Cathy MacConnachie

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 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 kn...

Stock Identification of Fraser River Sockeye Salmon Using Microsatellites and Major Histocompatibility Complex Variation

Abstract The utility of DNA-based variation for stock identification was evaluated for Fraser River sockeye salmon Oncorhynchus nerka. For this evaluation, the variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was determined from approximately 13,000 fish from 47 populations in the drainage. Genetic differentiation among the populations was observed, the overall F ST value for the 14 microsatellite loci surveyed being 0.054 and that for the MHC locus being 0.215. The variation among regions and populations within regions was approximately 20 times as great as that of the annual variation within populations for the microsatellite loci and 28 times as great for the MHC locus. The power of a microsatellite locus for population-specific identification in simulated mixture samples was positively correlated with the number of observed alleles at the locus. Analysis of simulated mixtures indicated that the mean percentage error of estimated stock compositions was less than ...

Coho Salmon Population Structure in North America Determined from Microsatellites

Abstract Population structure of coho salmon Oncorhynchus kisutch from Russia to California was examined with a survey of microsatellite variation to describe the distribution of genetic variation. Variation at 17 microsatellite loci was surveyed for approximately 50,000 coho salmon sampled from 318 localities. The genetic differentiation index (F ST) over all populations and loci was 0.058, with individual locus F ST values ranging from 0.027 to 0.143. The least genetically diverse coho salmon were observed from Russia, the Porcupine River in the Yukon River drainage, and the middle Fraser and Thompson rivers in southern British Columbia. Coho salmon from Vancouver Island, British Columbia; Puget Sound, Hood Canal, and Juan de Fuca Strait, northern Washington; and Oregon displayed the greatest number of alleles compared with coho salmon in other regions. Differentiation in coho salmon allele frequencies among regions and among populations within regions was approximately seven times greater than that of ...

Use of Microsatellites to Determine Population Structure and Migration of Pacific Herring in British Columbia and Adjacent Regions

Abstract This study assessed genetic population structure of Pacific herring Clupea pallasii in British Columbia and adjacent regions by analyzing microsatellite variation; the utility of microsatellites for stock identification applications was also evaluated. Variation at 14 loci was surveyed in approximately 26,000 Pacific herring from 90 sampling locations. Estimates of the genetic differentiation index F ST by locus varied between 0.000 and 0.014, and the mean across all loci was 0.003. Four stocks of Pacific herring were defined in British Columbia, and stocks were also identified in southeast Alaska, Washington, and California. In British Columbia, differences in timing of spawning are the main isolating mechanisms among stocks, although geographic isolation of the spawning populations may also have some effect in maintaining the genetic distinctiveness of each stock. The limited genetic differentiation among Pacific herring populations in British Columbia is consistent with among-population strayi...

Population Structure of Sockeye Salmon from Russia Determined with Microsatellite DNA Variation

Abstract The population structure of sockeye salmon Oncorhynchus nerka from Russia was determined from a survey of the variation of 14 microsatellite loci among approximately 3,750 sockeye salmon from 56 populations. The populations from Avacha Bay and the Palana River were quite distinct. Genetic differentiation among the populations surveyed was observed, the mean value of the differentiation index (F ST) for all loci being 0.038 (SD = 0.007). Regional structuring of the populations surveyed was observed, multiple populations sampled within a lake being more similar to each other than to populations in other lakes or rivers. River drainage of origin was a significant unit of population structure. Populations spawning in rivers without access to a nursery lake for juvenile rearing displayed greater genetic variation than did populations with access to nursery lakes. Within Kurilskoye Lake, genetic differentation was observed between populations spawning in tributaries to the lake and those populations sp...

DNA-Level Variation of Sockeye Salmon in Southeast Alaska and the Nass and Skeena Rivers, British Columbia, with Applications to Stock Identification

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. Estim...

Population Structure and Run Timing of Sockeye Salmon in the Skeena River, British Columbia

AbstractDetermination of run timing is an important component of salmonid fisheries management and was the major focus of the current study. Population structure of Sockeye Salmon Oncorhynchus nerka was examined in the Skeena River, northern British Columbia. Variation at 14 microsatellites was surveyed for 27 populations in the drainage. There were 9,473 individuals sampled in a lower river test fishery during 2000–2011 in order to provide information on relative abundance and time of arrival of specific populations or stocks near the mouth of the river. Within-lake or within-river tributary structuring of populations was the general pattern observed, with 10 populations from Babine Lake clustering together in 91% of dendrograms evaluated, and two populations from Lakelse Lake clustering together in 100% of dendrograms evaluated. The 27 populations sampled were arranged in 12 reporting groups for genetic stock identification applications. The estimated stock composition of known-origin mixtures was withi...

Microsatellite Mixed-Stock Identification of Coho Salmon in British Columbia

Abstract Variation at 17 microsatellite loci was analyzed for about 50,000 coho salmon Oncorhynchus kisutch sampled from 274 locations ranging from Russia to California (but largely from British Columbia), and the variation was applied to estimate stock composition in mixed-stock fishery samples. High resolution of mixed-stock samples was possible; accurate estimates of stock composition were available for coho salmon originating from 39 regions (Russia, 1 region; Yukon River, 1; southeast Alaska, 1; British Columbia, 28; Washington, 5; Columbia River, 1; Oregon, 1; California, 1). The power of a locus in providing accurate estimates of stock composition of simulated single-population mixtures was related to the number of alleles observed at the locus. Approximately 800 alleles were observed across the 17 microsatellites. Analysis of known-origin samples indicated that accurate regional estimates of stock composition were obtained; estimates from 37 of 39 regions had accuracy greater than 90%. Estimated stock compositions of five mixed-fishery samples collected in British Columbia and the San Juan Islands (Washington) reflected the presence and timing of migration of the local populations. Microsatellites provided accurate estimates of stock composition from many locations in the British Columbia distribution of coho salmon.

Population Structure and Run Timing of Sockeye Salmon in the Skeena River, British Columbia: Response to Comment

The use of genetic stock identification together with abundances estimated from a test fishery is fairly standard in the management of ocean mixed-stock salmon fisheries in British Columbia (Beacha...