Rypel, A. L. | bioRxiv Science

bioRxiv2026

Community assembly dynamics in a regulated stream: Insights from environmental DNA

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.

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bioRxiv2026

Quantifying catch inequality in recreational fisheries: a case study with California steelhead (Oncorhynchus mykiss)

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 (range 0.74-0.86) 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 especially influential for 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. High catch inequality may complicate traditional management efficacy and catch-per-unit-effort data utilization, emphasizing its consideration in fisheries management.

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bioRxiv2026

Smoothing over "rough" mismanagement: establishing protective harvest limits for native nongame fishes

There is growing interest in establishing more protective regulations for native fishes historically classified as "rough fish"- a term ascribed to species of low-to-zero perceived commercial value. Yet high-quality population data are lacking for most species and populations, precluding 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 key instrument for gauging sustainable harvest. P/B 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 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 USA. For each species and population, we leveraged the above statistical model to predict and compare mean P/B across species. Results show most native fishes express P/B values similar to, or lower than, 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. Model uniformly showed non-linear trends with high residuals (suggesting excessive bag limits) common for panfish species and low residuals (suggesting overly conservative bag limits) common for trout species. Managers can use the results of this study to estimate harvest limits native fishes.

ecology↗

bioRxiv2023

Reservoir ecosystems support large pools of fish biomass

Humans increasingly dominate Earths natural freshwater ecosystems, and many freshwater fisheries resources are imperiled and at-risk of collapse. Yet despite this, the productive capacity of intensively modified freshwater ecosystems is rarely studied. We digitized, and provide open access to, a legacy database containing empirical fish biomass from 1,127 surveys on 301 USA reservoirs. In parallel, we developed a slate of reservoir classification schemas that were deployed to better understand distributions of biomass and secondary production. By fusing these data products, we generated a predictive capacity for understanding the scope of fisheries biomass and secondary production across all USA reservoirs. We estimate total potential fish total standing stock in USA reservoirs is 3.4 billion (B) kg, and annual secondary production is 4.5 B kg y-1. In southern USA alone, total standing stock and secondary production are 1.9 B kg and 2.5 B kg y-1, respectively. We also observe non-linear trends in reservoir fish production and biomass over time, indicating that these ecosystems are quite dynamic. Results demonstrate that reservoirs represent globally relevant pools of freshwater fisheries, in part due to their immense spatial and limnetic footprint. This study further shows that reservoir ecosystems play major roles in food security, and fisheries conservation, even though they are frequently overlooked by freshwater scientists. We encourage additional effort be expended to effectively manage reservoir environments for the good of humanity, biodiversity, and fishery conservation. Significance StatementGlobally, many freshwater fishes and fisheries resources are imperiled and at-risk of collapse. However, previous research overwhelmingly focuses on freshwater fisheries in natural rivers and lakes. This study provides evidence that novel and reconciled ecosystems, such as reservoirs, hold massive pools of freshwater fisheries biomass and may have higher ecological value than previously thought. While dams are patently ecological catastrophes, ecosystem services including secondary fish production provided by reservoirs are nonetheless substantial. Indeed, in many locations (e.g., arid regions), reservoirs are the only remaining fisheries resource. We suggest considerable conservation management is warranted for reservoir fisheries worldwide. Data DepositionCode is available on GitHub (https://github.com/caparisek/res_biomass_USA; DOI 10.5281/zenodo.8316696). All data and reservoir classifications are available on Zenodo (DOI 10.5281/zenodo.8317007). Furthermore, data will also be deposited in the Environmental Data Initiative repository upon acceptance of this manuscript.

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bioRxiv2022

Habitat use differences mediate anthropogenic threat exposure in white sturgeon

Understanding intraspecific variation in habitat use, particularly of long-lived fishes across multiple life history stages, is core to improved conservation management. Here, we present results from a synthesis of acoustic telemetry data for large juvenile and adult white sturgeon (Acipenser transmontanus) from 2010 to 2017 in the San Francisco Estuary and Sacramento River ecosystems. We focused primarily on uncovering spatial patterns of inferred habitat occupancy across life stages, and on linking habitat use to population threats. We found substantial differences in habitat use across individuals and over time that was related to fish age class. However, differences in habitat use were not explained by fish sex or water year flow conditions. We estimated an index of angling exposure, which showed that fish entering reproductive maturity, which historically were of harvestable size, were detected less often than other sizes in areas with high angler pressure, suggesting possible behavioral avoidance of areas of high angler pressure. Additionally, we used historical data to evaluate potential exposure of white sturgeon to a severe red tide event in late summer 2022. We found that >50% of reproductive-age fish may have been residing in areas affected by the red tide. Future monitoring and management of white sturgeon might benefit from examining multiple phases of white sturgeon life history. For example, additional tracking studies could improve understanding of juvenile habitat use, adult survival rates, patterns of anadromy, and cross-basin habitat utilization.

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bioRxiv2022

Life-history diversity in lakes is associated with ecosystem size

In this study, I inspect how ecosystem size drives fish life-history strategies in north temperate lakes. Species were classified as equilibrium, periodic, or opportunistic strategists according to Winemiller and Rose (1992), and species-area curves assembled and compared among strategy types. The smallest lakes were often dominated by only one species, usually an opportunistic strategist. Overall, species richness rose with ecosystem size, but larger ecosystems tended to be dominated by more periodic and equilibrium strategists. Richness of periodic species increased with ecosystem size at a faster rate compared to opportunistic species. Similarly, life-history niche space increased with ecosystem size in accord with species-area relationships, but showed saturation behavior (i.e., life-history niche space became increasingly packed in large lakes). As predicted by theory, relative abundances of opportunistic strategists were extremely variable over space and time, whereas abundances of equilibrium and periodic strategists were more stable. Integration of species-area relationships with life-history theory provides insights into community assembly at multiple scales, and has broad conservation applications.

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bioRxiv2021

Intraspecific variation in migration timing of green sturgeon in the Sacramento River system

BackgroundUnderstanding movement patterns of anadromous fishes is critical to conservation management of declining wild populations and preservation of habitats. Yet, infrequent observations of individual animals fundamentally constrain accurate descriptions of movement dynamics. MethodsIn this study, we synthesized over a decade (2006-2018) of acoustic telemetry tracking observations of green sturgeon (Acipenser medirostris) in the Sacramento River system to describe major anadromous movement patterns. ResultsWe observed that green sturgeon exhibited a unimodal in-migration during the spring months but had a bimodal distribution of out-migration timing, split between an early out-migration (32%) group during May - June, or alternatively, holding in the river until a late out-migration (68%), November - January. Focusing on these out-migration groups, we found that river discharge, but not water temperature, may cue the timing of migration, and that fish showed a tendency to maintain out-migration timing between subsequent spawning migration events. ConclusionsWe recommend that life history descriptions of green sturgeon in this region reflect the distinct out-migration periods described here. Furthermore, we encourage the continued use of biotelemetry to describe migration timing and life history variation, not only this population but other green sturgeon populations and other species.

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bioRxiv2021

Survival of a threatened salmon is linked to spatial variability in river conditions

Extirpation of the Central Valley spring-run Chinook Salmon ESU (Oncorhynchus tshawytscha) from the San Joaquin River is emblematic of salmonid declines across the Pacific Northwest. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook Salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. There were two regional mortality sinks evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll-, fDOM, turbidity and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Importantly, our data generation and modeling methods can be applied to a wide variety of fish species that transit heterogeneous and diverse habitat types.

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bioRxiv2021

Growth of Lahontan Cutthroat Trout from multiple sources re-introduced into Sagehen Creek, CA

Lahontan Cutthroat Trout Oncorhynchus clarkii henshawi have experienced massive declines in their native range and are now a threatened species under the US Endangered Species Act. A key management goal for this species is re-establishing extirpated populations using translocations and conservation hatcheries. In California USA, two broodstocks (Pilot Peak and Independence Lake) are available for translocation, in addition to potential wild sources. Yet suitability of these sources for re-introduction in different ecosystem types and regions remains an open and important topic. We conducted growth experiments using Lahontan Cutthroat Trout stocked into Sagehen Creek, CA USA. Experiments evaluated both available broodstocks and a smaller sample of wild fish translocated from a nearby creek. Fish from the Independence Lake source had significantly higher growth in weight and length compared to the other sources. Further, Independence Lake fish were the only stock that gained weight on average over the duration of the experiment. Our experiments suggest fish from the Independence Lake brood stock may be useful for re-introduction efforts into small montane headwater streams in California.

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bioRxiv2020

Reconciling fish and farms: Methods for managing California rice fields as salmon habitat

The rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in Californias Central Valley have emerged as promising habitat for rearing juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods for rearing fall-run Chinook Salmon on winter-flooded rice fields in the Yolo Bypass, a modified floodplain of the Sacramento River in California. These included: 1) influence of field substrate differences from previous season rice harvest; 2) effects of depth refugia from avian predators (trenches); 3) field drainage methods to promote efficient egress of fish; and 4) in-field salmon survivorship over time. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant when directly compared to the adjacent Sacramento River. Correspondingly, somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater versus fish in the adjacent Sacramento River. Post-harvest field substrate treatments had little effect on the lower trophic food web and had an insignificant effect on growth rates of in-field salmon. Though depth refugia did not directly increase survival, it buffered maximum water temperatures in the trenches and facilitated outmigration from fields during draining. Rapid field drainage methods yielded the highest survival and were preferable to drawn-out drainage methods. High initial mortality immediately after stocking was observed in the survival over time experiment with stable and high survival after the first week. In-field survival ranged 7.4-61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in Californias recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. The abundance of food resources and exceptionally high growth rates observed during these experiments illustrate the benefits associated with reconciling off-season agricultural land use with fish conservation practices. Without any detriment to flood control or agricultural yield, there is great promise for reconciliation ecology between agricultural floodplains and endangered fish conservation where minor alterations to farm management practices could greatly enhance the effectiveness of fish conservation outcomes.

ecology↗

bioRxiv2020

Reconciling fish and farms: Methods for managing California rice fields as salmon habitat

The rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in Californias Central Valley have emerged as promising habitat for rearing juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods for rearing fall-run Chinook Salmon on winter-flooded rice fields in the Yolo Bypass, a modified floodplain of the Sacramento River in California. These included: 1) influence of field substrate differences from previous season rice harvest; 2) effects of depth refugia from avian predators (trenches); 3) field drainage methods to promote efficient egress of fish; and 4) in-field salmon survivorship over time. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant when directly compared to the adjacent Sacramento River. Correspondingly, somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater versus fish in the adjacent Sacramento River. Post-harvest field substrate treatments had little effect on the lower trophic food web and had an insignificant effect on growth rates of in-field salmon. Though depth refugia did not directly increase survival, it buffered maximum water temperatures in the trenches and facilitated outmigration from fields during draining. Rapid field drainage methods yielded the highest survival and were preferable to drawn-out drainage methods. High initial mortality immediately after stocking was observed in the survival over time experiment with stable and high survival after the first week. In-field survival ranged 7.4-61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in Californias recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. The abundance of food resources and exceptionally high growth rates observed during these experiments illustrate the benefits associated with reconciling off-season agricultural land use with fish conservation practices. Without any detriment to flood control or agricultural yield, there is great promise for reconciliation ecology between agricultural floodplains and endangered fish conservation where minor alterations to farm management practices could greatly enhance the effectiveness of fish conservation outcomes.

ecology↗