Salmonid distribution and abundance in the context of Elwha River dam removals

Removal of two dams on the Elwha River, Washington from 2011 to 2014 has begun to restore natural sediment processes to the coastal environment near the river mouth. Since 2006, we have been collecting data on shallow subtidal (nearshore) fish communities near the Elwha River and at reference sites in the Strait of Juan de Fuca to assess fish response to sediment changes resulting from dam removal. Juvenile salmon (Chinook, coho, pink and chum salmon) migrate through this region, which also supports ecologically important forage fish and endemic benthic fauna. Beach seine samples collected annually from April through September from over 20 sites span pre-removal, high impact (during dam removal), and post-removal years. Annual catches included 23,093 to 92,677 individuals from 45-55 species. Trends in species richness and abundance were variable over this time period. Forage fish dominated our catches followed by salmonids. In this analysis we explored patterns of juvenile salmonid abundance in relation to dam removal, environmental variables, site characteristics (including community composition), and year/season using a Bayesian hierarchical modeling framework and multivariate analyses. Chinook salmon show a tenfold variation in abundance over the years examined. Catches of Chinook and coho salmon were dominated by locally released hatchery fish with high variability between sampling sites. Throughout this region we have seen a marked decrease in coho salmon catches in recent years. Understanding what biotic and abiotic factors contribute most to this variability in salmon abundance and distribution may help tailor future dam removal processes or reframe management decisions

Armoring on Puget Sound: Progress towards a better baseline

The construction of seawalls and similar structures along Puget Sound’s shoreline impacts geomorphic processes and ecological functions. The extent of shoreline armor has been adopted by the Puget Sound Partnership as a vital sign indicator, is used by local, state, and federal groups as a measure of ecosystem function, and has been employed as a tool for prioritizing restoration actions. As a result, we recognized the importance of accurately characterizing the extent, character, and distribution of shoreline armor. The objectives of our project were to review existing data sources, assess methodologies, identify gaps in data quality or coverage, and to recommend steps for developing a reliable baseline for future monitoring and analyses. Previous efforts have suggested that approximately 27% of the region’s 4000 km of shoreline is armored, but our ability to answer important questions has been hampered by the quality and consistency of datasets, poorly documented methodologies, and the ability to relate armor with other shoreline information. In particular, we had difficulty associating armor with its geomorphic setting – bluffs and spits, small estuaries, river deltas, and artificial human landscapes – which greatly influences ecological impacts, management decisions, and restoration strategies. We noted the need for clear definitions and protocols for mapping and characterizing shoreline structures. Some attributes, such as condition and waterward extent, are ecologically important but difficult to measure. Environmentally friendlier soft or hybrid structures are particularly hard to identify and categorize. Our preliminary results provide a clearer picture of where armoring occurs and where there remain significant problems with data reliability and geographic consistency. We have begun a collaborative process to develop a high quality regional dataset of shoreline armor that will provide better understanding of the impacts of existing armor, a reliable baseline for assessing future change, and a tool to support prioritization for protection and restoration

Spatio-temporal variation in the nearshore forage fish community in the Strait of Juan de Fuca

Nearshore marine habitats in the Salish Sea support populations of many fish species including migrating juvenile salmon, benthic sculpins, and rearing and spawning forage fish. The Strait of Juan de Fuca (SJF) is critical as a corridor between the Pacific Ocean and inland water bodies. Though known to utilize this area, the population dynamics of ecologically important forage fish are poorly understood. Over 9 years of monthly beach seine sampling (April – September) at 24 sites along 70 km of coastline in the SJF, we have observed high variability in fish catch across years, sites, and seasons. Annual catches ranged from 23,093 to 92,677 individual fish divided among 45 to 55 species. Forage fish were represented by 9 species and were numerically the dominant group, accounting for 87.8% of the catch from all sampling areas combined. Three forage fish species dominated, thus warranting in-depth investigation: Pacific Herring (Clupea pallasii), Pacific Sand Lance (Ammodytes hexapterus), and Surf Smelt (Hypomesus pretiosus). Influence of individual species varied, yet drove the fish assemblage structure. We explored effects of temporal and spatial variability on forage fish occurrence, abundance, and community composition using descriptive statistics and a Bayesian hierarchical modeling framework. Additionally, the removal of two large dams on the adjacent Elwha River, which released stored sediment into our sampling area, provided us an opportunity to examine forage fish response to a localized habitat perturbation. Spatially, individual species may avoid regions of high perturbation but dramatic variations in distribution and abundance of the greater forage fish community are temporally driven by larger scale changes. Management plans directed at forage fish should take into consideration how variation in abundance at regional scales and consistent population responses to large-scale environmental fluctuations may drive forage fish populations over time

Applied Fisheries Oceanography: Ecosystem Indicators of Ocean Conditions Inform Fisheries Management in the California Current

Fisheries oceanography is the study of ecological relationships between fishes and the dynamics of their marine environments and aims to characterize the physical, chemical, and biological factors that affect the recruitment and abundance of harvested species. A recent push within the fisheries management community is toward ecosystem-based management. Here, we show how physical and biological oceanography data can be used to generate indicators of ocean conditions in an ecosystem context, and how these indicators relate to the recruitment of salmonids, sablefish, sardines, and rockfish in the California Current

Movements of sub-adult Chinook salmon, Oncorhynchus tshawytscha, in Puget Sound, Washington, as indicated by ultrasonic tracking

Salmonids show a wide variety of migration patterns. Such variation is especially prevalent in Chinook salmon, Oncorhynchus tshawytscha. This species migrates to coastal and open ocean waters, and the tendency to use these different marine environments varies markedly among populations. For example, some Chinook salmon that enter Puget Sound do not migrate to the sea as juveniles in their first year but rather remain as “residents” through (at least) the following Spring. Known locally as blackmouth, these fish are the focus of extensive sport fisheries. In this study, we used acoustic telemetry to examine questions surrounding resident Chinook salmon in Puget Sound. The overall objective of this study was to determine the extent to resident and migratory behavior patterns are distinct or ends of a continuum of movement patterns, and then characterize the movements of resident fish. We first assessed the proportion of fish, caught and tagged as immature residents (inferred from the locations and dates of capture), that remained within Puget Sound and the proportion that moved to the coastal region, and tested the hypotheses that origin (wild or hatchery), location and season of tagging, fish size and condition factor would influence the tendency to remain resident. Second, we characterized the movements by resident fish with Puget Sound at a series of different spatial scales: movement among the major basins, travel rates, and areas of concentration within Puget Sound. Third, we tested the model of seasonal north-south movement patterns by examining the distribution of detections over the whole area and year. Because residents represent a significant portion of the Puget Sound Chinook salmon Evolutionarily Significant Unit, currently listed as Threatened under the U. S. Endangered Species Act, better understanding of their movements in Puget Sound will help identify critical habitat use patterns and evaluate fishery management objectives as the species crosses jurisdictional boundaries

Trends in Developed Land Cover Adjacent to Habitat for Threatened Salmon in Puget Sound, Washington, U.S.A.

For widely distributed species at risk, such as Pacific salmon (Oncorhynchus spp.), habitat monitoring is both essential and challenging. Only recently have widespread monitoring programs been implemented for salmon habitat in the Pacific Northwest. Remote sensing data, such as Landsat images, are therefore a useful way to evaluate trends prior to the advent of species-specific habitat monitoring programs. We used annual (1986-2008) land cover maps created from Landsat images via automated algorithms (LandTrendr) to evaluate trends in developed (50-100% impervious) land cover in areas adjacent to five types of habitat utilized by Chinook salmon (O. tshawytscha) in the Puget Sound region of Washington State, U.S.A. For the region as a whole, we found significant increases in developed land cover adjacent to each of the habitat types evaluated (nearshore, estuary, mainstem channel, tributary channel, and floodplain), but the increases were small (<1% total increase from 1986 to 2008). For each habitat type, the increasing trend changed during the time series. In nearshore, mainstem, and floodplain areas, the rate of increase in developed land cover slowed in the latter portion of the time series, while the opposite occurred in estuary and tributary areas. Watersheds that were already highly developed in 1986 tended to have higher rates of development than initially less developed watersheds. Overall, our results suggest that developed land cover in areas adjacent to Puget Sound salmon habitat has increased only slightly since 1986 and that the rate of change has slowed near some key habitat types, although this has occurred within the context of a degraded baseline condition

Ultrasonic Telemetry Reveals Seasonal Variation in Depth Distribution and Diel Vertical Migrations of Sub-Adult Chinook and Coho Salmon in Puget Sound

Seasonal and diel vertical movement (DVM) patterns in aquatic systems have been well documented for many aquatic organisms but little is known about salmon distributions in marine waters. In this study, we examined the vertical distributions of sub-adult coho and Chinook salmon in Puget Sound using acoustic telemetry to: 1) compare the depths occupied by the two species, 2) determine whether either species displayed DVM, and if these patterns differed between the two species, and 3) ascertain if changes in depth distributions changed seasonally. To evaluate these objectives, we tagged coho and Chinook salmon in Puget Sound from 2005-2012 with ultrasonic transmitters that positioned the fish in three dimensions in the water column. Detections were compiled from a set of receivers located throughout Puget Sound. We modeled data on individual fish depths as a function of species, time of day, and time of year, considering both the proximity of the fish to the surface and to the bottom. Results indicated that the salmon species differed in average depth and also in the seasonal and diel patterns. The mean depth of Chinook (40.6 m) was deeper than coho (28.3 m). Coho exhibited diel movements during the spring with fish deeper at night (often to 100 m) and closer to the surface (6.6 -21.8 m) during the day (a pattern opposite of DVM reported for other organisms), but this pattern disappeared during other times of the year. Chinook salmon showed less pronounced diel movement, and were shallowest in June (23.6 m), moving deeper each month until a maximum in October (64.7 m). Depth distributions of salmon were complex and changed dramatically between seasons and may be a result of several physical and biological factors. Combined with data on environmental conditions in the water column throughout the year, these results provide new insights into how and why salmon are vertically distributed within Puget Sound

Evaluating Responses of Nearshore Fish to Removal of the Elwha River Dams

Removal of two dams on the Elwha River began in late 2011 and will restore sediment processes in the near coastal environment adjacent to the river\u27s mouth. Since 2005, we have been collecting data on intertidal/sub-tidal fish communities near the mouth of the River where we expect sediment changes to occur. We have also sampled in reference areas. Samples were collected by beach seining in the spring and summer. Our primary objective has been to determine if attributes of the nearshore fish community (notably species assemblage structure and size distribution) changed in response to sediment restoration. Potential shifts in fish assemblage structure and size distribution of ecologically important species such as forage fish and juvenile salmon are of particular interest because sediment changes will likely be significant in these intertidal and sub-tidal habitats. Trends in species richness and abundance were consistent prior to and following dam removal (2012 is thus far the only year where we have post dam removal information) with reference areas generally possessing more species and a greater overall abundance of fish than treatment areas. Forage fish were the numerically dominate species group in all areas. Using multivariate analysis, we found considerable overlap in fish community composition between years but there was some separation in fish assemblage structure between the different areas prior to dam removal. Regional differences were primarily a result of several forage fish species (notably Pacific sandlance, and surf smelt) and juvenile salmonid species (notably chum salmon). There were also seasonal differences in all regions with salmonids and forage fish the dominate fish in the spring and flatfish, sculpins, perch, and greenlings the primary species occurring in summer. Inclusion of post-dam removal data from 2012 did not significantly change these observed patterns. We plan to continue monitoring in the future. However, our ability to detect responses of fish communities to sediment changes will ultimately depend on both biotic factors (such as species and life stages being considered) and abiotic factors, such as when sediment reaches the coastal environment; the quantity, composition and distribution of the material that reaches the Salish Sea; and how long it takes material to distribute from the river’s mouth