Animal populations are frequently infected by pathogens, but it is not always easy to determine the importance of pathogens to overall population dynamics. It is especially difficult to detect the effects of disease in population time series data because the effects are often local while overall population dynamics are also affected by larger-scale environmental factors. We overcame this difficulty by applying multivariate time series analysis to extract local effects from spawning abundance data and by comparing the survival rate of juvenile fall-run Chinook salmon Oncorhynchus tshawytscha from two locations in the Klamath River basin of California, one of which is affected by a high concentration of the myxozoan parasite Ceratomyxa shasta. To assess the effect of the disease (ceratomyxosis) caused by C. shasta on the population dynamics, we analyzed spatially structured abundance data for naturally spawning salmon and survival data for hatchery-released salmon for associations with exposure to C. shasta and stream discharge, another important factor with respect to ceratomyxosis in juvenile salmon. The results suggest that ceratomyxosis reduces the survival of the Chinook salmon that migrate through the location where parasite densities are highest and that this effect is also detectable in spawning abundance estimates.

a b s t r a c tWe apply genetic stock identification (GSI) data and models of the catch and sampling process to describe spatial and temporal patterns in the stock composition and stock-specific catch-per-unit-effort (CPUE) of both tagged and untagged stocks encountered in California recreational ocean Chinook salmon fisheries during the period 1998-2002. Spatial and temporal distributions inferred from GSI sampling of stocks with tagged hatchery components were broadly consistent with those previously inferred from studies of tag recoveries alone, while GSI provided additional insight into untagged stocks of conservation concern. The catch in all times and areas was dominated (typically ≥90%) by the "Central Valley Fall" genetic reporting group, which is comprised primarily of Sacramento River fall run Chinook. Other contributing stocks were more spread out in space and time with the exception of Central Valley winter run Chinook, which were rarely encountered by boats fishing in port areas north of Point Reyes. Localized stock-specific CPUE appeared to increase near a stock's respective natal river while decreasing in other port areas at the time of adult return to freshwater for spawning. We describe methods for quantifying uncertainty in stock proportions, stock-specific catch, and determining the statistical support for proposed management boundaries hypothesized to represent "break points" in the spatial distributions for stocks of concern, and find at most equivocal support for a proposed delineation line at Point Reyes in north-central California.Published by Elsevier B.V.

Lipid class dynamics and the relationship between weight and length were analysed during early life stage (ELS) development in wild populations of shortbelly rockfish Sebastes jordani to investigate their utility in a condition or nutritional status assessment. Analyses from more than 3000 field-captured shortbelly rockfish indicated little variation in weight for a given length and provided limited application in the assessment of condition. The fractionation of total lipids into individual classes revealed trends in lipid metabolism throughout development. These trends were described best using a stage-specific regression model, since Sebastes show defined early life history transitions. Among developmental stages, triacylglycerols (TAG) and polar lipids (PL) were the dominant lipid classes and cholesterol (CHOL), sterol/wax esters, and nonesterified fatty acids were found in lower concentrations. In the preflexion stage, low concentrations and constant levels of TAG along with the combined influence of endogenous and exogenous sources of energy compromised the use of TAG as an index of nutritional status. However, during flexion through juvenile stages, TAG levels increased indicating an accumulation of energy reserves with development, thus providing a valid indicator of nutritional status in later stages. Large fluctuations in PL concentrations during development suggested complex metabolism which may be due to changes in cell volume and cell membrane proliferation with development as well as catabolism. CHOL declined in larval stages, then remained constant with increasing size through the juvenile stage, negating its use as a normalizer for variations of mass in a TAG/CHOL ratio prior to juvenile transformation. This study provides the first documentation of lipid dynamics during early life stages following parturition in a marine viviparous teleost.