Stephanie M. Carlson’s research while affiliated with University of California, Berkeley and other places

Climate change is redistributing life on Earth, with profound impacts for ecosystems and human well-being. While repeat surveys separated by multidecadal intervals can determine whether observed shifts are in the expected direction (e.g., poleward or upslope due to climate change), they do not reveal their mechanisms or time scales: whether they were gradual responses to environmental trends or punctuated responses to disturbance events. Here, we document population reductions and temporary range contractions at multiple sites resulting from drought for three Pacific salmonids at their ranges’ trailing edge. During California’s 2012 to 2016 historic multiyear drought, the 2013 to 2014 winter stood apart because rainfall was both reduced and delayed. Extremely low river flows during the breeding season (“flow–phenology mismatch”) reduced or precluded access to breeding habitat. While Chinook ( Oncorhynchus tshawytscha) experienced a down-river range shift, entire cohorts failed in individual tributaries (steelhead trout, O. mykiss ) and in entire watersheds (coho salmon, O. kisutch) . Salmonids returned to impacted sites in subsequent years, rescued by reserves in the ocean, life history diversity, and, in one case, a conservation broodstock program. Large population losses can, however, leave trailing-edge populations vulnerable to extinction due to demographic stochasticity, making permanent range contraction more likely. When only a few large storms occur during high flow season, the timing of particular storms plays an outsized role in determining which migratory fish species are able to access their riverine breeding grounds and persist.

Evaluating progress toward achieving freshwater conservation and sustainability goals requires transforming diverse types of data into useful information for scientists, managers, and other interest groups. Despite substantial increases in the volume of freshwater data collected worldwide, many regions and ecosystems still lack sufficient data collection and/or data access. We illustrate how these data challenges result from a diverse set of underlying mechanisms and propose solutions that can be applied by individuals or organizations. We discuss creative approaches to address data scarcity, including the use of community science, remote‐sensing, environmental sensors, and legacy datasets. We highlight the importance of coordinated data collection efforts among groups and training programs to improve data access. At the institutional level, we emphasize the power of prioritizing data curation, incentivizing data publication, and promoting research that enhances data coverage and representativeness. Some of these strategies involve technological and analytical approaches, but many necessitate shifting the priorities and incentives of organizations such as academic and government research institutions, monitoring groups, journals, and funding agencies. Our overarching goal is to stimulate discussion to narrow the data disparities hindering the understanding of freshwater processes and their change across spatial scales.

Intrapopulation variation in movement is common in nature but its effects on population dynamics are poorly understood. Using movement data from 3270 individually‐marked fish representing nine cohorts of coho salmon (Oncorhynchus kisutch) in California, we show that bimodal intrapopulation variation in the timing of juvenile down‐migration from their natal habitat and subsequent residence in non‐natal habitat affects growth, emigration timing, and the abundance and stability of adult returns. Non‐natal fish (early down‐migrants) exhibited more variable growth and more variable but earlier emigration to the estuary than natal fish (late down‐migrants). While natal rearing was more common, non‐natal fish were overrepresented among adult returns, and total returns were 1.4 times more stable than natal returns alone. Our results demonstrate that variation in migratory behaviour bolsters population stability. However, non‐natal rearing is reduced in low water years, suggesting that drought exacerbates population instability by reducing critical intrapopulation variation.

Although the eco‐evolutionary consequences of dispersal and exploitation are increasingly recognised, consideration of these effects and how they interact for management and conservation remains limited. We addressed this gap by examining population exploitation within a metapopulation framework, using Atlantic salmon as a case study. We compared eco‐evolutionary consequences of alternative exploitation strategies by incorporating selective exploitation based on life‐history traits and spatial dimension of exploitation (i.e., whether populations were net exporters or importers of individuals). We used a demo‐genetic agent‐based model to examine demographic and evolutionary consequences of these strategies across a gradient of population‐specific exploitation rates. At the metapopulation scale, we found both lower abundance and earlier sexual maturation with increasing exploitation, particularly when fishing was selective on larger individuals. The spatial selectivity of exploitation had an overall additional detrimental effect on metapopulation performance and fisheries yield, and induced stronger evolutionary changes than when exploitation was evenly spread over all populations. We discuss the implications of metapopulation functioning for species management and how considering dispersal patterns and intensity might change how we apply harvest. Nevertheless, our findings suggest that the safest approach remains to distribute exploitation efforts evenly across all populations, especially in the absence of variation in intrinsic productivity. However, this strategy might not completely prevent negative consequences at the local scale. Therefore, we advise managers to critically assess the relevance of our results and dispersal assumptions in the specific cases they may have to deal with.

Climate change is shifting the timing of organismal life‐history events. Although consequential food‐web mismatches can emerge if predators and prey shift at different rates, research on phenological shifts has traditionally focused on single trophic levels. Here, we analysed >2000 long‐term, monthly time series of phytoplankton, zooplankton, and fish abundance or biomass for the San Francisco, Chesapeake, and Massachusetts bays. Phenological shifts occurred in over a quarter (28%) of the combined series across all three estuaries. However, phenological trends for many taxa (ca. 29–68%) did not track the changing environment. While planktonic taxa largely advanced their phenologies, fishes displayed broad patterns of both advanced and delayed timing of peak abundance. Overall, these divergent patterns illustrate the potential for climate‐driven trophic mismatches. Our results suggest that even if signatures of global climate change differ locally, widespread phenological change has the potential to disrupt estuarine food webs.

Climate-induced flow alteration is subjecting mountain streams to more frequent and severe low-flow periods due to lower snowpack and earlier snowmelt. Yet, anticipating how stream ecosystems respond to prolonged low flows remains challenging because trophic levels can respond differently, and non-native predators could dampen or amplify responses. Here, we conducted a large-scale experiment to examine how early, prolonged low flows projected by the end of the century in California's Sierra Nevada will alter mountain stream food webs and emerging insect flux--a critical stream-to-land cross-ecosystem linkage. Additionally, we tested whether Brown trout (Salmo trutta), a widespread non-native top predator, would change food-web responses to low-flow conditions. We found that early low flows and non-native fish effects were additive rather than synergistic or antagonistic. Early low flows did not alter the overall rate of emerging insects but they did shift community structure and reduce the prevalence of small-sized individuals--possibly reflecting larger size at emergence and faster growth rates due to warming. In contrast, non-native fish presence increased seasonally-aggregated abundance of stream insects up to 12%, mainly by increasing abundance of Chironomidae and small-sized Ephemeroptera and Trichoptera. In channels with fish, benthic algal biomass doubled and scraper-grazer and collector-gatherer insects emerged 60% and 55% more than channels without fish, likely benefiting from trout keeping mesopredators at bay. This experiment illustrates that prolonged low flows and invasions can profoundly alter mountain river food webs even when operating additively; and shows how mesocosm-based research may help understand global-change driven disruption of cross-ecosystem linkages.

Conservation scientists have long used population viability analysis (PVA) on species count data to quantify trends and critical decline risk, thereby informing conservation actions. These assessments typically focus on single species rather than assemblages and assume that risk is consistent within a given life stage (e.g., across the different seasons or months of a year). However, if risk is assessed at too broad a temporal or spatial scale, it may overlook diverging population declines between predators and prey that disrupt biotic interactions. In this study, we used time-series based PVA for age-0 forage fishes and their potential zooplankton prey for each month of the year in the San Francisco Estuary, over 1995-2023 (N = 175 time series). We used Multivariate Autoregressive (MAR) models that estimate long-term population trends and variability (i.e., process error) for each population. We found widespread negative population trends across fish species (56.6%) and observed that critical decline risk is often higher in months when species abundances peak compared to ‘shoulder’ months. Although current decline risk is somewhat balanced between predators and their prey (mean 21.8% for fish and 21.4% for zooplankton), our time-series models indicate trophic levels are poised to diverge over the next 10 years, with fish generally accumulating risk faster than their prey. Additionally, zooplankton showed 11.5% higher uncertainty about their near-term critical decline risk relative to fish. These observations suggest strong, previously unreported potential for future trophic mismatches. Our results underscore the need to assess risk over finer temporal scales within and across trophic levels to better understand vulnerability, and thus inform conservation of imperiled species. Our approach is transferable and highlights the benefits of time-series based PVA to understand risk of food-web collapse in the face of climate-induced phenological shifts.

Captive‐breeding programs are increasingly implemented to curb population declines but can have unintended negative effects on genetic diversity and phenotypes. Through an analysis of ~10 years of genetic monitoring, pedigree information, and phenotypic data, we evaluated a captive‐breeding program that uses adaptive management to reduce inbreeding and improve captive broodstock performance. A captive‐breeding program was established in 2012 to reintroduce spring‐run Chinook salmon to the southern edge of their range in California's San Joaquin River (SJR), using fish produced each year at the nearby Feather River Hatchery (FRH). We found that the SJR program adequately captured the genetic diversity of the FRH source population and that mate pairings guided by genetic relatedness reduced inbreeding. However, the SJR broodstock reared in captivity had smaller body size at maturity in comparison to the FRH source broodstock which matures at sea, but this effect disappeared when SJR juveniles were released from captivity to mature at sea. Phenotypic traits of SJR female parents also influenced reproductive performance; older mothers and those with smaller eggs had offspring with lower survival. These findings demonstrate that adaptive genetic monitoring and pedigree information can be powerful tools for reducing risks of captive breeding and evaluating program effectiveness.

More than half of the world’s rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.

Dispersal is a ubiquitous ecological process that has been extensively studied in many plants and animals. Anadromous salmonids are an interesting system for examining dispersal, in part because of their well‐known philopatric behaviour, but also because of the conservation challenges related to the dispersal of hatchery‐origin fish. Building on earlier work, we provide an updated systematic review of dispersal and gene flow in anadromous salmonids. In particular, we compared studies on the dispersal of anadromous salmonids from wild and hatchery origins, including studies providing estimates of dispersal rates, observations of dispersal and results from modelling studies. We reviewed 228 studies and found these were unevenly distributed among species, with Atlantic salmon, Chinook salmon and sea trout being well‐represented. Our results showcase considerable variability in estimated dispersal rates within and across studies, which is likely related to the different methodologies, dispersal propensities across species and populations, and spatial extents considered. Overall, our results confirmed a higher tendency of hatchery fish to disperse relative to wild fish, but we also found some variation across species that warrants further study. Moreover, we found that dispersal propensity tended to decline exponentially with distance and that the drivers of dispersal varied considerably among studies. Additionally, we highlight various facets of dispersal captured across this suite of studies, including variation in terminology, methods and metrics for characterising dispersal, and the spatio‐temporal scales considered. Finally, our review revealed that few studies considered, and even fewer assessed, the implications of dispersal for the conservation and management of anadromous salmonids.