The environmental requirements of salmon and trout in fresh water

This article is a summary for the general reader, rather than an in-depth review, and attempts to define, as quantitatively as possible, the habitat requirements of salmon and trout and then to relate them to the main ways in which man's activity can influence the survival and growth of these fishes. Frequent text references to an extensive body of published work have been avoided, although a selective bibliography has been included which lists some of the main work upon which the text depends. This article deals only with the freshwater part of the life cycle, and the coverage has some bias towards England and Wales.

1976 step in the Pacific climate: forty environmental changes between 1968-1975 and 1977-1984

Examination of 40 time series of multidisciplinary environmental variables from the Pacific Ocean and the Americas, collected in 1968 to 1984, demonstrated the remarkable consistency of a major climate-related, step-like change in 1976. To combine the 40 variables (e.g., air and water temperatures, Southern Oscillation, chlorophyll, geese, salmon, crabs, glaciers, atmospheric dust, coral, carbon dioxide, winds, ice cover, Bering Strait transport) into a single time series, standard variants of individual annual values (subtracting the mean and dividing by a standard deviation) were averaged. Analysis of the resulting time series showed that the single step in 1976, separating the 1968-1975 period from the 1977-1984 period, accounted for 89% of variance within the composite time series. Apparently, one of the Earth's large ecosystems occasionally undergoes large abrupt shifts.

Report on the 1994 juvenile salmon stocking study of Foxhouses and Grizedale Becks, River Wyre

The aim of this study was to assess the suitability of Foxhouses and Grizedale Becks as nursery habitat for juvenile salmon. A comprehensive fish stock assessment survey of the Wyre catchment was carried out by the NRA in 1992. This survey found that juvenile salmon were absent from two sites studied in Foxhouses Beck. In one site in Grizedale Beck, 0+ salmon were found at very low densities. Juvenile trout were found in all three sites studied in 1992. On the basis of the results of the 1992 survey, these two becks were stocked in 1994 with 0+ salmon reared from Lune broodstock at the NRA's Witcherwell Hatchery. These salmon were stocked at a known density, following a pre-stocking survey. This report examines and compares the results of the pre-stocking survey consisting of fourteen sites in the two becks, carried out between 12/04/94 and 27/04/94 and a post- stocking survey of six sites, carried out between 12/10/94 and 19/10/94. Flow, habitat and in-river obstructions have been shown to affect juvenile salmonid densities. A habitat description is provided for each site surveyed during the course of this study.

A working guide to the assessment, implementation and post project monitoring of fisheries habitat improvement schemes in South Cumbria

Due to changes in land use over the last century, the physical nature of many streams and rivers in the British Isles has probably changed. In some cases this change may be large for example as a result of flood defence schemes and is easily observed, whilst in other cases altered land use, farming, forestry or urbanization may have resulted in more subtle changes to river features. This working guide draws together a way of assessing habitat in any stream or river and determine sites or reaches on the assessed watercourse that may benefit from habitat improvement schemes. It will determine a method of measuring existing habitat in a broad sense, whilst referring to R and D studies currently being undertaken in this area. A method of prioritising any proposed habitat restoration work will be suggested. The limitations of fisheries improvement schemes in terms of cross functional acceptance (flood defence and conservation) will be examined along with suggested proposals for some example watercourses. The need for pre and post enhancement monitoring will be discussed as will the requirement for maintenance programs on schemes. Finally methods for determining the cost benefits of small schemes will be examined, compared to other currently used enhancement strategies. This will allow small scale revenue schemes to be used to back up pre project cost benefit analysis as required in future capital submissions.

Rivers Ribble and Hodder - habitat improvement

In order to improve the habitat of the Rivers Ribble and Hodder in the north west of England it is necessary to assess existing fish stocks. To assist the Ribble Fisheries Association a test census of stock has been made on the rivers Hodder and Ribble. The fish have been taken by electro fishing techniques. The following fish were collected over six days in September 1965: dace, chub, grayling, eel, salmon and trout. This short report summarises the findings of the survey.

River Wyre salmon action plan December 2003

In 1996 a Strategy for the Management of Salmon in England and Wales was launched by the National Rivers Authority setting out objectives for the management of Salmon fisheries. These objectives are to be met through local Salmon Action Plans which are to be produced for each of the 68 principal salmon rivers in England and Wales by December 2003. A consultation document was produced for the river Wyre and released publicly during October 2003. This document: • Determined an egg deposition figure of 1.27 million eggs which would allow maximum gain from the fisheries • Raised a number of issues which are though to limit existing salmon production. • Identified actions which may be undertaken by the Environment Agency and other bodies to improved stocks. The document looks at the issues in the consultation document and also highlights some important changes to historic egg deposition rates following further analysis of the data. Some of the major issues addressed in the plan are: • Severe low flows on specific tributaries • Reduced juvenile production caused by insufficient habitat. • Changes in flow regime resulting in the wash out of gravels and redds. • The impact of man made structures preventing access to suitable spawning areas, and preventing the downstream distribution of spawning gravels.

Effect of environmental conditions on the distribution of Pacific mackerel (Scomber japonicus) larvae in the California Current system

We modeled the probability of capturing Pacif ic mackerel (Scomber japonicus) larvae as a function of environmental variables for the Southern California Bight (SCB) most years from 1951 through 2008 and Mexican waters offshore of Baja California from 1951 through 1984. The model exhibited acceptable fit, as indicated by the area under a receiver-operating-characteristic curve of 0.80 but was inconsistent with the zero catches that occurred frequently in the 2000s. Two types of spawners overlapped spatially within the survey area: those that exhibited peak spawning during April in the SCB at about 15.5°C and a smaller group that exhibited peak spawning in August near Punta Eugenia, Mexico, at 20°C or greater. The SCB generally had greater zooplankton than Mexican waters but less appropriate (lower) geostrophic f lows. Mexican waters generally exhibited greater predicted habitat quality than the SCB in cold years. Predicted quality of the habitat in the SCB was greater from the 1980s to 2008 than in the earlier years of the survey primarily because temperatures and geostrophic flows were more appropriate for larvae. However, stock size the previous year had a larger effect on predictions than any environmental variable, indicating that larval Pacific mackerel did not fully occupy the suitable habitat during most years.

Distributions and abundances of Pacific sardine (Sardinops sagax) and other pelagic fishes in the California Current Ecosystem during spring 2006, 2008, and 2010, estimated from acoustic–trawl surveys

The abundances and distributions of coastal pelagic fish species in the California Current Ecosystem from San Diego to southern Vancouver Island, were estimated from combined acoustic and trawl surveys conducted in the spring of 2006, 2008, and 2010. Pacific sardine (Sardinops sagax), jack mackerel (Trachurus symmetricus), and Pacific mackerel (Scomber japonicus) were the dominant coastal pelagic fish species, in that order. Northern anchovy (Engraulis mordax) and Pacific herring (Clupea pallasii) were sampled only sporadically and therefore estimates for these species were unreliable. The estimates of sardine biomass compared well with those of the annual assessments and confirmed a declining trajectory of the “northern stock” since 2006. During the sampling period, the biomass of jack mackerel was stable or increasing, and that of Pacific mackerel was low and variable. The uncertainties in these estimates are mostly the result of spatial patchiness which increased from sardine to mackerels to anchovy and herring. Future surveys of coastal pelagic fish species in the California Current Ecosystem should benefit from adaptive sampling based on modeled habitat; increased echosounder and trawl sampling, particularly for the most patchy and nearshore species; and directed-trawl sampling for improved species identification and estimations of their acoustic target stren

Ontogenetic patterns and temperature-dependent growth rates in early life stages of Pacific cod (Gadus macrocephalus)

Pacific cod (Gadus macrocephalus) is an important component of fisheries and food webs in the North Pacific Ocean and Bering Sea. However, vital rates of early life stages of this species have yet to be described in detail. We determined the thermal sensitivity of growth rates of embryos, preflexion and postflexion larvae, and postsettlement juveniles. Growth rates (length and mass) at each ontogenetic stage were measured in three replicate tanks at four to five temperatures. Nonlinear regression was used to obtain parameters for independent stage-specific growth functions and a unified size- and temperature-dependent growth function. Specific growth rates increased with temperature at all stages and generally decreased with increases in body size. However, these analyses revealed a departure from a strict size-based allometry in growth patterns, as reduced growth rates were observed among preflexion larvae: the reduction in specific growth rate between embryos and free-swimming larvae was greater than expected based on body size differences. Growth reductions in the preflexion larvae appear to be associated with increased metabolic rates and the transition from endogenous to exogenous feeding. In future studies, experiments should be integrated across life transitions to more clearly define intrinsic ontogenetic and size-dependent growth patterns because these are critical for evaluations of spatial and temporal variation in habitat quality.

Growth and survival of sockeye salmon (Oncorhynchus nerka) from Karluk Lake and River, Alaska, in relation to climatic and oceanic regimes and indices, 1922–2000

We examined whether the relationship between climate and salmon production was linked through the effect of climate on the growth of sockeye salmon (Oncorhynchus nerka) at sea. Smolt length and juvenile, immature, and maturing growth rates were estimated from increments on scales of adult sockeye salmon that returned to the Karluk River and Lake system on Kodiak Island, Alaska, over 77 years, 1924–2000. Survival was higher during the warm climate regimes and lower during the cool regime. Growth was not correlated with survival, as estimated from the residuals of the Ricker stock-recruitment model. Juvenile growth was correlated with an atmospheric forcing index and immature growth was correlated with the amount of coastal precipitation, but the magnitude of winter and spring coastal downwelling in the Gulf of Alaska and the Pacific Northwest atmospheric patterns that influence the directional bifurcation of the Pacific Current were not related to the growth of Karluk sockeye salmon. However, indices of sea surface temperature, coastal precipitation, and atmospheric circulation in the eastern North Pacific were correlated with the survival of Karluk sockeye salmon. Winter and spring precipitation and atmospheric circulation are possible processes linking survival to climate variation in Karluk sockeye salmon.

Abundance, condition, and diet of juvenile Pacific ocean perch (Sebastes alutus) in the Aleutian Islands

T he relative value of pelagic habitat for three size classes of juvenile Pacific ocean perch (Sebastes alutus) was investigated by comparing their abundance and condition in two areas of the Aleutian Islands. Diet, zooplankton biomass, and water column temperatures were examined as potential factors affecting observed differences. Juvenile Pacific ocean perch abundance and condition, and zooplankton biomass varied significantly between areas, whereas juvenile Pacific ocean perch diet varied only by size class. Observed differences in fish condition may have been due to the quantity or quality of pelagic prey items consumed. For the delineation of essential demersal fish habitat, important ecological features of the pelagic habitat must therefore be considered.

Assessment of habitat quality for juvenile California halibut (Paralichthys californicus) in a seasonally arid estuary

We evaluated habitat quality for juvenile California halibut (Paralichthys californicus) in a Pacific Coast estuary lacking in strong salinity gradients by examining density, recent otolith growth rates, and gut fullness levels of wild-caught and caged juveniles for one year. Juveniles <200 mm standard length were caught consistently in the inner, central, and outer sections of the estuary. The density of juveniles was two times higher in the inner estuary during most of the year, consistent with active habitat selection by part of the population. A generalized linear model indicated temperature, sampling time, and the interaction between salinity and temperature were significantly related to density. However, the model explained only 21% of the variance. Gut fullness levels of wild-caught juveniles were highest during the summer, but recent otolith growth rates were not related to temperature. The proportion of individuals feeding successfully indicated that seasonal differences in food availability are more important than spatial variation in prey abundance in driving feeding success. Feeding success of caged fishes was limited, precluding the use of growth rates as indicators of local habitat quality. However, marginal increment widths were reliable indicators of somatic growth at low growth rates over two-week periods. The relatively high growth rates and abundance of small wild-caught juveniles found throughout the estuary indicates that the entire estuary system has the potential for serving as nursery habitat.

Spatial and seasonal relationships between Pacific harbor seals (Phoca vitulina richardii) and their prey, at multiple scales

Knowing where pinnipeds forage is vital to managing and protecting their populations, and for assessing potential interactions with fisheries. We assessed the spatial relationship between the seasonal distribution of Pacific harbor seals (Phoca vitulina richardii) outfitted with satellite transmitters and the seasonal distributions of potential harbor seal prey species in San Francisco Bay, California. Pearson’s correlation coefficients were calculated between the number of harbor seal locations in an area of the San Francisco Bay and the abundance of specific prey species in the same area. The influence of scale on the analyses was assessed by varying the scale of analysis from 1 to 10 km. There was consistency in the prey species targeted by harbor seals year-round, although there were seasonal differences between the most important prey species. The highest correlations between harbor seals and their prey were found for seasonally abundant benthic species, located within about 10 km of the primary haul-out site. Probable foraging habitat for harbor seals was identified, based on areas with high abundances of prey species that were strongly correlated with harbor seal distribution. With comparable local data inputs, this approach has potential application to pinniped management in other areas, and to decisions about the location of marine reserves designed to protect these species.

Ichthyoplankton community in the Columbia River plume off Oregon: effects of fluctuating oceanographic conditions

Ichthyoplankton samples were collected at approximately 2-week intervals, primarily during spring and summer 1999−2004, from two stations located 20 and 30 km from shore near the Columbia River, Oregon. Northern anchovy (Engraulis mordax) was the most abundant species collected, and was the primary species associated with summer upwelling conditions, but it showed significant interannual and seasonal fluctuations in abundance and occurrence. Other abundant taxa included sanddabs (Citharichthys spp.), English sole (Parophrys vetulus), and blacksmelts (Bathylagidae). Two-way cluster analysis revealed strong species associations based primarily on season (before or after the spring transition date). Ichthyoplankton abundances were compared to biological and environmental data, and egg and larvae abundances were found to be most correlated with sea surface temperature. The Pacific Decadal Oscillation changed sign (from negative to positive) in late 2002 and indicated overall warmer conditions in the North Pacific Ocean. Climate change is expected to alter ocean upwelling, temperatures, and Columbia River flows, and consequently fish eggs and larvae distributions and survival. Long-term research is needed to identify how ichthyoplankton and fish recruitment are affected by regional and largescale oceanographic proces

Abundance, distribution, and habitat of leatherback turtles (Dermochelys coriacea) off California, 1990−2003

Leatherback turtles (Dermochelys coriacea) are regularly seen off the U.S. West Coast, where they forage on jellyfish (Scyphomedusae) during summer and fall. Aerial line-transect surveys were conducted in neritic waters (<92 m depth) off central and northern California during 1990−2003, providing the first foraging population estimates for Pacific leatherback turtles. Males and females of about 1.1 to 2.1 m length were observed. Estimated abundance was linked to the Northern Oscillation Index and ranged from 12 (coefficient of variation [CV] =0.75) in 1995 to 379 (CV= 0.23) in 1990, averaging 178 (CV= 0.15). Greatest densities were found off central California, where oceanographic retention areas or upwelling shadows created favorable habitat for leatherback turtle prey. Results from independent telemetry studies have linked leatherback turtles off the U.S. West Coast to one of the two largest remaining Pacific breeding populations, at Jamursba Medi, Indonesia. Nearshore waters off California thus represent an important foraging region for the critically endangered Pacific leatherback turtle.