Andrew L. Rypel

Flow regime alteration is among the most pervasive threats to freshwater ecosystems globally, and migratory species are particularly vulnerable to these impacts. Despite this, specific aspects of flow regimes that shape spawning migrations remain poorly understood for most threatened species. Functional flow frameworks offer a promising tool for identifying ecologically meaningful flow targets, especially for threatened species, like the Sacramento River population of green sturgeon ( Acipenser medirostris ). Aspects of this species' life‐history are highly flow‐dependent, and its migratory corridor overlaps with heavily regulated waterways, making it an interesting case study for understanding how flow dynamics shape migratory behavior. We used an acoustic telemetry dataset (2007–2022) to explore how river flows impact spawning migration behavior of green sturgeon ( n = 220) through the California Sacramento‐San Joaquin Delta. A cluster analysis identified three migration patterns: mainstem Sacramento River routing, Delta routing, and incomplete migrants. Increased discharge during migration was positively associated with migration success and fish selecting the Sacramento River, with a threshold near 10,000 cfs, below which fish frequently routed through the Delta where water diversions and altered hydrology may pose additional risks. Higher pre‐migration temperatures were positively correlated with greater Delta use and strongly negatively correlated with migration success. Functional flow metrics related to wet season magnitude, wet season timing, and spring recession characteristics were the strongest predictors of route selection, migration success, and duration. Overall, this study demonstrates how functional flow frameworks combined with telemetry can uncover critical linkages between flow dynamics and spawning migrations, with direct implications for management in regulated rivers.

Degradation of freshwater habitats, including the alteration of natural flow regimes by impoundment, is a major threat to native fishes. When dam removal is not possible, management actions to recover natural flow regimes can benefit native species, but monitoring community responses is crucial to show efficacy. We used eDNA metabarcoding to quantify spatiotemporal trends in fish assemblages along the longitudinal profile of a regulated stream where a court-ratified environmental flows framework is used to benefit native fishes. At a subset of sites, we also compared eDNA results with concurrent surveys conducted using long-term standardized fisheries monitoring techniques to evaluate concordance. From 59 eDNA samples collected over approximately 2 years, we detected 26 fish taxa, including 8 native species, with 25 taxa resolving to species level using a custom reference sequence database; one taxon could not be resolved between closely related species. Fish assemblages varied predictably along the longitudinal profile of the stream and by season (fall and spring). Diversity indices were higher at downstream sites and in fall, reflecting greater richness of warm-water non-native species. Evenness was similar among sites but shifts in species ranks suggests reordering processes drive spatiotemporal variation in assembly. Gradient forest analysis identified thirteen species associated with spatiotemporal gradients, including both native cold-water species and non-native warm-water species. Overall, eDNA results were concordant with conventional fisheries monitoring but eDNA detected significantly greater species richness through increased detection of rare species. eDNA results align with long-term monitoring that demonstrated assemblage shifts in upper, but not lower stream reaches, and extends the insights into spatial responses, species reordering, and ecology of rare species. These findings demonstrate the value of eDNA as a complementary tool for understanding community assembly dynamics, including responses to stream rehabilitation and ecosystem management.

There is growing interest in establishing more protective regulations for native fishes that historically have been classified as “rough fish,” a term ascribed to species of low-to-zero commercial value. Yet high-quality population data are lacking for most species and populations, precluding the determination of sustainable harvest limits using standard methods. Here, we present an inductive and ecosystem-based approach for comparing and aligning harvest limits of diverse fish species. Our approach centers on the production/biomass (P/B) ratio as the main instrument for gauging sustainable harvest. Production/biomass is the biomass turnover rate in populations and, therefore quantifies the return rate of any removed biomass in populations. We extracted and summarized data from existing studies, representing a total of 517 empirical estimates of secondary production, biomass, and P/B ratios. We subsequently developed a highly predictive statistical model (R2 = 0.90), demonstrating that P/B is largely a function of maximum age across species. We then developed a separate database on age, growth, and longevity data for most native fishes of interest across the United States. For each species and population, we leveraged the above statistical model to predict and compare mean P/B across species. The results show that most native fishes express P/B values that are similar to or lower than those for traditional game fish species. Accordingly, harvest limits across species groups can be harmonized with those of other managed species. For example, native nongame species like Bigmouth Buffalo Ictiobus cyprinellus and Freshwater Drum Aplodinotus grunniens are long-lived with slow replacement rates that are statistically clustered with those observed in Lake Sturgeon Acipenser fulvescens and trophy Muskellunge Esox masquinongy populations, two popular game fish species. Harvest limits for these nongame species would therefore need to be similarly low for these species to ensure comparable sustainability. To understand broad patterns of harvest limit alignment, we modeled relationships between daily bag limits of managed species and P/B for five test states. The models uniformly showed nonlinear trends with high residuals (suggesting excessive bag limits) being common for panfish species and low residuals (suggesting overly conservative bag limits) being common for trout species. Managers can adapt the results and approach from this study to complement the social limit-setting process, especially in absence of more robust biological data.

Freshwater ecosystems are hotspots of biodiversity and contribute significantly to food security. Yet freshwater habitats throughout the world remain plagued by overfishing, which depletes populations and diminishes provisioning of ecosystem services. There is growing interest in the use of freshwater protected areas (FPAs), which are freshwater ecosystems managed under long‐term fishing bans and conservation‐oriented regulations, to promote ecosystem recovery. Yet empirical evidence on the efficacy of FPAs indicates that ecological recovery can be complicated by non‐native species, which may also benefit from reduced harvest pressure and improved habitat conditions. To evaluate effects of targeted fish removals (TFRs) under fully implemented FPAs, we conducted exhaustive field surveys across five Chinese lakes with and without removal efforts and assessed multiple dimensions of fish assemblage diversity. Results showed multidimensional diversity metrics for native fishes improved significantly in FPAs with TFRs (e.g. non‐native fish removals in invasion hotspots), while these same metrics declined in control lakes. Moreover, TFRs appeared to strengthen top‐down regulation and alleviate eutrophication, as indicated by altered trophic cascade relationships and reduced phytoplankton biomass (PB) in FPAs with TFR. Synthesis and applications. Our results indicate combining FPAs with TFRs is essential to achieve effective biodiversity recovery in these ecosystems. This integrated strategy should be prioritized in invasion‐prone or eutrophic systems, where passive protection alone is unlikely to deliver desired ecological outcomes.

Catch inequality—the disproportionate distribution of catch across anglers— is a fundamental but overlooked driver of recreational fisheries dynamics. Here, we use 11 years (2012-2022) of compulsory angler report cards to characterize long-term catch dynamics in the specialized recreational steelhead ( Oncorhynchus mykiss ) fishery in California, U.S.A. Spatialized catch data reveal the fishery is principally supported by wild fish, despite evidence of widespread hatchery straying. California steelhead appear to represent the most catch-unequal recreational fishery studied yet, exhibiting a statewide Gini coefficient of 0.81. Across basins, inequality varies substantially but remains relatively stable over time and flow conditions; high inequality is primarily driven by significant proportions of zero-catch anglers. We find the relationship between sample size and inequality measures is especially influential in fisheries data. Hence, we develop a three-prong approach for identifying minimal sample sizes required for robust Gini estimation. Across basins and years, an average minimum of 77 report cards were required for the present fishery. Collectively, these findings demonstrate the necessity of considering catch inequality in fisheries management, particularly when utilizing angler data. Graphical N.a.

Freshwater ecosystems in mountain landscapes are threatened by climate change. Accumulated heat can result in lethal short-term heat exposure, while velocity of change governs severity and rates of long-term heat exposure. Here, we novelly integrate heat accumulation and velocity of change approaches to classify climate-vulnerable USA mountain watersheds. We combine watershed position and air temperature data to calculate degree-days. We then calculate the current velocity of this change and used discriminant function analyses to classify watershed vulnerability through 2100. Our results demonstrate how rates of heat accumulation are increasing across mountain landscapes. We estimate 19% of watersheds are at greatest vulnerability to accumulated heat, and this will increase to 33% by 2100. Further, mean killing degree days (i.e., region-specific mean number of days above 90th temperature percentile) are projected to increase 215-254% (mean = 236%) over this same time frame. Together, results indicate heat accumulation will increase substantially over the next 75 years; changes are projected to be most severe in lower elevation landscapes and those with greatest historical velocity of change. These changes will likely restructure species' distributions. Decision-makers can use these classifications to better understand landscapes, species' needs, and ecosystem services, thereby enabling effective allocation of conservation resources.

To advance our understanding of freshwater biodiversity in data‐limited systems, this study used multispecies occupancy models to predict species richness and individual species occupancy, providing critical insights for the conservation of these rapidly declining ecosystems. Chilean watersheds were chosen as the study system as they support a highly endemic and vulnerable assemblage of freshwater fishes in need of increased research and management. We tested several model types and ultimately pursued latent spatial multispecies occupancy models, which gained popularity in wildlife ecology, but are relatively underutilized in fisheries ecology. Advantages include simultaneously modeling multiple species to infer both species‐specific and assemblage‐level responses to hydro‐geomorphological conditions while also accounting for imperfect species detections. Model results showed that fish species richness is primarily driven by negative relationships with elevation; however, individual species responses were variable across all environmental drivers. We present maps of predicted occupancies, representing niche model results for selected native and nonnative species. Finally, to put our results in the context of the rapid development in hydropower taking place throughout Chile, we analyzed predicted species richness and occupancy patterns in relation to aquatic ecosystem fragmentation risk from current and planned dams throughout Chile. Results showed a large number of dams are planned for the diverse lower elevation areas of the Biobio, Valdivia, and Puelo River Basins, highlighting the potential for negative impacts to the species that inhabit them. As over half the species modeled are currently listed as endangered, critically endangered, or data deficient by the International Union for Conservation of Nature (IUCN), model outputs could aid in conservation planning. This approach not only enhances our ability to protect Chile's unique and vulnerable freshwater fish species but also provides a robust framework for integrating modeled ecological insights of data‐limited systems into conservation planning.

Climate change is transforming the ecology of lakes at a rapid pace, shifting some lakes toward warmwater‐dominant habitats. As a result, warmwater fishes are increasingly becoming more prevalent in lakes where they already existed, altering the patterning and strength of species interactions. Understanding shifting species interactions (e.g., competition, predation), and the role of lake management in shaping these interactions, will be critical for lake stewardship in response to climate change. Here, we present results from an intensive 5‐year experimental removal of ~285,000 warmwater fishes from a north‐temperate lake. The goal of the experiment was to test whether warmwater fish reduction is effective for rewiring lake food webs to reverse undesirable conditions for coolwater species, leading to increased recruitment and abundance of coolwater fishes. Throughout the experiment, warmwater fishes were resilient to reductions, with biomass declines of 23% averaged across five species. Among coolwater fishes, the top predator walleye showed no biomass response, while yellow perch biomass increased by ~914%. Fish species biomass changes translated to food web shifts, including a yellow perch trophic position decline of 0.4, decreased zooplankton abundances, and increased zoobenthos abundances. Our results highlight differential species responses to a management action aimed at adapting to climate change. Despite similar thermal tolerances, two coolwater species responded differently to removal of warmwater fishes, highlighting the characteristics (e.g., life history strategies, adaptive capacity) that contribute to species resilience. Given the importance of biotic interactions, climate adaptation may need to go beyond a “one‐size‐fits‐all” approach even when species have similar thermal tolerances.

Motivation: Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database.Main Types of Variables Included: The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years.Spatial Location and Grain: Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size.Time Period and Grain: The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample‐level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric.Major Taxa and Level of Measurement: The database includes any eukaryotic taxa, with a combined total of 56,400 taxa.Software Format: csv and. SQL.

As fish populations face compounding pressures under climate change, highly modified rivers are receiving increasing research and conservation attention as important sites for restoration. Across the North Pacific Ocean, Chinook salmon (Oncorhynchus tshawytscha) have experienced unprecedented declines and extirpations because of habitat loss and fragmentation and climate variability. Here, we studied a rare example of a novel salmon population developing in Putah Creek, California, a dam‐controlled stream flowing through an area of intensive agriculture where salmon were unlikely to occur prior to the rehabilitation of a more natural flow regime. We used otoliths from adult Chinook salmon carcasses recovered from Putah Creek to determine river or hatchery of origin for five spawning year classes. Our results provide evidence of successful salmon reproduction, outmigration survival, and natal homing of individuals back to Putah Creek in recent years. Although hatchery‐origin fish that strayed to Putah Creek to spawn dominated returns each year, this study documents life‐cycle completion required for the potential development of a self‐sustaining salmon population. This study demonstrates that targeted restoration and flow rehabilitation efforts can generate viable new salmon spawning habitat in dam‐controlled river systems, which could help mitigate habitat lost to dams and developments. Further, successful anadromous life‐cycle completion can occur in new spawning habitat within the first several generations, which will help inform efforts to restore or reintroduce salmon in other altered river systems.