David A. Boughton

Population genetic structure and ancestry of Oncorhynchus mykiss populations above and below dams in south-central California.

Genetic analyses of coastal Oncorhynchus mykiss, commonly known as steelhead/rainbow trout, at the southern extreme of their geographic range in California are used to evaluate ancestry and genetic relationships of populations both above and below large dams. Juvenile fish from 20 locations and strains of rainbow trout commonly planted in reservoirs in the five study basins were evaluated at 24 microsatellite loci. Phylogeographic trees and analysis of molecular variance demonstrated that populations within a basin, both above and below dams, were generally each other’s closest relatives. Absence of hatchery fish or their progeny in the tributaries above dams indicates that they are not commonly spawning and that above-barrier fish are descended from coastal steelhead trapped at dam construction. Finally, no genetic basis was found for the division of populations from this region into two distinct biological groups, contrary to current classification under the US and California Endangered Species Acts.

Incorporating Climate Science in Applications of the U.S. Endangered Species Act for Aquatic Species

Aquatic species are threatened by climate change but have received comparatively less attention than terrestrial species. We gleaned key strategies for scientists and managers seeking to address climate change in aquatic conservation planning from the literature and existing knowledge. We address 3 categories of conservation effort that rely on scientific analysis and have particular application under the U.S. Endangered Species Act (ESA): assessment of overall risk to a species; long-term recovery planning; and evaluation of effects of specific actions or perturbations. Fewer data are available for aquatic species to support these analyses, and climate effects on aquatic systems are poorly characterized. Thus, we recommend scientists conducting analyses supporting ESA decisions develop a conceptual model that links climate, habitat, ecosystem, and species response to changing conditions and use this model to organize analyses and future research. We recommend that current climate conditions are not appropriate for projections used in ESA analyses and that long-term projections of climate-change effects provide temporal context as a species-wide assessment provides spatial context. In these projections, climate change should not be discounted solely because the magnitude of projected change at a particular time is uncertain when directionality of climate change is clear. Identifying likely future habitat at the species scale will indicate key refuges and potential range shifts. However, the risks and benefits associated with errors in modeling future habitat are not equivalent. The ESA offers mechanisms for increasing the overall resilience and resistance of species to climate changes, including establishing recovery goals requiring increased genetic and phenotypic diversity, specifying critical habitat in areas not currently occupied but likely to become important, and using adaptive management. Incorporación de las Ciencias Climáticas en las Aplicaciones del Acta Estadunidense de Especies en Peligro para Especies Acuáticas.

Seasonal weather patterns drive population vital rates and persistence in a stream fish

Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark-recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout (Salvelinus fontinalis) at a broad spatial scale using a novel stage-structured population model. The data were a 15-year record of brook trout abundance from 72 sites distributed across a 170-km-long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site-specific conditions. Specifically, young-of-year survival was most strongly affected by spring temperature, adult survival by elevation and per-capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel-scouring flows on eggs and newly hatched individuals. However, high-elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density-dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage-structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics.

A Practical Comparison of Viability Models Used for Management of Endangered and Threatened Anadromous Pacific Salmonids

Abstract This study considered whether different population viability analyses give similar estimates of extinction risk across management contexts. We compared the performance of population viability analyses developed by numerous scientific teams to estimate extinction risk of anadromous Pacific salmonids listed under the U.S. Endangered Species Act and challenged each analysis with data from 34 populations. We found variation in estimated extinction risk among analytical techniques, which was driven by varying model assumptions and the inherent uncertainty of risk forecasts. This result indicates that the scientific teams developed techniques that perform differently. We recommend that managers minimize uncertainty in risk estimates by using multiple models tailored to the local ecology. Assessment of relative extinction risk was less sensitive to model assumptions than was assessment of absolute extinction risk. Thus, the former method is better for comparing population status and raises caution about...

Thermal Potential for Steelhead Life History Expression in a Southern California Alluvial River

AbstractSteelhead Oncorhynchus mykiss (anadromous Rainbow Trout) near the southern limit of the species’ range commonly use shallow alluvial rivers for migration, spawning, and rearing. These rivers have been widely modified for water management, and an enduring question is whether their rehabilitation would create summer nursery habitat for steelhead. We used process-based models to evaluate the thermal potential for steelhead nursery habitat in the Santa Ynez River, California, a regulated alluvial river that currently supports few steelhead. We assessed (1) how well a calibrated model of river heat fluxes predicted summer temperature patterns for a warm year and an average year; (2) whether those patterns created thermal potential for the rapid growth that is characteristic of steelhead nursery habitat; and (3) whether manipulation of flows from an upstream dam significantly altered thermal potential. In the heat flux model, the root mean square error for 15-min temperatures was 1.51°C, about three tim...

River response to large-dam removal in a Mediterranean hydroclimatic setting: Carmel River, California, USA: River response to large-dam removal

Dam removal provides a valuable opportunity to measure the fluvial response to changes in both sediment supply and the processes that shape channel morphology. We present the first study of river response to the removal of a large (32-m-high) dam in a Mediterranean hydroclimatic setting, on the Carmel River, coastal California, USA. This before-after/control-impact study measured changes in channel topography, grain size, and salmonid spawning habitat throughout dam removal and subsequent major floods. During dam removal, the river course was re-routed in order to leave most of the impounded sediment sequestered in the former reservoir and thus prevent major channel and floodplain aggradation downstream. However, a substantial sediment pulse occurred in response to base-level fall, knickpoint migration, and channel avulsion through sediment in the former reservoir above the newly re-routed channel. The sediment pulse advanced ~3.5 km in the first wet season after dam removal, resulting in decreased riverbed grain size downstream of the dam site. In the second wet season after dam removal, high flows (including a 30-year flood and two 10-year floods) transported sediment > 30 km downstream, filling pools and reducing cross-channel relief. Deposition of gravel in the second wet season after dam removal enhanced salmonid spawning habitat downstream of the dam site. We infer that in dam removals where most reservoir sediment remains impounded and where high flows follow soon after dam removal, flow sequencing becomes a more important driver of geomorphic and fish-habitat change than the dam removal alone.

Size-conditional smolting and the response of Carmel River steelhead to two decades of conservation efforts

Threshold effects are common in ecosystems and can generate counterintuitive outcomes in management interventions. A threshold effect proposed for steelhead trout (Oncorhynchus mykiss) is size-conditional smolting and marine survival. Steelhead are anadromous, maturing in the ocean but migrating to freshwater to spawn, where their offspring reside for one or more years before smolting—physiologically transforming to a saltwater form—and migrating to the ocean. In conditional smolting, juveniles transform only if growth exceeds a threshold body size prior to migration season, and subsequent marine survival correlates with size at ocean entry. Conditional smolting suggests that efforts to improve freshwater survival of juveniles may reduce smolt success if they increase competition and reduce growth. Using model-selection techniques, we asked if this effect explained declining numbers of adult Carmel River steelhead. This threatened population has been the focus of two decades of habitat restoration, as well as active translocation and captive-rearing of juveniles stranded in seasonally dewatered channels. In the top-ranked model selected by information-theoretic criteria, adult decline was linked to reduced juvenile growth rates in the lower river, consistent with the conditional smolting hypothesis. According to model inference, since 2005 most returning adult steelhead were captively-reared. However, a lower-ranked model without conditional smolting also had modest support, and suggested a negative effect of captive rearing. Translocations of juvenile fish to perennial reaches may have reduced the steelhead run slightly by raising competition, but this effect is confounded in the data with effects of river flow on growth. Efforts to recover Carmel River steelhead will probably be more successful if they focus on conditions promoting rapid growth in the river. Our analysis clearly favored a role for size-conditional smolting and marine survival in the decline of the population, but did not definitively rule out alternative explanations.