtsClock1a PolyQ was highly conserved. We found evidence of a latitudinal cline in average allele length and frequency of the two most common OtsClock1b alleles. The shorter 335 bp allele increases in frequency with decreasing latitude while the longer 359 bp allele increases in frequency at higher latitudes. Comparison to 13 microsatellite loci showed that 335 and 359 bp deviate significantly from neutral expectations. Furthermore, a hierarchical gene diversity analysis based on OtsClock1b PolyQ variation revealed that run ...
Research Interests: Geography, Polymorphism, Biology, Medicine, Biological Sciences, and 15 moreCircadian Rhythm, Animals, Animal migration, Peptides, Salmon, North America, Genotype, Amino Acid Sequence, Chinook Salmon, Molecular Sequence Data, alleles, Genetic control, microsatellite loci, Gene frequency, and Medical and Health Sciences
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Accurate evaluation of remnant Ostrea conchaphila/lurida population structure is critical for developing appropriate restoration efforts. Here we report 19 polymorphic microsatellites suitable for analyses of population differentiation,... more
Accurate evaluation of remnant Ostrea conchaphila/lurida population structure is critical for developing appropriate restoration efforts. Here we report 19 polymorphic microsatellites suitable for analyses of population differentiation, pedigree reconstruction and linkage map construction. We screened clones from four enriched genomic libraries, identified 73 microsatellite-containing sequences and designed polymerase chain reaction primers for 44 of these loci. We successfully optimized polymerase chain reaction conditions for 20 loci, including one monomorphic locus. In a Willapa Bay reference sample, mean observed and expected heterozygosities were 0.6729 and 0.8377. Nine loci deviated from Hardy-Weinberg equilibrium. These markers have proven useful for genetic studies of the Olympia oyster.
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Research Interests: Genetics, Geography, Polymorphism, Biology, Medicine, and 15 moreMolecular Ecology, Biological Sciences, California, Circadian Rhythm, Genetic Structure, Animals, New Zealand, Animal migration, Genetic Differentiation, Local adaptation, Genetic variation, Base Sequence, Chinook Salmon, Molecular Sequence Data, and Gene frequency
Research Interests: Genetics, Geography, Oceanography, Gene Flow, Marine Protected Areas, and 15 moreMarine Reserves, Molecular Ecology, Biological Sciences, California, Copper, Animals, Fishes, Larval Dispersal, Ecosystem, Analysis of Variance, Marine Protected Area, Marine Reserve, Genetic variation, Microsatellite DNA, and Isolation by distance
Research Interests: Geography, Polymorphism, Population Genetics, Biology, Medicine, and 15 moreMolecular Ecology, Biological Sciences, Molecular, Phylogeny, Microsatellites, Animals, Salmon, Differentiation, North America, Information Content, Single Nucleotide Polymorphism, Snps, Statistical Test, Chinook Salmon, and Genetic Markers
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The biological and taxonomic separation of the Pacific oyster Crassostrea gigas (Thunberg, 1793) from the Kumamoto oyster C. sikamea (Amemiya, 1928) is affirmed by three concordant lines of evidence: (1) fixed differences in 2% of a mtDNA... more
The biological and taxonomic separation of the Pacific oyster Crassostrea gigas (Thunberg, 1793) from the Kumamoto oyster C. sikamea (Amemiya, 1928) is affirmed by three concordant lines of evidence: (1) fixed differences in 2% of a mtDNA sequence coding for large subunit rRNA; (2) a genetic distance of 0.440 based on 19 allozyme loci, including 5 diagnostic loci (Aat-1, Idh-1,