Migration and Residence Patterns of Salmonids in Puget Sound, Washington

Thesis (Ph.D.)--University of Washington, 2016-08Diadromy is an unusual but widely distributed form of migration in fishes, and thus understanding these fishes requires a full knowledge of their behavior in both marine and freshwater environments. Freshwater ecology is easier to study and so our understanding is more advanced compared to our understanding of their marine ecology. This dissertation was focused on anadromous salmonids that were hypothesized to express a range of marine migration patterns from estuarine resident to ocean-bound migrants, in a suite of species native to Puget Sound: steelhead trout (Oncorhynchus mykiss), coastal cutthroat trout (O. clarkii clarkii), bull trout (Salvelinus confluentus), and Chinook salmon (O. tshawytscha). The study results will help inform a general model of the marine migrations of these salmonids within the Puget Sound. The study is organized into chapters by species. Abstracts for each chapter are described below. This dissertation describes the movements of individual anadromous salmonids of four species to determine the extent to which migration patterns vary among the species, populations and marine sub-basins within Puget Sound. The study took a comparative approach between species and was part of a larger suite of studies that investigated 1) marine migrations of ocean-bound stream-type fish (steelhead); 2) marine distribution, residency, and movement of resident and semi-resident pelagic species (Chinook and coho salmon, conducted by other researchers and reported in other publications); 3) movement and habitat use of two different estuarine and nearshore resident species (cutthroat and bull trout); and 4) movement and habitat use in estuarine and freshwater areas by maturing pelagic species (Chinook and sockeye salmon). Enhanced understanding of marine migrations and habitat use by anadromous salmonids is necessary for their conservation. The Puget Sound’s estuaries and shorelines have been affected in many ways by human actions including industrial and agricultural development of estuaries, construction of docks and marinas, and armoring of beaches. The tendency for salmonids to use these estuarine and marine habitats may cause their populations to decline if preferred habitats are degraded or lost. Information on movements and habitat use patterns is an essential component of conservation plans for these species and provides important links to species that prey on salmon, notably killer whales and other marine mammals. Three species considered in this study are listed as threatened under the Endangered Species Act; information on their life history and habitat use will provide essential information to sustain and recover Puget Sound populations. The study resulted in collaborative relationships between tribes, agencies and sporting groups acting as a nexus for organizations interested in research needed to manage Puget Sound salmonids. The results fostered research in other areas that will be useful for generating an understanding of marine life histories elsewhere. Comparative migratory behavior and survival of wild and hatchery steelhead (Oncorhynchus mykiss) smolts in riverine, estuarine, and marine habitats of Puget Sound, Washington Declines in the survival of steelhead (Oncorhynchus mykiss) populations in protected waters of Washington and British Columbia have drawn attention to the need for more information on migratory patterns and losses in river, estuary, and nearshore habitats. Accordingly, acoustic telemetry was used to quantify movements by wild and hatchery steelhead smolts released from 2006-2009 in the Green River, and tracked through Puget Sound, Washington. Survival varied by release group and migration segment but overall survival rates from release to the Strait of Juan de Fuca were 9.7% for wild and 3.6% for hatchery fish. These rates are low relative to similar studies on steelhead. Survival was higher for wild fish along all migration segments than hatchery-origin fish; the greatest loss for both groups coincided with the slowest travel rates as fish first entered the estuary and as they exited Puget Sound. Wild fish travelled faster than hatchery fish in the river (15.1 vs. 4.4 km/d) with the fastest travel in the lower river (41 vs. 20.2 km/d) and slowest immediately after release (3.7 vs. 2.4 km/d). The travel rates of wild and hatchery fish became progressively more similar over time: 15.4 vs. 10.6 km/d in the estuary, and 10.3 vs. 9.3 km/d in nearshore areas. Movement was primarily nocturnal in the river, nearly equal between day and night in the upper estuary, and predominately diurnal in the lower estuary and nearshore waters, with no difference between wild and hatchery fish. The migration in marine water showed an early offshore movement and a strong northward and westward orientation, and all fish exited the Strait of Juan de Fuca rather than the Strait of Georgia. The findings support research suggesting that declines in wild and hatchery steelhead populations may be caused primarily by factors in the early marine period. Diversity of movements by individual anadromous coastal cutthroat trout in Hood Canal, Washington Wild, downstream-migrating cutthroat trout, Oncorhynchus clarkii clarkii, smolts and adults were captured at a weir in Big Beef Creek, Hood Canal, Washington, surgically implanted with acoustic tags and tracked to identify spring and summer movements using stationary receivers to test the assumption that the species moves little while in marine waters. Overall, 93-96% migrated from the stream into the east side of the long narrow fjord, where they dispersed north and south along the shoreline. Most O. clarkii clarkii were detected near shore within 10 km of the release site, with declining detection rates to 77 km. Over one third (36%) crossed ~ 2-4 km of deep water to the other side but only one O. clarkii clarkii left the Hood Canal basin. Movements and behaviour patterns did not differ between smolts and adults but cluster analysis revealed two modes of distribution, here categorized as residents and migrants. Within these categories of overall distribution, a range of finer-scale behaviour patterns was observed, including sedentary individuals, daily “commuting” between proximate sites, and more continuous long-distance travel. Diel movement patterns varied markedly among individuals but overall activity increased near dawn, peaked around mid-day, and declined but continued at night. These patterns contrast with sympatric and closely related steelhead trout, O. mykiss, providing new insights into the diversity of trout behaviour Migrations of anadromous bull trout in estuarine and marine waters of Puget Sound, Washington: Thermal constraints on foraging opportunities Anadromous fishes migrate to sea to take advantage of superior opportunities for foraging and growth compared to less productive freshwater habitats but the species vary greatly in the temporal duration and spatial extent of marine migrations. Char, Salvelinus spp., characteristically display short migrations and it has been hypothesized that thermal constraints may affect migration timing. Our objective was to study the timing, period of marine residence, and major habitats occupied by anadromous bull trout, S. confluentus, during their migrations to and from Puget Sound, Washington. We predicted that bull trout would have a well-defined period of estuary and marine habitation and that fish would undertake “premature migrations” back to freshwater in early summer to avoid rising temperatures, prior to spawning in the fall. We used a combination of traps and beach seining to capture juveniles and adults, and acoustic telemetry to quantify movements in river, estuary, and marine waters in relation to thermal regimes. The overall period of marine residence was similar among fish from different river basins and life stages; larger bull trout entered marine waters in late winter-early spring, juveniles in late spring, and most fish migrated back into rivers by late spring-early summer as temperatures were increasing. However, the timing of return migration was similar among rivers despite differences in their thermal regimes. Some fish entered and exited the rivers in the fall but few overwintered in marine areas. Most fish occupied estuary and nearshore areas near natal rivers but some moved over 100 km from the river mouth. These timing patterns and use of marine habitats contrast strongly with those of other salmonids in Puget Sound, revealing the diversity in migratory behavior under the broad category of anadromy, and emphasizing the importance of estuarine and nearshore habitats for the conservation of bull trout, listed as Threatened under the U. S. Endangered Species Act. Behavioral thermoregulation by adult Chinook salmon (Oncorhynchus tshawytscha) and comparison to sockeye salmon (O. nerka) in estuary and freshwater habitats prior to spawning The movements and thermal experience of Pacific salmon during their homeward migration through marine waters and into freshwater systems pose challenges for their physiology, especially in river basins altered by human structures and activities, and under regimes of increasingly high temperatures. This study determined the thermal regimes experienced by maturing Chinook salmon, Oncorhynchus tshawytscha, entering the Lake Washington basin via a navigational locks and canal, and migrating through the lake to spawning grounds or hatcheries. We then compared these patterns, determined from a combination of acoustic tracking and temperature loggers attached to the fish, with comparable data on sockeye salmon collected in an independent study in overlapping years. Chinook salmon exhibited complex patterns, occupying cool water refuges in stratified marine and freshwater areas: 1) in Puget Sound (28-30 ppt, 12-15 oC), 2) in deeper water in the salt wedge (upper estuary) above the locks (12-15 ppt, 18-21 oC), and 3) intermittently in deeper fresh water in Lake Washington (9-21 oC). Most Chinook salmon (> 75%) left the estuary after tagging and spent a short period (mean 4.6 d) in Puget Sound). Upon return to the upper estuary Chinook salmon either held in a small, cool area in the salt wedge (mean 11.1 d) or went back to Puget Sound twice to hold in tidally influenced saltwater. Sockeye salmon exhibited a fairly simple migration pattern, holding for a short period in warm water (median 18.4 oC) in the upper estuary and canal (mean 3.6 d), then migrating to the lake and residing in cold-water areas (mean 10.3 oC) at depths of 40 m (mean 88.3 d). Sockeye and Chinook salmon travelled through a 10.8 km canal to Lake Washington in relatively short periods, 2 d and 0.5 d (mean) respectively, but Chinook salmon experienced higher temperatures (20-22.5 oC) because they migrated later in summer. In Lake Washington Chinook salmon exhibited vertical migrations above and below the thermocline and used the lake as a thermal refuge to a lesser extent than did sockeye salmon, which remained below the thermocline almost exclusively until they ascended rivers to spawn. Individual fish utilized different migration paths and so had distinct thermal experiences but survived to reach breeding sites. The ability to exploit multiple refuges in this highly modified migratory corridor may be essential for the persistence of these species and especially the Chinook salmon. In the face of climate change, understanding how fish use available thermal refuges may help identify management alternatives to retain or increase these areas in the future