Brenda McIntosh

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 ...

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...

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...

Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage‐based tagging (PBT) may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded‐wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774—individual, 267—population baseline available for assignment. Coho salmon from un‐CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT‐GSI system of identification to individuals in 2017 fisheries and escapements provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian‐origin coho salmon relative to CWTs, and an opportunity for a genetic‐based system to replace the current CWT system for coho salmon assessment.