The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage.

Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)

Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of the utility of the microsatellite variation for population-specific stock identification applications indicated that the accuracy of the stock composition estimates generally improved with an increasing number of loci used in the estimation procedure, but an increase in accuracy was generally marginal after eight loci were used. With 10–14 populations in a simulated fishery sample, the mean error in population-specific estimated stock composition with a 50-popula-tion baseline was <1.4%. Identification of individuals to specific populations was highest for lower Fraser River and lower and North Thompson River populations; an average of 70% of the individual fish were correctly assigned to specific populations. The average error of the estimated percentage for the seven populations present in a coded-wire tag sample was 2% per population. Estimation of stock composition in the lower river commercial net fishery prior to June is of key local fishery management interest. Chinook salmon from the Chilcotin River and Nicola River drainages were important contributors to the early commercial fishery in the lower river because they comprised approximately 50% of the samples from the net fishery prior to mid April.

Quantifying annual variation in catchability for commercial and research fishing

Biomass indices, from commercial catch per unit of effort (CPUE) or random trawl surveys, are commonly used in fisheries stock assessments. Uncertainty in such indices, often ex-pressed as a coefficient of variation (CV), has two components: observation error, and annual variation in catchability. Only the former can be estimated directly. As a result, the CVs used for these indices either ignore the annual-variation component or assume a value for it (often implicitly). Two types of data for New Zealand stocks were examined: 48 sets of residuals and catchability estimates from stock assessments using either CPUE or trawl survey indices; and biomass estimates from 17 time series of trawl surveys with between 4 and 25 species per time series. These data show clear evidence of significant annual variation in catchability. With the trawl survey data, catchability was detectably extreme for many species in about one year in six. The assessment data suggest that this annual variability typically has a CV of about 0.2. For commercial CPUE the variability is slightly less, and a typical total CV (including both components) of 0.15 to 0.2. This is much less than the values of 0.3 to 0.35 that have commonly been assumed in New Zealand. Some estimates of catchability are shown to be implausible.

The effect of intensive line fishing on the virgin biomass of a tropical deepwater snapper, the crimson jobfish (Pristipomoides filamentosus)

An intensive commercial hook-and-line fishing operation targeted the demersal fisheries resources at Saya de Malha Bank in the Southwest Indian Ocean. Fishing was conducted with 12 dories that were equipped with echo sounders and electric fishing reels and supported by a refrigerated mothership. Over a 13-day period in the 55–130 m depth range, a total of 74.3 metric tons (t) of fish were caught, of which the crimson jobfish (Pristipomoides filamentosus) represented 80%. Catch rates decreased with time and could not be attributed to changes in location, climatic conditions, fishing depth, fishing method, or bait type. The initial virgin biomass of P. filamentosus available to a line fishery at the North Western promontory of Saya de Malha Bank was estimated at 72.6 t through application of the Leslie model to daily catch and effort data. Biomass densities of 2364 kg/km2 and 1206 kg/km were obtained by applying the initial biomass estimates to the surface area and to the length of the dropoff that was fished. The potential sustainable yield prior to exploitation was estimated at 567 kg/km2 per year. The quantity of P. filamentosus caught by the mother-ship-dory fishing operation represented 82% of the initial biomass available to a hook-and-line fishery, equivalent to more that three times the estimated maximum sustainable yield. The results of the study are important to fisheries managers because they demonstrate that intensive line fishing operations have the potential to rapidly deplete demersal fisheries resources.

Modeling the effect of striped bass (Morone saxatilis) on the population viability of Sacramento River winter-run chinook salmon (Onchorhynchus tshawytscha)

We estimated the impact of striped bass (Morone saxatilis) predation on winter-run chinook salmon (Oncorhynchus tshawytscha) with a Bayesian population dynamics model using striped bass and winter-run chinook salmon population abundance data. Winter-run chinook salmon extinction and recovery probabilities under different future striped bass abundance levels were estimated by simulating from the posterior distribution of model parameters. The model predicts that if the striped bass population declines to 512,000 adults as expected in the absence of stocking, winter-run chinook salmon will have about a 28% chance of quasi-extinction (defined as three consecutive spawning runs of fewer than 200 adults) within 50 years. If stocking stabilizes the striped bass population at 700,000 adults, the predicted quasi-extinction probability is 30%. A more ambitious stocking program that maintains a population of 3 million adult striped bass would increase the predicted quasi-extinction probability to 55%. Extinction probability, but not recovery probability, was fairly insensitive to assumptions about density dependence. We conclude that winter-run chinook salmon face a serious extinction risk without augmentation of the striped bass population and that substantial increases in striped bass abundance could significantly increase the threat to winter-run chi-nook salmon if not mitigated by increasing winter chinook salmon survival in some other way.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

Physiological ecology of juvenile chinook salmon (Oncorhynchus tshawytscha) at the southern end of their distribution, the San Francisco Estuary and Gulf of the Farallones, California

Juvenile chinook salmon, Oncorhynchus tshawytscha, from natal streams in California’s Central Valley demonstrated little estuarine dependency but grew rapidly once in coastal waters. We collected juvenile chinook salmon at locations spanning the San Francisco Estuary from the western side of the freshwater delta—at the confluence of the Sacramento and San Joaquin Rivers—to the estuary exit at the Golden Gate and in the coastal waters of the Gulf of the Farallones. Juveniles spent about 40 d migrating through the estuary at an estimated rate of 1.6 km/d or faster during their migration season (May and June 1997) toward the ocean. Mean growth in length (0.18 mm/d) and weight (0.02 g/d) was insignificant in young chinook salmon while in the estuary, but estimated daily growth of 0.6 mm/d and 0.5 g/d in the ocean was rapid (P≤0.001). Condition (K factor) declined in the estuary, but improved markedly in ocean fish. Total body protein, total lipid, triacylglycerols (TAG), polar lipids, cholesterol, and nonesterified fatty acids concentrations did not change in juveniles in the estuary, but total lipid and TAG were depleted in ocean juveniles. As young chinook migrated from freshwater to the ocean, their prey changed progressively in importance from invertebrates to fish larvae. Once in coastal waters, juvenile salmon appear to employ a strategy of rapid growth at the expense of energy reserves to increase survival potential. In 1997, environmental conditions did not impede development: freshwater discharge was above average and water temperatures were only slightly elevated, within the species’ tolerance. Data suggest that chinook salmon from California’s Central Valley have evolved a strong ecological propensity for a ocean-type life history. But unlike populations in the Pacific Northwest, they show little estuarine dependency and proceed to the ocean to benefit from the upwelling-driven, biologically productive coastal waters.