Population structure of pink salmon (Oncorhynchus gorbuscha) in British Columbia and Washington, determined with microsatellites

Population structure of pink salmon (Oncorhynchus gorbuscha) from British Columbia and Washington was examined with a survey of microsatellite variation to describe the distribution of genetic variation. Variation at 16 microsatellite loci was surveyed for approximately 46,500 pink salmon sampled from 146 locations in the odd-year broodline and from 116 locations in the even-year broodline. An index of genetic differentiation, FST, over all populations and loci in the odd-year broodline was 0.005, with individual locus values ranging from 0.002 to 0.025. Population differentiation was less in the even-year broodline, with a FST value of 0.002 over all loci, and with individual locus values ranging from 0.001 to 0.005. Greater genetic diversity was observed in the odd-year broodline. Differentiation in pink salmon allele frequencies between broodlines was approximately 5.5 times greater than regional differentiation within broodlines. A regional structuring of populations was the general pattern observed, and a greater regional structure in the odd-year broodline than in the even-year broodline. The geographic distribution of microsatellite variation in populations of pink salmon likely ref lects a distribution of broodlines from separate refuges after the last glaciation period

2006c) Pacific rim population structure of Sockeye salmon as determined from microsatellite analysis

Abstract.-The Pacific Rim population structure of sockeye salmon Oncorhynchus nerka was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed for over 48,000 sockeye salmon sampled from 299 localities ranging from the Columbia River to Japan. The value of the genetic differentiation index F ST over all populations and loci was 0.097; individual locus values ranged from 0.038 to 0.154. Sockeye salmon from the Queen Charlotte Islands and the Columbia River displayed the least number of alleles relative to sockeye salmon from other regions in the Pacific Rim distribution of the species. Conversely, sockeye salmon displaying the greatest allelic diversity were observed in Southeast Alaska and the central coast of British Columbia. Sockeye salmon from these two regions displayed approximately 30% more alleles than did sockeye salmon from the Queen Charlotte Islands and the Columbia River. Sockeye salmon from Russia and western Alaska were, on average, less diverse than sockeye salmon from Southeast Alaska and more southerly locations in North America. A regional structuring of populations was generally observed among the sockeye salmon populations sampled, and populations were clustered within lakes and river drainages. At the Pacific Rim scale of population structure, there were two major groups of populations. The first group included populations from Russia, Bristol Bay, Kodiak Island, the Alsek River, and the Queen Charlotte Islands. The second group generally included populations from Southeast Alaska, British Columbia, and Washington. The distribution of microsatellite variation of sockeye salmon on a Pacific Rim basis reflected the origins of sockeye salmon radiating from refuges after the last glaciation period

Population and individual identification of Chinook Salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms

A study was undertaken to evaluate whether a parentage-based tagging (PBT) and genetic stock identification (GSI) program has the potential to emulate the results from an existing coded-wire tag (CWT) assessment program in British Columbia. A PBT/GSI approach was used to identify Chinook Salmon (Oncorhynchus tshawytscha) to specific populations and broodyears where 36,241 individuals from 45 populations were genotyped at 321 single nucleotide polymorphisms (SNPs). Known-origin and known-age age 1 juveniles from seven test populations were assigned via PBT (two-parental genotypes required, 538 of 656 juveniles assigned; one parental genotype required, 636 of 656 juveniles assigned) with a minimum accuracy of 99.9%. Assignment accuracy via PBT of 1,026 age 1, 2 or 3 Chinook Salmon returning to nine populations in 2015 or 2016 (two-parental genotypes required, 556 of 1,026 individuals assigned; one parental genotype required, 898 of 1,026 individuals assigned) was a minimum of 99.8%. A PBT/GSI or PBT system of identification may provide an alternate cost-effective method of identification in the assessment and management of Canadian-origin Chinook Salmon relative to the existing CWT program.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Population and individual identification of Coho Salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags

Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual Coho Salmon (Oncorhynchus kisutch) to specific populations and broodyears. In total, 20,242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho Salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1,939 Coho Salmon to the correct population was 100%, and to correct broodyear within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2,101 individuals, with an accuracy of 99.95% (2,000/2,001) to population and 100.0% to age. With 23 regions defined by the CWT program, and individuals displaying an assignment probabilityThe accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Coho Baseline Data - Genepop Format

Genotypic data for the 117 population, 302 SNP Baseline Data - genepop format

Data from: Population and individual identification of Coho Salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags

Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2101 individuals, with an accuracy of 99.95% (2000–2001) to population and 100.0% to age. With 23 regions defined by the coded-wire tag (CWT) program, and individuals displaying an assignment probability <0.85 excluded from the analysis, mean regional assignment accuracy of individuals via GSI was 98.4% over all 23 regions. A PBT–GSI or PBT system of identification will provide an alternate method of identification in the assessment and management of Canadian-origin coho salmon relative to the existing CWT program