ObjectiveThe Redeye Bass Micropterus coosae is a piscivore introduced into California, which has become a threat to the state's endemic freshwater fishes. It has eliminated native fishes from the middle reaches of the Cosumnes River, our study stream, which is the largest stream without a major dam on its main stem in the Sacramento-San Joaquin River drainage, central California, USA. We thoroughly documented its novel life history and ecology in California to shed light on why it has been such a successful invader despite its relatively small native range.MethodsOver 4000 stable carbon and nitrogen isotope samples were utilized to refine our understanding of fish trophic position within the river food web, along with a stable isotope mixing model that accounts for uncertainty in trophic enrichment data.ResultGrowth was slow, with an adult size range of 9-25 cm standard length (SL), although few were larger than 15-cm SL (5-6 years old). Stable isotope analyses showed that Redeye Bass dominate the river ecosystem to the exclusion of most native fishes, occupying multiple trophic levels and microhabitats. Adults largely consumed non-native crayfish and large aquatic insects, while juveniles consumed aquatic insects, the size of prey increasing with Redeye Bass length. There was no evidence of cannibalism. Redeye Bass have effectively occupied the diverse trophic positions of at least four native fish species and have altered the trophic position of Rainbow Trout Oncorhynchus mykiss in sites where they co-occur with bass.ConclusionThe introduction of Redeye Bass poses a continuing threat to native stream fishes in California and elsewhere. The Redeye Bass is a predatory fish that is endemic to the Coosa River system, spanning Georgia and Alabama, in the southeastern United States, but introduced into California. It now dominates a California river ecosystem, eliminating native fishes and simplifying the food web. Its success demonstrates the unintended consequences of introducing even fish with a small native range into a region with an already stressed native fish fauna.

The removal of two large dams on the Elwha River was completed in 2014 with a goal of restoring anadromous salmonid populations. Using observations from ongoing field studies, we compiled a timeline of migratory fish passage upstream of each dam. We also used spatially continuous snorkeling surveys in consecutive years before (2007, 2008) and after (2018, 2019) dam removal during summer baseflow to assess changes in fish distribution and density over 65 km of the mainstem Elwha River. Before dam removal, anadromous fishes were limited to the 7.9 km section of river downstream of Elwha Dam, potamodromous species could not migrate throughout the river system, and resident trout were the most abundant species. After dam removal, there was rapid passage into areas upstream of Elwha Dam, with 8 anadromous species (Chinook, Coho, Sockeye, Pink, Chum, Winter Steelhead, Summer Steelhead, Pacific Lamprey, and Bull Trout) observed within 2.5 years. All of these runs except Chum Salmon were also observed in upper Elwha upstream of Glines Canyon Dam within 5 years. The spatial extent of fish passage by adult Chinook Salmon and Summer Steelhead increased by 50 km and 60 km, respectively, after dam removal. Adult Chinook Salmon densities in some previously inaccessible reaches in the middle section of the river exceeded the highest densities observed in the lower section of the river prior to dam removal. The large number (>100) of adult Summer Steelhead in the upper river after dam removal was notable because it was among the rarest anadromous species in the Elwha River prior to dam removal. The spatial extent of trout and Bull Trout remained unchanged after dam removal, but their total abundance increased and their highest densities shifted from the lower 25 km of the river to the upper 40 km. Our results show that reconnecting the Elwha River through dam removal provided fish access to portions of the watershed that had been blocked for nearly a century.

Our study describes newly discovered spawning and rearing habitats of Longfin Smelt (Spirinchus thaleichthys) in brackish tidal wetlands near Silicon Valley, California. The Longfin Smelt is a threatened estuarine forage fish native to the San Francisco Estuary. Prior to our observations, it was not known that Longfin Smelt utilized and spawned in these brackish tidal marshes, likely because such habitats are often understudied and highly degraded. Our results suggest that a more comprehensive assessment of the ecological niche of Longfin Smelt is needed in order to assess their habitat needs and population dynamics. Photo credit: Levi Lewis. Photo credit: Levi Lewis. Photo credit: Levi Lewis. Photo credit: Levi Lewis. Photo credit: Levi Lewis. These photographs illustrate the article “Newly discovered spawning and recruitment of threatened Longfin Smelt in restored and under-explored tidal wetlands” by Levi S. Lewis, Malte Willmes, Arthur Barros, Patrick K. Crain, and James A. Hobbs published in Ecology. https​://doi.org/10.1002/ecy.2868

A comprehensive understanding of the life-history strategies and habitat use of species is essential for developing accurate ecological models and effective management and conservation strategies. For example, omitting critical habitats of endangered species when estimating their abundance and when designing conservation plans can severely limit our understanding of population dynamics and lead to poor management outcomes. Here we describe important new observations of the distribution and habitat use of Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary, California, USA. Longfin Smelt are planktivorous forage fish found in estuarine and coastal waters from San Francisco Bay, California to the Aleutian Islands, Alaska (Garwood 2017). This species was once a dominant forage fish in the estuary, even supporting a small commercial fishery prior to the 1970s (Skinner 1962, Moyle 2002); however, this genetically distinct population has collapsed to approximately 1% of its historic (pre-1980) abundance, and details regarding its life history and drivers of population dynamics remain uncertain (Nobriga and Rosenfield 2016). Longfin Smelt are thought to live for 1–2 yrs in the coastal Pacific Ocean before returning to tidal freshwater habitats of the Sacramento–San Joaquin Delta ("upper estuary"), where they are believed to spawn (Moyle 2002, Rosenfield and Baxter 2007; Fig. 1a). Though the San Francisco Estuary is a well-studied system, long-term fishery surveys were designed for other species (e.g., striped bass); thus population models for Longfin Smelt have depended largely on data from the upper estuary and open-water bay habitats. Targeted studies are needed to assess whether existing data sets and resultant models accurately describe Longfin Smelt distributions, behaviors, and population dynamics. For example, a recent study observed high densities of Longfin Smelt larvae in previously unsampled wetland habitats in the upper estuary (Grimaldo et al. 2017). Similarly, it has been hypothesized that Longfin Smelt may also inhabit shallow tidal wetlands of the many smaller watersheds throughout San Francisco Bay and San Pablo Bay for spawning, rearing, and feeding (Fig. 1b). From October through April, which encompasses the spawning season, and in all years from 2011 to 2019, we observed persistent and occasionally dense aggregations of adult Longfin Smelt in marshes and sloughs of the Coyote Creek watershed in the southernmost part of San Francisco Bay (Figs. 1b, 2a,b). Many of the adults were in late-stage spawning condition and expressed eggs and milt upon capture (Fig. 2c). Postlarval recruits (Fig. 2d) were also observed in April–May of 2017 and 2019, with each of these years characterized by anomalously high precipitation and freshwater outflow (and persistent low-salinity spawning and rearing habitat). Thus, the potential for spawning was apparent in all years, whereas recruitment success appeared to be limited by freshwater outflow, as has been described for Longfin Smelt in the upper estuary (Kimmerer 2002, Nobriga and Rosenfield 2016). The highest catches of recruits and adults were often within shallow recently restored tidal marshes and adjacent sloughs (Fig. 2a), suggesting that (1) previous surveys have likely omitted substantial fractions of the San Francisco Estuary Longfin Smelt population and (2) that tidal marsh restoration may benefit all life stages of this threatened species. Surveys were conducted monthly from 2011 to 2019 at 2–3 m depth in marsh and slough habitats of the lower Coyote Creek watershed, including two restored tidal marshes and two open-water bay stations. The Coyote Creek watershed of South San Francisco Bay drains much of Silicon Valley and feeds directly into the Alviso Marsh Complex—a macrotidal Mediterranean-type estuary with a 4-m tidal range that is composed of several major tidal sloughs (Upper and Lower Coyote Creek, Alviso Slough, and Artesian Slough) networked throughout historically expansive salt marsh habitats. Sampling was conducted by towing an otter trawl with a 4.3 × 1.5 m opening and 0.6-cm cod end mesh into the current at 3 km/h for 5–10 min and counting the number of fish in each tow. High abundances of Longfin Smelt were unexpected in these habitats, let alone evidence for successful spawning and recruitment. Most of the historic wetland habitats in the region were dredged, diked, and converted to solar evaporation ponds for salt production in the mid-1900s (Nichols et al. 1986) and little freshwater runoff reaches the estuary because of numerous upstream dams and diversions that capture and redirect most instream flows for human use (Grossinger et al. 2007). Alviso Marsh also receives over 100 million gallons per day of low-salinity, warm, and nutrient-rich wastewater effluent directly into its sloughs (San Jose–Santa Clara Regional Wastewater Facility [SJSCRWF] 2018). Historically, there has been little interest in studying ecological communities in this highly degraded ecosystem. However, recent commitments to restore 15,000 acres of wetland habitat in the region (Valoppi 2018) have provided the motivation to establish baselines and document changes in aquatic communities in response to restoration efforts over the past decade. Surprisingly, our observations suggest that Longfin Smelt are relatively abundant and can successfully spawn and rear in wetlands of South San Francisco Bay, and that restoration of marsh habitats and increases in freshwater outflow to these smaller watersheds could benefit this threatened species. How important are brackish wetland habitats to Longfin Smelt? To answer this, future studies should build upon these observations, expanding the geographic scope of sampling to encompass other brackish marshes and sloughs, and assessing the relative importance of these habitats to the adult population. Estuary-wide sampling of brackish wetland habitats should be conducted during spawning and recruitment periods and in years with different precipitation, temperature, and other climate parameters. Multiple gear types should be deployed to quantify both larval and adult abundances, and methods should match or be calibrated against long-term monitoring programs so that relative contributions can be directly compared among habitat types and regions. Future modeling efforts could assess sensitivity and elasticity of population dynamics to production and survival of young-of-the-year age classes in different regions and habitats of the estuary. Can tidal marsh and watershed restoration benefit Longfin Smelt? To address this, it is important to quantify the conservation value of tidal marsh habitats to Longfin Smelt. Comparative studies of abundance, feeding rates, growth rates, diets, and mortality rates of Longfin Smelt in marshes versus open-water habitats would be valuable. Trace-element chemistry of otoliths (fish ear bones) could be used to quantify the relative contributions of different regions and habitat types to adult Longfin Smelt populations (Hobbs et al. 2007). Isotopes of Sr and O in otoliths can be used to reconstruct time-resolved histories of salinity, providing key information about habitat requirements and ontogenetic movement patterns and behaviors (Hobbs et al. 2010). Additional chemical tools (e.g., δ34S and Mn) could prove useful for reconstructing the use of wetland versus open-water habitats by Longfin Smelt. Longfin Smelt are at record low abundance and likely no longer serve their historic ecological function in the San Francisco Estuary. The population was listed as "threatened" in 2009 under the California Endangered Species Act (CESA) and designated as "warranted but precluded" for listing in 2012 under the federal Endangered Species Act (ESA). For 7 years, the species has remained precluded from ESA protections despite rapid and continuous declines in abundance. In the face of numerous ecological impacts, a warming climate (Cloern et al. 2011, Jeffries et al. 2016), and precluded protection, the future of longfin smelt remains bleak in the estuary (Hobbs et al. 2017). For nine consecutive years, however, we have observed previously undescribed aggregations of Longfin Smelt that were attempting to spawn in restored and under-explored tidal wetlands of South San Francisco Bay. Furthermore, we observed successful recruitment in years of high freshwater outflow. These observations may help explain the positive recruitment–freshwater outflow relationship and long-term decline of Longfin Smelt (Kimmerer 2002, Kimmerer et al. 2009, Nobriga and Rosenfield 2016). For example, expansion of shallow low-salinity spawning and rearing habitats throughout the entire estuary in wet years may explain in part the positive relationship between interannual variation in freshwater outflow and Longfin Smelt recruitment. Similarly, the historic degradation of lesser watersheds and brackish wetlands throughout the San Francisco Estuary may have contributed to the long-term decline of this species. Thus, the observations reported herein could transform our fundamental understanding of the habitat needs of Longfin Smelt and the interventions needed to conserve and restore this distinct and imperiled population.

Recently, Hand et al. (2018) discussed the socio-ecological complexities surrounding natural resource policy, science, and management in the Columbia River Basin, using a case study of dam removal on the Elwha River in Washington State (WebFigure 1a). We feel compelled to provide additional historical context and correct some of the information provided by Hand et al. about the Elwha. The historic removals of the two Elwha River dams – a long-anticipated project that was decades in the making – have been touted by some as an environmental success story following the project's completion in 2014. As with any complex endeavor, critical analyses and lessons learned continue to emerge, and will likely benefit future projects. Dam construction along the Elwha effectively limited five Pacific salmon species, steelhead, and other migratory fish to the lower 8 km of the river, starting a steady decline of what was a highly productive salmon-producing river. In the decades following the completion of the Elwha Dam in 1913 and the Glines Canyon Dam in 1927, systematic channelization, wood removal, regulated flow/temperature fluctuations, diminished gravel recruitment, and floodplain alterations reduced the available habitat to <10% of its historical extent and led to further population declines of native salmonids and other anadromous fishes (WebFigure 1b). An important contextual element missing from their article is the massive amount of sediment released during and after dam removal (Warrick et al. 2015). Cumulatively, the dams' two reservoirs contained 21 million cubic meters of sediment, 66% of which has since been released (Randle et al. 2015; Ritchie et al. 2018) and transported downstream to the coast (Foley et al. 2017). Because of expected high and prolonged suspended sediment concentrations during and after dam removal, a desire to re-establish functioning floodplains in the former reservoirs, and requirements to protect fishes listed under the US Endangered Species Act, a staged dam removal lasting 3 years was necessary. Preserving salmon stocks from high sediment levels (approaching 1000 times greater than background; Magirl et al. 2015), unstable bed conditions, filling of pools, and the loss of downstream floodplain channels (East et al. 2015) was accomplished through the use of an integrated program that included hatcheries, adult relocations, and natural recolonization (Figure 1), an approach that is not new to salmon reintroduction efforts (Anderson et al. 2014). A tagged adult coho salmon released into a tributary of the Elwha River in 2017 as part of a long-term program to protect fish from high suspended-sediment affected areas downstream of the dam removal project. M McHenry, Lower Elwha Klallam Tribe While not disputing the science demonstrating the potential for negative consequences of fish hatcheries, we feel that Hand et al. may have mischaracterized the role and recent history of the two Elwha hatcheries. While claiming that the use of hatcheries has created an obstacle to fish recovery, they imply that the influence of hatchery origin fish is new to the Elwha because of dam removal; this is not the case. Recent otolith marking data revealed that natural Chinook spawners were failing to replace themselves (Weinheimer et al. 2017), suggesting that the hatchery played a role in conserving native Elwha River Chinook prior to dam removal. Most Chinook and coho salmon currently recolonizing areas upstream of the former dams were born in the hatcheries. Importantly, members of the natural-origin progeny of those post-dam removal colonizers, particularly for coho, are returning to upstream areas to spawn (Liermann et al. 2017). Thus far, a positive response in terms of increased spatial distribution, fry density, and smolt production has been observed in areas that have not had anadromous fishes for decades (Liermann et al. 2017; McHenry et al. 2017). Continued monitoring and adaptive management of the Elwha River's salmon populations will be necessary to track the evolution of this response. Guidelines for such adaptive management, which recommend biologically based phases of recovery and levels of management intervention necessary to achieve restoration success, are outlined in Peters et al. (2014). The numbers of hatchery releases during and after dam removal (1.3–3.4 million per year) are lower than pre-dam removal levels (WebFigure 1c) and those prescribed during pre-dam removal planning. This contrasts with the 7 million annual releases cited by Hand et al. Additionally, other migratory species that are not and have never been in hatcheries (eg bull trout, Pacific lamprey) are also recolonizing upstream of the dams (eg Moser and Paradis 2017; Quinn et al. 2017). Lastly, a commercial and sport-fishing moratorium, in place for the past 6 years, was designed to aid in the recovery of fish populations. Hand et al.'s statement that hatchery construction or operation costs have siphoned funds away from research and monitoring budgets is inaccurate, with the Elwha being among the best-studied dam removals in the world. Funding for dam removal began in 1995 and was provided by multiple congressional appropriation bills through 2015 to cover costs associated with acquisition, dam removal, and project mitigation. Reconstruction of the tribal fish hatchery to mitigate dam removal effects to the original hatchery's water supply was provided by the American Recovery and Reinvestment Act of 2009, federal funding made available for "construction-ready" projects in response to the 2008 financial crisis. Our era's natural resource issues are inherently complex and fraught with interconnected social, legal, cultural, and ecological entanglements. For any project, a foundation built on complete information and proper context must be used within translational scientific approaches (Enquist et al. 2017) and multidisciplinary collaborations to bridge the gap between research and practice. Steeped in a complex socio-ecological history, the Elwha River restoration has seen both early successes and setbacks, with the ultimate outcomes and lessons unfolding in the decades to come. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

First posted April 1, 2019 For additional information, contact: Director, Forest and Rangeland Ecosystem Science CenterU.S. Geological Survey777 NW 9th St., Suite 400Corvallis, Oregon 97330 Salmon populations spawning in the Lake Ozette watershed of northwestern Washington were once sufficiently abundant to support traditional Tribal fisheries, and were later harvested by settlers. However, in 1974 and 1975, the sockeye salmon (Oncorhynchus nerka) harvest decreased to 0 from a high of more than 17,500 in 1949, thus stimulating research into the causes of decrease, which resulted in eventual listing of the population as threatened under the Endangered Species Act in 1999. The listing status was upheld in 2005 and 2014 following 5-year reviews. Meanwhile, research results were compiled in a limiting factors analysis (LFA) and a recovery plan was developed. Although there has been some improvement in sockeye abundance since listing, the numbers remain too low to allow harvest and it is not yet clear which of the many potential limiting factors are most consequential.As part of the LFA process, a population model was developed to determine values of life-history parameters that would enable the population to survive for 100 years. The model was based on the best available data, but data are limited for the Lake Ozette system. Results informed the qualitative assessment of the importance of limiting factors used to develop the recovery plan for Lake Ozette sockeye. The model was built in Microsoft Excel® and is difficult to use. The purpose of the model described herein is to synthesize the results of the LFA in a form that can be manipulated by resource managers and the public to create scenarios, test hypotheses, and observe sensitivities of results to changes in parameters. The goal is to provide a tool that enables research, monitoring and management to be focused on the most impactful elements and processes, including identifying the information gaps that are most critical to fill.

Life-cycle models combine several strengths for estimating population parameters and biological reference points of harvested species and are particularly useful for those exhibiting distinct habitat shifts and experiencing contrasting environments. Unfortunately, time series data are often limited to counts of adult abundance and harvest. By incorporating data from other populations and by dynamically linking the life-history stages, Bayesian life-cycle models can be used to estimate stage-specific productivities and capacities as well as abundance of breeders that produce maximum sustained yield (MSY). Using coho salmon (Oncorhynchus kisutch) as our case study, we show that incorporating information on marine survival variability from nearby populations can improve model estimates and affect management parameters such as escapement at MSY. We further show that the expected long-term average yield of a fishery managed for a spawner escapement target that produces MSY strongly depends on the average marine survival. Our results illustrate the usefulness of incorporating information from other sources and highlight the importance of accounting for variation in marine survival when making inferences about the management of Pacific salmon.

Knowledge about population responses to environmental variability, including extreme climatic events, is crucial for understanding their current status and likely fate under future environmental change. The frequency and intensity of extreme events is projected to increase, especially in freshwater ecosystems. Anadromous fishes depend on freshwater habitats for spawning and juvenile rearing, making them sensitive to altered hydrologic regimes. Here, we evaluate the effect of past and projected variability in river hydrology on freshwater production of naturally spawning coho salmon populations from coastal river systems in Washington, USA . Using a stage‐based life‐cycle model, we show that juvenile production during freshwater residence depends on river flow characteristics. Most importantly, juvenile production is reduced by low minimum stream flows during summer. Based on climate model projections suggesting more extreme summer droughts in the region, we then simulate changes in river flow characteristics and quantify the effects of more frequent and severe low flows during summer on juvenile production as well as the harvest that can be sustained in these populations. Our results demonstrate that changes in hydrologic regimes due to environmental change, especially extreme low flows during summer, may significantly affect juvenile production in anadromous fishes such as coho salmon and the services these populations provide to their ecosystems and humans. Understanding population responses to extreme climatic events is thus essential for improving species conservation and risk assessments.

Conservation and recovery of endangered species requires timely and defensible data to predict their responses to management actions. In the Sacramento-San Joaquin Delta, the population of Delta Smelt Hypomesus transpacificus, a species of management concern, has declined to a record low. Alternative research strategies are now sought to determine the efficacy of management actions. In this study, we assessed the feasibility of tagging cultured adult Delta Smelt as a potential surrogate for wild fish in field experiments. Preliminary experiments determined that anesthesia of Delta Smelt in 35 mg/L AQUI-S 20E for 4 min best facilitated tagging. The 28-d survival of Delta Smelt (n = 39) intracoelomically injected with passive integrated transponder (PIT) tags (8.4 mm, 0.03 g) was high (95%) and did not differ from untagged control fish; tag retention was 97%. Survival of Delta Smelt with injected (n = 40) and surgically inserted (n = 40) dummy acoustic transmitters (15.0 mm, 0.22 g) was significantly lower than PIT-tagged and control fish, with only 60% surviving tag injection and 50% surviving surgical tag insertion. Surviving fish had high tag retention (injected: 95%; surgically inserted: 100%). Although not quantified, observational data suggested that the swimming ability of fish with acoustic tags was impaired. These results indicate that cultured Delta Smelt injected with PIT tags provide resource managers with a readily available wild surrogate to examine management actions in the delta. However, acoustic tags, which provide more detailed information on movement patterns, must be made smaller to reduce effects on survival before they can be used successfully in Delta Smelt. Logistic regression suggested that achievement of high survival (>90%) would require a tag mass: body mass ratio below 0.02.

Frequent invasions in coastal ecosystems result in novel species interactions that have unknown ecological consequences. Largemouth Bass Micropterus salmoides and Brazilian waterweed Egeria densa are introduced species in the Sacramento-San Joaquin River Delta (the Delta) of California, a highly modified estuary. In this system, Brazilian waterweed and Largemouth Bass have seen marked increases in distribution and abundance in recent decades, but their association has not been specifically studied until now. We conducted a 2-year, bimonthly electrofishing survey with simultaneous sampling of water quality and submerged aquatic vegetation (SAV) biomass at 33 locations throughout the Delta. We used generalized linear mixed models to assess the relative influences of water temperature, conductivity, Secchi depth, and SAV biomass density on the abundance of both juvenile-sized and larger Largemouth Bass. Water temperature had a positive relationship with the abundance of both size-classes, but only juvenile-sized fish had a positive association with SAV biomass density, with highest abundances at intermediate SAV densities. In contrast, larger fish were generally ubiquitous across all sampling conditions, even when SAV was absent or present at low densities. Our results on the Largemouth Bass-SAV relationship are consistent with those of previous studies from lake systems within the Largemouth Bass's native range, where they interact with a different SAV species assemblage. These results are supportive of the hypothesis that the proliferation of Brazilian waterweed has expanded Largemouth Bass rearing habitat in the Delta. Finally, this study has implications for tidal wetland restoration plans for the Delta, suggesting that the larger-sized Largemouth Bass may still inhabit restored areas even if invasive SAV establishment is limited.

The estuary of the Elwha River, on Washington’s Olympic Peninsula, has been degraded and simplified over the past century from sediment retention behind two large dams, levee construction, and channelization. With the removal of Elwha Dam and initiation of Glines Canyon Dam’s removal in fall 2011, sediment deposits will change the estuary and affect anadromous and nearshore marine fishes. Juvenile Chinook salmon commonly use estuaries and the river’s population is part of an Evolutionarily Significant Unit listed as Threatened under the U.S. Endangered Species Act. This study reports on monthly sampling in part of the river’s estuary from March 2007 through September 2011 to characterize the seasonal changes in relative abundance of yearlings and sub-yearlings, and size distributions prior to dam removal. Most (69 %) of the yearlings were caught in April, when this life history type was released from the hatchery, and to a lesser extent in May (28 %) and June (3 %). Yearlings caught in the estuary were smaller than those released from the hatchery (means: 153 mm ± 28 SD vs. 175 mm ± 5 SD), suggesting more rapid departure by larger fish. Sub-yearlings were much more abundant in the estuary, and were caught from March through November, increasing in mean fork length by 8.7 mm month-1. The hatchery-origin sub-yearlings were not marked externally and so were not distinguishable from natural origin fish. However, 39 % of the sub-yearlings were caught prior to June, when sub-yearlings were released from the hatchery, indicating substantial use of the estuary by natural-origin fish. Thus, even in a reduced state after a century of dam operation, the highly modified estuary was used over many months by juvenile Chinook salmon. The information on juvenile Chinook salmon prior to dam removal provides a basis for comparison to patterns in the future, when the anticipated increase in estuarine complexity may further enhance habitat use by juvenile Chinook salmon.

Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a systematic assessment approach that incorporates expert knowledge was developed to determine status and future vulnerability to climate change of freshwater fishes in California, USA. The method uses expert knowledge, supported by literature reviews of status and biology of the fishes, to score ten metrics for both (1) current status of each species (baseline vulnerability to extinction) and (2) likely future impacts of climate change (vulnerability to extinction). Baseline and climate change vulnerability scores were derived for 121 native and 43 alien fish species. The two scores were highly correlated and were concordant among different scorers. Native species had both greater baseline and greater climate change vulnerability than did alien species. Fifty percent of California’s native fish fauna was assessed as having critical or high baseline vulnerability to extinction whereas all alien species were classified as being less or least vulnerable. For vulnerability to climate change, 82% of native species were classified as highly vulnerable, compared with only 19% for aliens. Predicted climate change effects on freshwater environments will dramatically change the fish fauna of California. Most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction. Fishes requiring cold water (<22°C) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with some species increasing in abundance and range. However, a few alien species will likewise be negatively affected through loss of aquatic habitats during severe droughts and physiologically stressful conditions present in most waterways during summer. Our method has high utility for predicting vulnerability to climate change of diverse fish species. It should be useful for setting conservation priorities in many different regions.

In addition to the downstream migration of smolts in spring, Coho Salmon Oncorhynchus kisutch also enter estuaries throughout the year but especially in the spring as fry and in the fall as parr. The removal of two large dams on the Elwha River, Washington, has increased the area accessible to salmon and is affecting many aspects of the system. For comparison with the postdam period, when the Elwha River estuary will likely expand in size and complexity, monthly sampling was conducted in the estuary during 2007-2011 to determine patterns of Coho Salmon presence and size prior to dam removal; Salt Creek, a nearby undammed stream, was also sampled to allow comparison of fish size and seasonal timing patterns. The spring smolt migration in the Elwha River included a large fraction of unmarked fish (primarily of natural origin) as well as marked fish from the Lower Elwha Klallam Tribe Fish Hatchery. Subyearlings entered both estuaries during much of the year, exhibiting a peak in September. Coho Salmon from the Elwha River (including wild and hatchery-origin fish) were larger and more heavily represented in the fall relative to the spring smolt migration compared to those from Salt Creek. Future patterns in the Elwha River may include reduced presmolt use of the estuary if the center of distribution is farther upriver, but improved estuarine habitat may make it more suitable for presmolts. Received November 21, 2012; accepted April 3, 2013

Author(s): Moyle, Peter B.; Kiernan, Joseph D.; Crain, Patrick K.; Quinones, Rebecca M. | Abstract: A methodology is presented that allows systematic evaluation of climate change impacts on freshwater fishes in California (121 native fish taxa and 43 aliens). The methodology uses expert opinions of the authors and literature reviews of status and biology of the fishes to score both status of each species (“baseline vulnerability”) and likely impact of climate change (“climate change vulnerability”). Baseline and climate change vulnerability scores were highly correlated with one another and were consistent among different scorers. Native species were found to have both greater baseline and greater climate change vulnerability than alien species. Fifty percent of natives had critical or high baseline vulnerability versus none for aliens; 83 percent had critical or high climate change vulnerability versus 19 percent for aliens. Fishes with high baseline vulnerability were also likely to have highest vulnerability to climate change. These results show that predicted climate change effects on fresh water environments will dramatically change the fish fauna at all scales and at all elevations. The research team concluded that most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction, if present trends continue. Fishes requiring cold water (

We examined the response of fishes to establishment of a new flow regime in lower Putah Creek, a regulated stream in California, U.S.A. The new flow regime was designed to mimic the seasonal timing of natural increases and decreases in stream flow. We monitored fish assemblages annually at six sample sites distributed over approximately 30 km of stream for eight years before and nine years after the new flow regime was implemented. Our purpose was to determine whether more natural stream flow patterns would reestablish native fishes and reduce the abundances of alien (nonnative) fishes. At the onset of our study, native fishes were constrained to habitat immediately (<1 km) below the diversion dam, and alien species were numerically dominant at all downstream sample sites. Following implementation of the new flow regime, native fishes regained dominance across more than 20 km of lower Putah Creek. We propose that the expansion of native fishes was facilitated by creation of favorable spawning and rearing conditions (e.g., elevated springtime flows), cooler water temperatures, maintenance of lotic (flowing) conditions over the length of the creek, and displacement of alien species by naturally occurring high-discharge events. Importantly, restoration of native fishes was achieved by manipulating stream flows at biologically important times of the year and only required a small increase in the total volume of water delivered downstream (i.e., water that was not diverted for other uses) during most water years. Our results validate that natural flow regimes can be used to effectively manipulate and manage fish assemblages in regulated rivers.

This paper is a review of the biology of Sacramento perch (Archoplites interruptus) based mainly on recent studies of their distribution, ecology, physiology, and genetics. The Sacramento perch is the only member of the family Centrarchidae that is endemic to California. It is most closely related to the rock basses (Ambloplites spp.) and is thought to have split from its eastern cousins during the Middle Miocene Period (15.5 to 5.2 million years ago, MYA). Their native range includes the Central Valley, Pajaro and Salinas rivers, tributaries to the San Francisco Estuary (e.g., Alameda Creek), and Clear Lake (Lake County). Today, they are most likely extirpated from all of their native range. They are known to persist in 28 waters outside their native range: 17 in California, nine in Nevada, and one each in Utah and Colorado. Disappearance from their native range coincided with massive changes to aquatic habitats in the Central Valley and with the introduction of alien species, including other centrarchids. Unfortunately, many populations established outside their native range have also disappeared and are continuing to do so.

In the Elwha River, two hydroelectric dams constructed nearly a century ago fragment previously continuous habitat and isolate migratory bull trout. Removal of the dams is scheduled to begin in 2011, and represents an opportunity to help recover this threatened species. Large-scale disturbance is expected when accumulated sediments behind the dams are released downstream, which may initially negatively affect bull trout. To inform restoration planning, we investigated levels of genetic variation within and among bull trout populations from six Olympic Peninsula watersheds with an emphasis on the Elwha River. We determined genetic relationships among Elwha bull trout from four distinct river sections and performed population assignments for fish collected from the lower Elwha and Dungeness rivers. There were greater levels of variation and gene flow in coastal watersheds (Hoh, South Fork Hoh, Kalaloch) compared to populations isolated by dams (Elwha, North Fork Skokomish). Elwha bull trout represented an independent spawning population and were highly differentiated from other populations. Bull trout from the Elwha (n = 21) and Dungeness (n = 18) estuaries all assigned to the river they there were collected from. Despite long-term fragmentation, there was no significant genetic variation among Elwha bull trout separated by the dams, although fish from the Elwha headwaters were genetically distinct. Results suggest that bull trout still migrate downstream through both Elwha River dams and that anadromous bull trout will likely help to recolonize the Elwha River following dam removal. Baseline data from this study will be useful for monitoring bull trout recovery following dam removal.

The purpose of the project is to improve our understanding about best management practices that can be utilized on diked managed wetlands in Suisun Marsh for reducing the occurrence of low dissolved oxygen (DO) and high methylmercury (MeHg) events associated primarily with fall flood-up practices. Low DO events are of concern because they can lead to undue stress and even mortality of sensitive aquatic organisms. Elevated MeHg levels are of concern because MeHg is a neurotoxin that bio-magnifies up the food chain and can cause deleterious effects to higher trophic level consumers such as piscivorous fish, birds, and mammals (including humans). This study involved two years (2007-2008) of intensive field data collection at two managed wetland sites in northwest Suisun Marsh and their surrounding tidal sloughs, an area with prior documented low DO events. In addition, the study collected limited soils and water quality field data and mapped vegetation for three managed wetland sites in the central interior of Suisun Marsh, for the purpose of examining whether wetlands at other locations exhibit characteristics that could indicate potential for similar concerns. In Year 1 of the study, the objective was to identify the baseline conditions in the managed wetlands and determine which physical management conditions could be modified for Year 2 to reduce low DO and MeHg production issues most effectively. The objective of Year 2 was to evaluate the effectiveness of these modified management actions at reducing production of low DO and elevated MeHg conditions within the managed wetlands and to continue improving understanding of the underlying biogeochemical processes at play. This Final Evaluation Memorandum examined a total of 19 BMPs, 14 involving modified water management operations and the remaining five involving modified soil and vegetation management practices. Some of these BMPs were previously employed and others have not yet been tested. For each BMP this report assesses its efficacy in improving water quality conditions and potential conflicts with wetland management. It makes recommendations for further study (either feasibility assessments or field testing) and whether to consider for future use. Certain previously used BMPs were found to be important contributors to poor water quality conditions and their continued use is not recommended. Some BMPs that could improve water quality conditions appear difficult to implement in regards to compatibility with wetland management; these BMPs require further elaboration and feasibility assessment to determine whether they should be field tested. In practice for any given wetland, there is likely a combination of BMPs that would together have the greatest potential to address the low DO and high MeHg water quality concerns. Consequently, this report makes no sweeping recommendations applicable to large groups of wetlands but instead promotes a careful consideration of factors at each wetland or small groups of wetlands and from that assessment to apply the most effective suite of BMPs. This report also identifies a number of recommended future actions and studies. These recommendations are geared toward improving the process understanding of factors that promote low DO and high MeHg conditions, the extent of these problems in Suisun Marsh, the regulatory basis for the DO standards for a large estuarine marsh, the economics of BMPs, and alternative approaches to BMPs on diked managed wetlands that may address the water quality issues. The most important of these recommendations is that future BMP implementation should be carried out within the context of rigorous scientific evaluation so as to gain the maximum improvement in how to manage these water quality issues in the diked managed wetlands of Suisun Marsh.

Nonnative brook trout Salvelinus fontinalis are abundant in Pine Creek and its main tributary, Bogard Spring Creek, California. These creeks historically provided the most spawning and rearing habitat for endemic Eagle Lake rainbow trout Oncorhynchus mykiss aquilarum. Three-pass electrofishing removal was conducted in 2007-2009 over the entire 2.8-km length of Bogard Spring Creek to determine whether brook trout removal was a feasible restoration tool and to document the life history characteristics of brook trout in a California meadow stream. After the first 2 years of removal, brook trout density and biomass were severely reduced from 15,803 to 1,192 fish/ha and from 277 to 31 kg/ha, respectively. Average removal efficiency was 92-97%, and most of the remaining fish were removed in the third year. The lack of a decrease in age-0 brook trout abundance between 2007 and 2008 after the removal of more than 4,000 adults in 2007 suggests compensatory reproduction of mature fish that survived and higher survival of age-0 fish. However, recruitment was greatly reduced after 2 years of removal and is likely to be even more depressed after the third year of removal assuming that immigration of fish from outside the creek continues to be minimal. Brook trout condition, growth, and fecundity indicated a stunted population at the start of the study, but all three features increased significantly every year, demonstrating compensatory effects. Although highly labor intensive, the use of electrofishing to eradicate brook trout may be feasible in Bogard Spring Creek and similar small streams if removal and monitoring are continued annually and if other control measures (e.g., construction of barriers) are implemented. Our evidence shows that if brook trout control measures continue and if only Eagle Lake rainbow trout are allowed access to the creek, then a self-sustaining population of Eagle Lake rainbow trout can become reestablished.