Khai D. Le

Population Structure and Stock Identification of Steelhead in Southern British Columbia, Washington, and the Columbia River Based on Microsatellite DNA Variation

Abstract The purpose of this study was to describe population structure and determine the potential for genetic stock identification for steelhead Oncorhynchus mykiss in British Columbia using microsatellite DNA markers. Variation at eight microsatellite DNA loci (Oki200, Omy77, Ots1, Ots3, Ssa85, Ots100, Ots103, and Ots108) was surveyed in approximately 1,500 steelhead from 22 populations in southern British Columbia, Washington, and the Columbia River drainage as well as in more than 450 steelhead from two commercial salmon fisheries conducted off the southwest coast of Vancouver Island. Nine populations were sampled for two or more years, and variation in allele frequencies among populations and regions was, on average, about 3.7 times greater than annual variation within populations. Regional structuring of populations was apparent, with Thompson River, upper Fraser River, and Columbia River populations forming distinct groups. Significant differences in allele frequencies were observed among regional...

Microsatellite DNA Population Structure and Stock Identification of Steelhead Trout (Oncorhynchus mykiss) in the Nass and Skeena Rivers in Northern British Columbia

Abstract: Population structure and the application to genetic stock identification for steelhead (Oncorhynchus mykiss) in the Nass and Skeena Rivers in northern British Columbia was examined using microsatellite markers. Variation at 8 microsatellite loci (Oki200, Omy77, Ots1, Ots3, Ssa85, Ots100, Ots103, and Ots108) was surveyed for approximately 930 steelhead from 7 populations in the Skeena River drainage and 850 steelhead from 10 populations in the Nass River drainage, as well as 1550 steelhead from test fisheries near the mouth of each river. Differentiation among populations within rivers accounted for about 1.9 times the variation observed among years within populations, with differences between drainages less than variation among populations within drainages. In the Nass River, winter-run populations formed a distinct group from the summer-run populations. Winter-run populations were not assessed in the Skeena River watershed. Simulated mixed-stock samples suggested that variation at the 8 microsatellite loci surveyed should provide relatively accurate and precise estimates of stock composition for fishery management applications within drainages. In the Skeena River drainage in 1998, Babine River (27%) and Bulkley drainage populations (31%) comprised the main components of the returns. For the Nass River in 1998 steelhead returning to Bell-Irving River were estimated to have comprised 39% of the fish sampled in the test fishery, with another 27% of the returns estimated to be derived from Cranberry River. The survey of microsatellite variation did not reveal enough differentiation between Nass River and Skeena River populations to be applied confidently in estimation of stock composition in marine fisheries at this time.

Population structure and stock identification of steelhead trout (Oncorhynchus mykiss) in British Columbia and the Columbia River based on microsatellite variation

Variation at 13 microsatellite loci was surveyed from ∼3 800 steelhead trout, Oncorhynchus mykiss, from 51 populations in British Columbia, Washington, and the Columbia River drainage. Mean FST over all 13 loci and 51 populations was 0.066. Regional structuring of populations was apparent, with Thompson River, upper Fraser River, and Columbia River populations forming distinct groups. In the Nass River, winter-run populations were distinct from the summer-run populations. Significant differences in allele frequencies were observed among regional stock groups at all loci. Analysis of variance components indicated that 5.7% of the total observed variation was distributed among 11 regions, and 2.3% of the variation was among populations within regions. Analysis of simulated mixed-stock samples suggested that variation at the microsatellite loci provided relatively accurate and precise estimates of stock composition for fishery management applications, and this was confirmed by application to actual fishery samples of known origin. Within the Fraser River drainage, individual steelhead trout can be identified to one of the three regions of origin with an accuracy of 94–97%. Microsatellites provided an effective way to determine population structure, and provided reliable estimates of stock composition in mixed-stock fisheries.

Population Structure and Stock Identification of Eulachon ( Thaleichthys pacificus ), an Anadromous Smelt, in the Pacific Northwest

The genetic structure of eulachon (Thaleichthys pacificus) populations was examined in an analysis of variation of 14 microsatellite loci representing approximately 1900 fish from 9 sites between the Columbia River and Cook Inlet, Alaska. Significant genetic differentiation occurred among the putative populations. The mean FST for all loci was 0.0046, and there was a significant correlation between population genetic differentiation (FST) and geographic distance. Simulated mixed-stock samples comprising populations from different regions suggested that variation at microsatellite loci provided reasonably accurate estimates of stock composition for potential fishery samples. Marine sampling indicated that immature eulachons from different rivers, during the 2 to 3 years of prespawning life in offshore marine waters, do not mix thoroughly. For eulachons captured incidentally in offshore trawl fisheries, there was a clear geographic cline in relative abundance of eulachons from different geographic areas. The sample from northern British Columbia was dominated by northern and central coastal populations of British Columbia, the sample from central British Columbia was composed of eulachons from all regions, and the sample from southern British Columbia was dominated by Columbia River and Fraser River populations. These results have implications for the management of trawl fisheries and conservation of spawning populations in some rivers where abundance is at historically low levels.

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...

Microsatellite Stock Identification of Chum Salmon on a Pacific Rim Basis

Abstract The variation at 14 microsatellite loci was analyzed for more than 53,000 chum salmon Oncorhynchus keta from 381 locations ranging from Korea to Washington State and used to estimate the stock composition of mixed-stock fishery samples. High resolution of the samples was possible, the number of reporting groups being distributed as follows: Korea = 1, Japan = 7, Russia = 8, Alaska = 15, Canadian Yukon River = 5, British Columbia = 16, and Washington State = 5. The number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of the stock composition of single population mixtures. Approximately 800 alleles were observed across the 14 microsatellites, providing the basis for high-resolution stock identification. Analysis of known-origin samples indicated that accurate regional estimates of stock composition were obtained. The estimated stock compositions of mixed-fishery samples from coastal Japan, the Sea of Okhotsk, the western Pacific Ocean, the Gulf...

Population structure and stock identification of chum salmon Oncorhynchus keta from Japan determined by microsatellite DNA variation

Variation at 14 microsatellite loci was surveyed in 26 chum salmon Oncorhynchus keta populations from Japan, one population from West Kamchatka and three populations from North America to determine population structure. Microsatellites were then applied to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (Fst) over all populations and loci was 0.031, with individual locus values ranging from 0.010 to 0.081. Seven regional populations were observed in Japanese chum salmon, with late-run populations from the Pacific Coast of Honshu the most distinct. Japanese populations displayed greater genetic diversity than did those in North America. Transplantation history in some Japanese river populations influenced their present genetic characteristics. Analysis of simulated mixtures from fishery sampling suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. Stock compositions for a 2005 sample of maturing, migrating chum salmon off the north-west coast of Hokkaido near the border of the Sea of Japan and the Sea of Okhotsk indicated that this region may be a migration corridor for Hokkaido populations from the Sea of Japan coast. Microsatellites have the ability to provide fine-scale resolution of stock composition in Japanese coastal fisheries.

Population structure and stock identification of chum salmon (Oncorhynchus keta) from British Columbia determined with microsatellite DNA variation

Variation at 14 microsatellite loci was surveyed in 205 populations of chum salmon (Oncorhynchus keta (Walbaum in Artedi, 1792)) from British Columbia to determine population structure and the possible application of microsatellites to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (FST) over all populations and loci was 0.016, with individual locus values ranging from 0.006 to 0.059. Sixteen regional stocks were defined in British Columbia for stock identification applications. Analysis of simulated fishery samples suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. The main stocks that constitute the October 2007 samples of migrating chum salmon through Johnstone Strait in southern British Columbia were Fraser River (45%–64%), southern British Columbia mainland (22%), and east coast Vancouver Island (13%–28%), within the range of those to be...

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

Abstract Identification of population-specific run timing is an important component of salmonid fisheries management and was a major focus of our study. Population structure of steelhead Oncorhynchus mykiss was examined in the Skeena River of northern British Columbia. Variation at 14 microsatellites was surveyed in 3,062 steelhead sampled from 17 populations in the drainage. During 1998–2010, 6,691 individuals were sampled in a lower river test fishery to obtain information on relative abundance and time of arrival of specific populations near the river mouth. The genetic differentiation index F ST calculated over all populations and loci was 0.021; individual locus values ranged from 0.017 to 0.045. Differentiation in steelhead allele frequencies among populations was approximately 14 times the differentiation observed among years within populations. A regional structuring of populations was the general pattern observed, with steelhead populations from the upper portion of the drainage clustering togeth...