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 F_ST 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.     

Discriminating coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia, using microsatellite DNA markers

Three microsatellite loci were used to examine genetic variation among 16 coho salmon ( Oncorhynchus kisutch ) populations within the Fraser River drainage system, in British Columbia, Canada. Each locus was highly polymorphic with 30 alleles at the Ots 101 locus, 15 alleles at the Ots 3 locus and 38 alleles at the Ots 103 locus. Average observed heterozygosities were 86.1%, 70%, and 56.1%, respectively. With the exception of the Dunn and Lemieux River populations, Chi-square tests and F _ST values indicated that all populations had significantly different allele frequencies. Two distinct population groups within the Fraser River drainage were observed. Lower Fraser River populations were strongly differentiated from populations spawning in the upper Fraser River, which includes the Thompson River (a tributary flowing into the upper Fraser) and the portion of the Fraser River beyond the precipitous Fraser River canyon. This regional population structure may have resulted from colonization of the upper and lower Fraser River regions by different founder populations following Pleistocene glaciation, and be maintained by adaptive differences between the two groups of coho salmon. Coho salmon populations in the upper Fraser and Thompson River drainages form an evolutionarily significant unit (ESU) of importance for conservation of biodiversity in coho salmon. Microsatellite DNA loci show promise as technically simple and highly informative genetic markers for coho salmon population management.     

Genetic variation in westslope cutthroat trout <Emphasis Type="Italic">Oncorhynchus clarkii lewisi</Emphasis>: implications for conservation

Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei’s D _S , populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention.     

Minisatellite DNA variation and stock identification of coho salmon

Geographic variation in minisatellite DNA variation was examined in 18 stocks of coho salmon Oncorhynchus kisutch from British Columbia and three stocks from Kamchatka or Western Alaska. Genomic DNA was restricted with Mbo I or Hae III and hybridized with two minisatellite probes (p Ssa -A34, Ots PBS-1). Allele frequencies and DNA band counts derived from the two probes were combined with band counts from the probe Ssa to show a regional stock structure. In British Columbia, stocks from the Fraser River were distinct from those on Vancouver Island, and all were differentiated from those on the mainland of British Columbia. Average heterozygosity at the Ssa -A34 locus was 71%. Compared with a previous study of British Columbia coho salmon population structure in which variation at 26 allozyme loci was examined, greater population differentiation and higher heterozygosity were observed at minisatellite loci. Estimated stock compositions of simulated mixtures of fishery samples from British Columbia stocks were accurate and precise, with the potential of identifying stocks within the drainage basin of a major river, the Fraser River. Minisatellite DNA variation may provide accurate and precise estimates of stock composition in actual fishery applications, and has the potential of identifying individual fish to region or stock of origin.     

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 F_ST for all loci was 0.0046, and there was a significant correlation between population genetic differentiation (F_ST) 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.     

Genetic mixed‐stock analysis of lake‐run brown trout Salmo trutta fishery catches in the Inari Basin,northern Finland: implications for conservation and management

Genetic mixed‐stock analysis (MSA) of wild lake‐run brown trout Salmo trutta fishery catches (n = 665) from the Inari Basin (northern Finland) between 2006 and 2008 was carried out using a previously characterized baseline with 30 populations (n = 813) and 13 microsatellite loci. Altogether, 12 populations contributed significantly to mixed‐stock fisheries, with the Ivalojoki system being the major contributor (70%) to the total catch. When catches were analysed regionally, geographically nearby populations were the main contributors to the local catches, indicating that a large proportion of S. trutta occupy lacustrine areas near the natal river mouth rather than dispersing throughout the lake. Similarly, far upstream populations contributed insignificantly to catches. These findings have important implications for the conservation and sustainable fishery management of the Inari system.     

Juvenile Salmon Usage of the Skeena River Estuary

Migratory salmon transit estuary habitats on their way out to the ocean but this phase of their life cycle is more poorly understood than other phases. The estuaries of large river systems in particular may support many populations and several species of salmon that originate from throughout the upstream river. The Skeena River of British Columbia, Canada, is a large river system with high salmon population- and species-level diversity. The estuary of the Skeena River is under pressure from industrial development, with two gas liquefaction terminals and a potash loading facility in various stages of environmental review processes, providing motivation for understanding the usage of the estuary by juvenile salmon. We conducted a juvenile salmonid sampling program throughout the Skeena River estuary in 2007 and 2013 to investigate the spatial and temporal distribution of different species and populations of salmon. We captured six species of juvenile anadromous salmonids throughout the estuary in both years, and found that areas proposed for development support some of the highest abundances of some species of salmon. Specifically, the highest abundances of sockeye (both years), Chinook in 2007, and coho salmon in 2013 were captured in areas proposed for development. For example, juvenile sockeye salmon were 2–8 times more abundant in the proposed development areas. Genetic stock assignment demonstrated that the Chinook salmon and most of the sockeye salmon that were captured originated from throughout the Skeena watershed, while some sockeye salmon came from the Nass, Stikine, Southeast Alaska, and coastal systems on the northern and central coasts of British Columbia. These fish support extensive commercial, recreational, and First Nations fisheries throughout the Skeena River and beyond. Our results demonstrate that estuary habitats integrate species and population diversity of salmon, and that if proposed development negatively affects the salmon populations that use the estuary, then numerous fisheries would also be negatively affected.     

Population structure of lake‐type and river‐type sockeye salmon in transboundary rivers of northern British Columbia

The population structure of 'lake‐type' and 'river‐type' sockeye salmon Oncorhynchus nerka , primarily in transboundary rivers in northern British Columbia, was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed from c . 3000 lake‐type and 3200 river‐type sockeye salmon from 47 populations in six river drainages in British Columbia. The mean F _ST for the 14 microsatellite loci and 47 populations was 0·068, and 0·034 over all river‐type populations. River‐type sockeye salmon were more genetically diverse than lake‐type sockeye salmon, with expected heterozygosity of river‐type sockeye salmon 0·72 and with an average 12·7 alleles observed per locus, whereas expected heterozygosity of lake‐type sockeye salmon was 0·65 with and average 10·5 alleles observed per locus. River drainage of origin was a significant unit of population structure. There was clear evidence of genetic differentiation among river‐type populations of sockeye salmon from different drainages over a broad geographic range in British Columbia.     

Conservation and management implications of fine-scale genetic structure of Gulf sturgeon in the Pascagoula River, Mississippi

The anadromous Gulf sturgeon occurs along the north central coast of the Gulf of Mexico and is federally listed as threatened. We analyzed fine‐scale patterns of Gulf sturgeon population structure, focusing on the Pascagoula River drainage of Mississippi, in reference to movement patterns as determined via telemetry and capture data. We genotyped 361 Gulf sturgeon using eight microsatellite loci including samples from the Pascagoula, Pearl, Escambia, Yellow, Choctawhatchee, and Apalachicola river drainages. Pairwise F_ST estimates indicated that genetic structure occurs at least at the drainage level. The Pascagoula and Pearl rivers form a western group, demonstrating 100% bootstrap support for a division with drainages to the east. Assignment tests detected non‐natal genotypes occurring in all drainages. According to assignment tests, the Pascagoula supports an admixture of individuals, containing minimal influence from drainages to the east (2%) and substantial interaction with the Pearl River (14.1%). The occurrence of Pascagoula River fish in the Pearl was non‐reciprocal, observed at 1.1%. After accounting for non‐natal genetic diversity within the Pascagoula, there remained a disparity between a pooled Pascagoula group and the only documented spawning site within the drainage located in the Bouie River. We interpret this as an indication of a second genetic stock within the Pascagoula River drainage. Radio telemetry data suggest that spawning likely occurs in the Chickasawhay River, in areas isolated from the Bouie River spawning site by about 350 river kilometers. We emphasize the utility of integrating field and molecular approaches when delineating fine‐scale patterns of population structure in anadromous fishes.     

DNA in Action: Rapid Application of DNA Variation to Sockeye Salmon Fisheries Management

Commitment to conservation-based management of exploited fish species imposes unprecedented requirements for adaptive, real-time management of biologically and socially complex mixed-stock fisheries such as those conducted for Pacific salmon. Stock identification is a key component of the management process, with population-specific timing and abundance information often incorporated into management decisions. By using both microsatellite and major histocompatibility complex genetic variation, we achieved highly accurate estimates of stock composition for Fraser River sockeye salmon. Over a 2-month period in 2002, we analyzed 9300 returning Fraser River sockeye salmon sampled in mixed-stock fisheries, and provided stock composition estimates to fishery managers within 9–30 h of sample delivery. Stock-specific exploitation targets governed by conservation concerns were achieved in this fishery.     

Assessment of genetic variation between reproductive ecotypes of Klamath River steelhead reveals differentiation associated with different run-timings

Seven microsatellite DNA loci were optimized to assess genetic differentiation in coastal steelhead (Oncorhynchus mykiss irideus) sampling groups from the lower Klamath River (California, USA). Genetic relationships among three winter‐run and two summer‐run groups were investigated. The different groups displayed high levels of allelic variation. Pairwise F_ST comparisons and Nei's genetic distance supported low, yet significant, genetic differentiation between summer and winter run‐timings similar to other studies of temporal variation in salmonids. Analysis of molecular variance showed that most of the genetic variation was at the individual level (97.9%), although significant genetic variation existed between timing of runs (2.59%). Additionally, at least one locus in each group was out of Hardy–Weinberg equilibrium due to a deficiency in heterozygotes, and significant F_IS values were observed in three temporal collections. Together, these results suggest stock admixture, caused by multiple populations of origin in each sampling group, better known as the Wahlund Effect. These observations are preliminary evidence for isolation by time between Klamath River steelhead runs during distinct periods.     

Hierarchical analysis of genetic structure in the habitat‐specialist Eastern Sand Darter (Ammocrypta pellucida)

Quantifying spatial genetic structure can reveal the relative influences of contemporary and historic factors underlying localized and regional patterns of genetic diversity and gene flow – important considerations for the development of effective conservation efforts. Using 10 polymorphic microsatellite loci, we characterize genetic variation among populations across the range of the Eastern Sand Darter (Ammocrypta pellucida), a small riverine percid that is highly dependent on sandy substrate microhabitats. We tested for fine scale, regional, and historic patterns of genetic structure. As expected, significant differentiation was detected among rivers within drainages and among drainages. At finer scales, an unexpected lack of within‐river genetic structure among fragmented sandy microhabitats suggests that stratified dispersal resulting from unstable sand bar habitat degradation (natural and anthropogenic) may preclude substantial genetic differentiation within rivers. Among‐drainage genetic structure indicates that postglacial (14 kya) drainage connectivity continues to influence contemporary genetic structure among Eastern Sand Darter populations in southern Ontario. These results provide an unexpected contrast to other benthic riverine fish in the Great Lakes drainage and suggest that habitat‐specific fishes, such as the Eastern Sand Darter, can evolve dispersal strategies that overcome fragmented and temporally unstable habitats.     

An analysis of genetic stock identification on a small geographical scale using microsatellite markers,and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed‐stock fishery to an almost exclusively single‐stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.     

Genetic diversity and population structure in the Barrens Topminnow (<Emphasis Type="Italic">Fundulus julisia</Emphasis>): implications for conservation and management of a critically endangered species

The Barrens Topminnow (Fundulus julisia) has undergone a rapid and dramatic decline. In the 1980s, at least twenty localities with Barrens Topminnows were known to exist in the Barrens Plateau region of middle Tennessee; currently only three areas with natural (not stocked) populations remain. The long-term survival of the Barrens Topminnow will depend entirely on effective management and conservation efforts. Captive propagation and stocking of captive-reared juveniles to suitable habitats have successfully established a handful of self-sustaining populations. However, very little is known about the genetic composition of source and introduced populations including levels of genetic diversity and structuring of genetic variation. Here we use both mitochondrial sequence data and genotypes from 14 microsatellite loci to examine patterns of genetic variation among ten sites, including all sites with natural populations and a subset of sites with introduced (stocked) populations of this species. Mitochondrial sequence analysis reveals extremely low levels of variation within populations and fixed differences between drainages. Microsatellite genotype data shows higher levels of genetic variability and a molecular signature consistent with a recent history of population bottlenecks. Measures of genetic diversity at microsatellite loci including allelic richness are similar within source and introduced populations. Bayesian assignment tests and analysis of molecular variation (AMOVA) support two distinct populations, consistent with drainage boundaries. Results from AMOVA analysis also suggest low levels of genetic connectivity between isolated populations within the same drainage. Here we propose two distinct evolutionary significant units (ESUs) and two management units that reflect this population substructure and warrant consideration in future management efforts.     

Mitochondrial DNA evidence for high levels of gene flow among populations of a widely distributed anadromous lamprey Entosphenus tridentatus (Petromyzontidae)

Mitochondrial DNA variation among 1246 individuals of Pacific lamprey ( Entosphenus tridentatus ) from 81 populations spanning 2600 km from the Skeena River, British Columbia, to the Ventura River, California, was surveyed using five restriction enzymes. A total of 29 composite haplotypes was detected in two gene fragments (ND2 and ND5). The three most common haplotypes, occurring in 91% of all samples, were present at similar frequencies in all regions. Samples were divided into six biogeographic regions based on sample distribution and geographical landmarks to assess geographic genetic structure. Analysis of molecular variance indicated that 99% of the genetic variation was explained by variability within drainages. The lack of geographical population structure is likely related to a life-history pattern that includes a prolonged larval freshwater stage, migration to oceanic feeding and return to fresh water to spawn. The lack of strong natal homing apparently promotes gene flow among drainages and regions.     

Population genetic structure of a rare unionid (<Emphasis Type="Italic">Lampsilis cariosa</Emphasis>) in a recently glaciated landscape

The yellow lampmussel (Lampsilis cariosa) is a rare unionid species in need of conservation, as it is declining throughout most of its Atlantic slope range in North America. Because freshwater mussels rely on a fish host for dispersal of their larvae, barriers to the movement of hosts, such as habitat fragmentation by dams, may indirectly affect population genetic structure. We used microsatellite loci to assess genetic variation for L. cariosa within and among three river drainages in the northern part of its range, which emerged from glaciation only ∼ ∼8–10 kya. Despite this relatively recent emergence, significant differences were observed among populations both within and among drainages, possibly because low effective population sizes meant that populations of these mussels achieved drift-migration equilibrium rapidly following glaciation. L. cariosa individuals could be assigned to their own drainages with 89.3% accuracy. Among-population differences were modest, however, in comparison to differences observed in another study of rare mussels south of the recently glaciated region. L. cariosa populations exhibited significant isolation by distance, but there was no additional variation explained by the number, size, or age of intervening dams. An understanding of mussel population genetic structure provides information, useful for conservation planning, on patterns of isolation and connectivity among populations.     

Discovery and characterization of single-nucleotide polymorphisms in steelhead/rainbow trout, Oncorhynchus mykiss

Single-nucleotide polymorphisms (SNPs) have several advantages over other genetic markers, including lower mutation and genotyping error rates, ease of inter-laboratory standardization, and the prospect of high-throughput, low-cost genotyping. Nevertheless, their development and use has only recently moved beyond model organisms to groups such as salmonid fishes. Oncorhynchus mykiss is a salmonid native to the North Pacific rim that has now been introduced throughout the world for fisheries and aquaculture. The anadromous form of the species is known as steelhead. Native steelhead populations on the west coast of the United States have declined and many now have protected status. The nonanadromous, or resident, form of the species is termed rainbow, redband or golden trout. Additional life history and morphological variation, and interactions between the forms, make the species challenging to study, monitor and evaluate. Here, we describe the discovery, characterization and assay development for 139 SNP loci in steelhead/rainbow trout. We used EST sequences from existing genomic databases to design primers for 480 genes. Sanger-sequencing products from these genes provided 130 KB of consensus sequence in which variation was surveyed for 22 individuals from steelhead, rainbow and redband trout groups. The resulting TaqMan assays were surveyed in five steelhead populations and three rainbow trout stocks, where they had a mean minor allele frequency of 0.15-0.26 and observed heterozygosity of 0.18-0.35. Mean F(ST) was 0.204. The development of SNPs for O. mykiss will help to provide highly informative genetic tools for individual and stock identification, pedigree reconstruction, phylogeography and ecological investigation.     

Stock structure of shovelnose sturgeon analyzed with microsatellite DNA and morphological characters

Shovelnose sturgeon (Scaphirhynchus platorhynchus) caviar fisheries exist in several states throughout the Mississippi River drainage. Management of these fisheries may benefit from information about genetic stock structure. Sixteen microsatellite loci and morphological analysis were used to examine geographic stock structure of shovelnose sturgeon among seven geographic locations: five within continuous shovelnose sturgeon habitat, and two isolated by artificial barriers. Tissue samples were collected from 1999 to 2006 from the upper Missouri, Platte, lower Missouri, middle Mississippi, Ohio, Wabash, and Atchafalaya rivers. Geographic samples of shovelnose sturgeon samples could be separated into three groups with discriminate function analysis of four morphological characters. The microsatellite loci were highly variable (allelic richness range 5.65–13, observed heterozygosity range 0.64–0.89). Bayesian clustering did not identify multiple groups in the genetic data. However, significant genetic differentiation (θ_ST = 0.017, P < 0.0001) was observed among a priori defined geographic samples and all pairwise estimates of θ_ST were significant. Assignment testing among a priori defined groups indicated that the sturgeon from the upper Missouri, Platte, and Atchafalaya rivers had the highest assignment scores and thus were most distinct, while the lower Missouri and the middle Mississippi were less distinct and a larger fraction of the sturgeon from these rivers was genetically assigned to other rivers. The Ohio and Wabash rivers were genetically most similar. A Mantel test revealed a positive relationship between genetic and geographic distance (r = 0.464, P = 0.055) that was not statistically significant. The level of genetic differentiation observed at both molecular and morphological characters suggests that multiple shovelnose sturgeon populations may exist within the studied area, yet demographic factors and possible gene flow may have minimized the amount of genetic differentiation among locations.