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The timing of anadromous migrations varies greatly among species, reflecting foraging opportunities, predation risk, and physical factors in freshwater and marine habitats. We studied the timing of bull trout, Salvelinus. confluentus, migrations downstream into Puget Sound, Washington, and the return migration using data from a combination of traps and beach seining to capture juveniles and adults, and acoustic telemetry to quantify movements in river, estuary, and marine waters. The period of marine residence overlapped among fish from different river basins and was generally brief; most bull trout entered marine waters from April to June and migrated back into rivers by July and August as temperatures were increasing, despite the increasing availability of prey fishes. The timing of return migration upriver occurred earlier in rivers with warmer temperatures than in cooler rivers, such that the fish entered at similar temperatures but different dates. However, the trapping and acoustic tag detections indicated that some exceptions occur, as individuals were in marine waters at times of the year when most of their populations were upriver. These timing patterns and other complex migration pathways and life history patterns indicated by the combination of sampling techniques, revealed the diversity in migratory behavior in this species, and the connections to the region’s abiotic and biotic conditions.

Species of conservation interest are often rare or elusive, and often require labor-intensive population surveys for management. Sampling genetic traces of such species from environmental media such as water, air, or soil (environmental DNA; eDNA) can provide noninvasive and cost-effective means of monitoring. However, eDNA results may not align with traditional survey methods (e.g., visual, net) making it difficult to interpret eDNA results. We present the results of parallel beach seine and quantitative-PCR (qPCR) surveys of a threatened Chinook salmon (Oncorhynchus tshawytscha) from Skagit Bay, an estuary in Washington, USA. Our replicated design and hierarchical statistical model assesses the abundance, biomass, and DNA concentration at two spatial scales (site- and population-) over five months. We find both eDNA- and seine-derived abundance indices reflect the seasonal migration of salmon; at the population-scale, eDNA and seines provide virtually identical quantitative information. At the site scale, the methods are less correlated, suggesting the methods reveal different information about a patchily distributed species. Environmental DNA may act to smooth otherwise patchy biological signals in space and time. Reduced within-site variability for eDNA relative to seines suggests that eDNA may offer more precise population estimates. We partition sources of variability in space and time and compare eDNA and seine surveys – a first, to our knowledge – and so reveal the behavior of eDNA in the field. Our results underscore the value of using eDNA in conjunction with traditional surveys. Combining eDNA and seine estimates should improve the population data on which management of threatened species depends.

To identify potential actions for conserving Chinook Salmon Oncorhynchus tshawytscha in the Skagit River, Washington, we used a 16-year time series of streamflow data, adult escapement, and out-migrant abundance to understand how out-migrant abundance and life history diversity were related to spawner abundance and incubation flows. Three freshwater rearing strategies were distinguished based on body size at out-migration: fry (≤45 mm FL), subyearling parr (46–100 mm FL), and yearling smolts (>100 mm FL). Density-independent and density-dependent processes were hypothesized to influence survival in sequence, with density-independent mechanisms operating during incubation and density-dependent mechanisms operating between emergence and out-migration. A model selection process compared spawner–recruit models with and without different incubation flow metrics. Density-independent models that included measures of flow duration and magnitude were strongly supported (Akaike's information criterion [AIC] difference ≤ 3). Sustained flow events of moderate magnitude (1-year recurrence interval) were an equivalent if not better predictor of freshwater survival than short-duration flow events of high magnitude (peak flows). A second model selection process evaluated density dependence of each life history type. The composition of out-migrants (fry, subyearling parr, and yearling smolts) was a density-dependent function of spawner abundance. Fry out-migrant abundance was density independent, and subyearling parr out-migrant abundance was density dependent. Neither model was supported for yearling smolts. At least one out-migrant life history, subyearling parr, should benefit from continued restoration of freshwater habitats in the Skagit River system. Factors contributing to the yearling smolt life history will benefit from additional study.Received October 12, 2014; accepted February 3, 2015

This study focuses on the use by juvenile Chinook salmon Oncorhynchus tshawytscha of the rarely studied neritic environment (surface waters overlaying the sublittoral zone) in greater Puget Sound. Juvenile Chinook salmon inhabit the sound from their late estuarine residence and early marine transition to their first year at sea. We measured the density, origin, and size of marked (known hatchery) and unmarked (majority naturally spawned) juveniles by means of monthly surface trawls at six river mouth estuaries in Puget Sound and the areas in between. Juvenile Chinook salmon were present in all months sampled (April–November). Unmarked fish in the northern portion of the study area showed broader seasonal distributions of density than did either marked fish in all areas or unmarked fish in the central and southern portions of the sound. Despite these temporal differences, the densities of marked fish appeared to drive most of the total density estimates across space and time. Genetic analysis and ...

We examined existing smolt trapping data from 30 constructed and natural floodplain habitats to determine whether the number (production), density, and length of coho salmon Oncorhynchus kisutch smolts varied by project type and area. At 13 of the 30 sites we conducted detailed physical surveys to examine how morphology (shoreline irregularity), depth, and cover influenced smolt density and length. Mean smolt production for all sites averaged 2,492, density 0.37 smolts/m2, and length 98.9 mm. We found no significant difference in smolt production or density between natural and constructed sites or among project types. Smolt length differed by project type and morphology, excavated ponds (gravel pits and mill ponds) producing significantly larger smolts than constructed groundwater or natural channels. Smolt production was positively correlated with wetted area. Smolt length was negatively correlated with density and distance from salt water, suggesting that sites further inland with cooler water ...

Incorporating parameter uncertainty into a Monte Carlo procedure for estimating spawning habitat capacity helped determine that spawning habitat availability is unlikely to limit recovery of six populations of Chinook salmon (Oncorhynchus tshawytscha) in Puget Sound. Spawner capacity estimates spanned up to four orders of magnitude, yet there was virtually no overlap of distributions of capacity estimates with distributions of current spawner abundance (

We predicted 22 years of return rates for wild Chinook salmon Oncorhynchus tshawytscha as a function of environmental conditions experienced during residency in freshwater, tidal delta, bay, and ocean habitats as well as as an indicator of density dependence (based on egg production) across life stages. The best predictors of return rate included the magnitude of floods experienced during incubation, a principal components factor describing environmental conditions during bay residency, a similar factor describing conditions experienced during the third ocean year, and an estimate of egg production. Our models explained up to 90% of the variation in return rate and had a very high forecasting precision, yet environmental conditions experienced during ocean residency explained only 5% of the variation. Our results suggest that returns of wild Chinook salmon can be predicted with high precision by incorporating habitat residency and that freshwater and nearshore environmental conditions strongly in...

We describe six habitat types for large rivers (>100 m bank-full width), including pools, riffles, and glides in midchannel and bank edges, bar edges, and backwaters along channel margins. Midchannel units were deeper and faster than edge units on average. Among edge habitat types, backwater units had the lowest velocities and contained complex cover consisting mainly of wood accumulations and aquatic plants. Banks and bars had similar velocity distributions, but banks had more complex cover such as rootwads and debris jams. Because sampling of juvenile salmonids was ineffective in the midchannel units (electrofishing capture efficiency was low, and the units were too deep and fast to snorkel), we focused our sampling efforts on juvenile salmonid use of edge habitats during winter, spring, and late summer. Densities of juvenile Chinook salmon Oncorhynchus tshawytscha and coho salmon O. kisutch were highest in bank and backwater units in winter, whereas age-0 and age-1 or older steelhead densities...

Consideration of fundamental channel processes, together with map-based and field investigations, indicates that stream channel type influences salmonid spawning distributions across entire channel networks and salmonid abundance within channel reaches. Our analysis suggests that salmonid spawning patterns in mountain drainage basins of the Pacific Northwest are adapted to, among other things, the timing and depth of channel bed mobility. We hypothesize that because the bed of pool-riffle and plane-bed reaches scours to a variable fraction of the thickness of alluvium, survival to emergence is favored by either burying eggs below the annual scour depth or avoiding egg burial during times of likely bed mobility. Conversely, annual mobility of all available spawning gravel in steeper step-pool and cascade channels favors either adaptations that avoid egg burial during times of likely bed mobility or selection of protected microhabitats. Consistent with these expectations, we find that salmonid spawning distributions track channel slope distributions in several west-slope Pacific Northwest watersheds, implying that spatial differences in channel processes influence community structure in these rainfall-dominated drainage basins. More detailed field surveys confirm that different channel types host differential use by spawning salmonids and reveal finer-scale influences of pool spacing on salmonid abundance.

To develop a habitat restoration strategy for the 8,270-km2 Skagit River basin, we estimated changes in smolt production of coho salmon Oncorhynchus kisutch since European settlement began in the basin, based on changes in summer and winter rearing habitat areas. We assessed changes in coho salmon smolt production by habitat type and by cause of habitat alteration. We estimated that the coho salmon smolt production capacity of summer habitats in the Skagit River basin has been reduced from 1.28 million smolts to 0.98 million smolts (–24%) and that the production capacity of winter habitats has been reduced from 1.77 million to 1.17 million smolts (–34%). The largest proportion of summer non-main-stem habitat losses has occurred in side-channel sloughs (41%), followed by losses in small tributaries (31%) and distributary sloughs (29%). The largest loss of winter habitats has occurred in side-channel sloughs (52%), followed by losses in distributary sloughs (37%) and small tributaries (11%). By typ...