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Population structure and stock identification of chum salmon from western Alaska determined with microsatellite and major histocompatibility complex variation. Pages 141-160. Pacific Salmon: ecology and management of western Alaska's populations
- In American Fisheries Society, Symposium 70
, 2009
"... Stock identification of chum salmon (Oncorhynchus keta) migrating through particular locations on the high seas can be of scientific and management interest. Although allozyme-based methods of stock identification have proven useful in estimation of chum salmon stock composition in mixed-stock fishe ..."
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Stock identification of chum salmon (Oncorhynchus keta) migrating through particular locations on the high seas can be of scientific and management interest. Although allozyme-based methods of stock identification have proven useful in estimation of chum salmon stock composition in mixed-stock fisheries (Shaklee et al. 1999), and differentiation at allozyme loci occurs among chum salmon (Beacham et al. 1987; Seeb and Crane 1999), the level of discrimination available in some applications is not sufficient for fisheries management decisions. Variation in microsatellite loci has been applied in other species requiring discrimination among salmonid populations within watersheds (Small et al. 1998; Beacham and Wood 1999; Beacham et al. 2001), and has been shown to be useful in stock discrimination in chinook salmon (Banks et al. 2000). Variation at microsatellite loci has been particularly useful for population-specific estimates of stock composition of Fraser River chinook salmon (Beacham et al. 2003), and may work well for chum salmon. In the present study, we survey variation at 13 microsatellite loci in chum salmon, and evaluate the utility of using microsatellite variation for stock identification on a regional and local basis. This is accomplished by analysis of simulated mixtures containing chum salmon from different regions, and on a local basis by incorporation of specific chum salmon populations. Tissue samples were collected from adult chum salmon from populations in Japan, the Yukon River, southeast
2005. DNA-level variation of sockeye salmon in Southeast Alaska and the Nass and Skeena rivers, British Columbia, with applications to stock identification
- North American Journal of Fisheries Management
"... Abstract.-The variation at 14 microsatellite loci and 1 major histocompatibility complex locus was surveyed in 12,000 sockeye salmon Oncorhynchus nerka from 35 populations in the Skeena and Nass River drainages in British Columbia and 20 populations from Southeast Alaska. Genetic differentiation am ..."
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Abstract.-The variation at 14 microsatellite loci and 1 major histocompatibility complex locus was surveyed in 12,000 sockeye salmon Oncorhynchus nerka from 35 populations in the Skeena and Nass River drainages in British Columbia and 20 populations from Southeast Alaska. Genetic differentiation among populations was observed, with an overall F ST of the microsatellite loci of 0.104. Evaluation of the utility of the microsatellite loci for stock identification applications indicated that the accuracy and precision of the estimated stock compositions generally increased as the number of observed alleles at the loci increased. Analysis of simulated mixtures of sockeye salmon from the Nass River, Skeena River, and Southeast Alaska indicated that DNA variation provides a practical way to estimate stock composition, yielding population and regional estimates within 1-3% of the actual values. The validity of the results from the simulated mixtures was evaluated with an analysis of a sample of known origin. Estimated stock compositions on a regional basis (derived from application of a 203-population baseline) were within 1% of the actual contributions, and for the Southeast Alaska component the individual population estimates were generally within 0.5% of the actual contributions. Analysis of fishery samples from a fishery near Tree Point in Southeast Alaska indicated that the major contributors to the fishery in 2001 were sockeye salmon of Nass River, Skeena River, and Southeast Alaska origin, with some components from the Stikine River. Analysis of fishery samples from a fishery near the entrance to Portland Inlet in northern British Columbia indicated that sockeye salmon of Nass River origin dominated the fishery in 2002. Thus, DNA variation provides an effective method for sockeye salmon stock identification.
Single Nucleotide Polymorphisms (SNPs) Provide Standard DNA Data for
"... Migratory studies of Chinook Oncorhynchus tshawytscha, chum O. keta, and sockeye O. nerka salmon require markers for which a large number of individuals can be processed in a relatively short time. Genetic markers, especially allozymes, have provided substantial insight into key questions asked by B ..."
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Migratory studies of Chinook Oncorhynchus tshawytscha, chum O. keta, and sockeye O. nerka salmon require markers for which a large number of individuals can be processed in a relatively short time. Genetic markers, especially allozymes, have provided substantial insight into key questions asked by BASIS investigators (see Kondzela et al. 2002; Urawa et al. 2004; Seeb et al. 2004). However, issues of sample collection and preservation as well as a desire for increased resolution have driven efforts to develop DNA markers to describe discrete aggregations of stocks. Given the multi-jurisdictional geographic range of these species, it is desirable that genetic markers and the corresponding data be transportable across laboratories. Allozymes meet these criteria while most DNA markers do not. To solve this DNA standardization dilemma, we are continuing to develop single nucleotide polymorphism (SNP) genotyping assays based upon the 5’-nuclease reaction. Various approaches to DNA analysis, each with advantages, were used to study Pacific salmon during the last decade. Initially the most common approach was the collection of SNP data that was obtained by restriction length polymorphism assays (RFLPs; e.g. Cronin et al. 1993; Park et al. 1993; Seeb and Crane 1999), amplification fragment length polymorphism assays (AFLPs; see Flannery et al. 2002), or DNA sequencing (e.g. Sato et al. 2004). SNP data were collected on mitochondrial DNA, nuclear DNA, neutral genes, and selected genes such as MHC
Mixed stock and landscape genetics analyses of sockeye salmon in the
, 2010
"... This is to certify that I have examined this copy of a master‟s thesis by ..."
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This is to certify that I have examined this copy of a master‟s thesis by
Listed under the Endangered
, 2011
"... Memorandum NMFS-NWFSC series to issue scientific and technical publications. Manuscripts have been peer reviewed and edited. Documents published in this series may be cited in the scientific and technical literature. The NMFS-NWFSC Technical Memorandum series of the Northwest Fisheries Science Cente ..."
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Memorandum NMFS-NWFSC series to issue scientific and technical publications. Manuscripts have been peer reviewed and edited. Documents published in this series may be cited in the scientific and technical literature. The NMFS-NWFSC Technical Memorandum series of the Northwest Fisheries Science Center continues the NMFS-F/NWC series established in 1970 by the Northwest & Alaska Fisheries Science Center, which has since been split into the Northwest Fisheries Science Center and the Alaska
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"... A future outlook on the effects of climate change on coho salmon (Oncorhynchus kisutch) habitats in the Cariboo-Chilcotin Study background Due to climate change by the 2050s average annual air temperatures and average annual precipitation in the Cariboo-Chilcotin are predicted to increase from 2.0-2 ..."
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A future outlook on the effects of climate change on coho salmon (Oncorhynchus kisutch) habitats in the Cariboo-Chilcotin Study background Due to climate change by the 2050s average annual air temperatures and average annual precipitation in the Cariboo-Chilcotin are predicted to increase from 2.0-2.5 °C and 5-20 % respectively, although in some locations summer precipitation is expected to decrease by as much as 5 % (Dawson et al. 2008). Such changes in air temperatures and precipitation are expected to lead to significant changes in hydrology and water
The numbering of the original series has been continued with the Sci en tific Re ports. Commissioners
"... Microsatellite screening in Pacific halibut (Hippoglossus stenolepis) and a preliminary examination of population structure based on observed DNA variation by ..."
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Microsatellite screening in Pacific halibut (Hippoglossus stenolepis) and a preliminary examination of population structure based on observed DNA variation by
Correspondence
, 2010
"... Using major histocompatibility complex markers to assign ..."
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DOI: 10.1577/T05-005.1 Estimation of Stock Composition and Individual Identification of Sockeye Salmon on a Pacific Rim Basis Using Microsatellite and Major Histocompatibility Complex Variation
"... Abstract.—The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a ..."
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Abstract.—The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of stock composition of single-population mixtures. In an analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 80 % accuracy for the average population was achieved by employing approximately 80 alleles in the analysis. Increasing the accuracy of estimated stock compositions to 90 % for the average population required approximately 400 microsatellite alleles. When all loci were used to estimate stock compositions, estimates were above 80 % for all sampling sites or populations, above 90 % for the lake of origin, and generally above 95 % for the region of origin. Analysis of known-origin samples indicated that accurate lake or regional estimates of stock composition were obtained. The accuracy of identification of individual fish to the correct lake of origin was above 90%, regardless of whether the lakes were geographically widespread or within a single watershed. The estimated stock com-positions of mixed-fishery samples from the western Bering Sea, from the continental shelf near
DOI: 10.1577/T04-040.1 Conservation Genetics of Inland Lake Trout in the Upper Mississippi River Basin: Stocked or Native Ancestry?
"... Abstract.—Although stocking for sport fishery enhancement has been practiced by resource managers for decades, the potential genetic effects of these stocking practices have remained largely unknown. We investigated the genetic contributions of stocking lake trout Salvelinus na-maycush in two inland ..."
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Abstract.—Although stocking for sport fishery enhancement has been practiced by resource managers for decades, the potential genetic effects of these stocking practices have remained largely unknown. We investigated the genetic contributions of stocking lake trout Salvelinus na-maycush in two inland lakes in Wisconsin (Trout and Black Oak lakes in Vilas County), which represent the only known indigenous lake trout populations in the upper Mississippi River basin. Exogenous sources of lake trout (Lake Michigan and Lake Superior strains) have been stocked into each of these lakes for decades, although the long-term effects of past stocking events on these populations are unknown. We used nine microsatellite loci and polymerase chain reaction– restriction fragment length polymorphism analysis of mitochondrial DNA to determine the dis-tinctiveness and genetic ancestry of lake trout in Trout and Black Oak lakes. Measures of allelic variance indicated that Trout and Black Oak lakes were significantly different (P, 0.05) from each other (FST 5 0.162) and all other populations evaluated in this study (FST 5 0.101 2 0.164). The combined microsatellite and mitochondrial DNA data indicate that upper Mississippi River basin lake trout have been minimally affected by past stocking practices. These populations should be managed as native gene pools, and interlake and interbasin stocking should be avoided.
