Daniel J. Isaak

Flow regime, temperature, and biotic interactions drive differential declines of trout species under climate change

Broad-scale studies of climate change effects on freshwater species have focused mainly on temperature, ignoring critical drivers such as flow regime and biotic interactions. We use downscaled outputs from general circulation models coupled with a hydrologic model to forecast the effects of altered flows and increased temperatures on four interacting species of trout across the interior western United States (1.01 million km2), based on empirical statistical models built from fish surveys at 9,890 sites. Projections under the 2080s A1B emissions scenario forecast a mean 47% decline in total suitable habitat for all trout, a group of fishes of major socioeconomic and ecological significance. We project that native cutthroat trout Oncorhynchus clarkii, already excluded from much of its potential range by nonnative species, will lose a further 58% of habitat due to an increase in temperatures beyond the species’ physiological optima and continued negative biotic interactions. Habitat for nonnative brook trout Salvelinus fontinalis and brown trout Salmo trutta is predicted to decline by 77% and 48%, respectively, driven by increases in temperature and winter flood frequency caused by warmer, rainier winters. Habitat for rainbow trout, Oncorhynchus mykiss, is projected to decline the least (35%) because negative temperature effects are partly offset by flow regime shifts that benefit the species. These results illustrate how drivers other than temperature influence species response to climate change. Despite some uncertainty, large declines in trout habitat are likely, but our findings point to opportunities for strategic targeting of mitigation efforts to appropriate stressors and locations.

Effects of climate change and wildfire on stream temperatures and salmonid thermal habitat in a mountain river network

Mountain streams provide important habitats for many species, but their faunas are especially vulnerable to climate change because of ectothermic physiologies and movements that are constrained to linear networks that are easily fragmented. Effectively conserving biodiversity in these systems requires accurate downscaling of climatic trends to local habitat conditions, but downscaling is difficult in complex terrains given diverse microclimates and mediation of stream heat budgets by local conditions. We compiled a stream temperature database (n = 780) for a 2500-km river network in central Idaho to assess possible trends in summer temperatures and thermal habitat for two native salmonid species from 1993 to 2006. New spatial statistical models that account for network topology were parameterized with these data and explained 93% and 86% of the variation in mean stream temperatures and maximas, respectively. During our study period, basin average mean stream temperatures increased by 0.38 degrees C (0.27 degrees C/decade), and maximas increased by 0.48 degrees C (0.34 degrees C/decade), primarily due to long-term (30-50 year) trends in air temperatures and stream flows. Radiation increases from wildfires accounted for 9% of basin-scale temperature increases, despite burning 14% of the basin. Within wildfire perimeters, however, stream temperature increases were 2-3 times greater than basin averages, and radiation gains accounted for 50% of warming. Thermal habitat for rainbow trout (Oncorhynchus mykiss) was minimally affected by temperature increases, except for small shifts towards higher elevations. Bull trout (Salvelinus confluentus), in contrast, were estimated to have lost 11-20% (8-16%/decade) of the headwater stream lengths that were cold enough for spawning and early juvenile rearing, with the largest losses occurring in the coldest habitats. Our results suggest that a warming climate has begun to affect thermal conditions in streams and that impacts to biota will be specific to both species and context. Where species are at risk, conservation actions should be guided based on considerations of restoration opportunity and future climatic effects. To refine predictions based on thermal effects, more work is needed to understand mechanisms associated with biological responses, climate effects on other habitat features, and habitat configurations that confer population resilience.

Climate change effects on stream and river temperatures across the northwest U.S. from 1980–2009 and implications for salmonid fishes

Thermal regimes in rivers and streams are fundamentally important to aquatic ecosystems and are expected to change in response to climate forcing as the Earth’s temperature warms. Description and attribution of stream temperature changes are key to understanding how these ecosystems may be affected by climate change, but difficult given the rarity of long-term monitoring data. We assembled 18 temperature time-series from sites on regulated and unregulated streams in the northwest U.S. to describe historical trends from 1980–2009 and assess thermal consistency between these stream categories. Statistically significant temperature trends were detected across seven sites on unregulated streams during all seasons of the year, with a cooling trend apparent during the spring and warming trends during the summer, fall, and winter. The amount of warming more than compensated for spring cooling to cause a net temperature increase, and rates of warming were highest during the summer (raw trend = 0.17°C/decade; reconstructed trend = 0.22°C/decade). Air temperature was the dominant factor explaining long-term stream temperature trends (82–94% of trends) and inter-annual variability (48–86% of variability), except during the summer when discharge accounted for approximately half (52%) of the inter-annual variation in stream temperatures. Seasonal temperature trends at eleven sites on regulated streams were qualitatively similar to those at unregulated sites if two sites managed to reduce summer and fall temperatures were excluded from the analysis. However, these trends were never statistically significant due to greater variation among sites that resulted from local water management policies and effects of upstream reservoirs. Despite serious deficiencies in the stream temperature monitoring record, our results suggest many streams in the northwest U.S. are exhibiting a regionally coherent response to climate forcing. More extensive monitoring efforts are needed as are techniques for short-term sensitivity analysis and reconstructing historical temperature trends so that spatial and temporal patterns of warming can be better understood. Continuation of warming trends this century will increasingly stress important regional salmon and trout resources and hamper efforts to recover these species, so comprehensive vulnerability assessments are needed to provide strategic frameworks for prioritizing conservation efforts.

CHINOOK SALMON USE OF SPAWNING PATCHES: RELATIVE ROLES OF HABITAT QUALITY, SIZE, AND CONNECTIVITY

Declines in many native fish populations have led to reassessments of management goals and shifted priorities from consumptive uses to species preservation. As management has shifted, relevant environmental characteristics have evolved from traditional metrics that described local habitat quality to characterizations of habitat size and connectivity. Despite the implications this shift has for how habitats may be prioritized for conservation, it has been rare to assess the relative importance of these habitat components. We used an information-theoretic approach to select the best models from sets of logistic regressions that linked habitat quality, size, and connectivity to the occurrence of chinook salmon (Oncorhynchus tshawytscha) nests. Spawning distributions were censused annually from 1995 to 2004, and data were complemented with field measurements that described habitat quality in 43 suitable spawning patches across a stream network that drained 1150 km2 in central Idaho. Results indicated that the most plausible models were dominated by measures of habitat size and connectivity, whereas habitat quality was of minor importance. Connectivity was the strongest predictor of nest occurrence, but connectivity interacted with habitat size, which became relatively more important when populations were reduced. Comparison of observed nest distributions to null model predictions confirmed that the habitat size association was driven by a biological mechanism when populations were small, but this association may have been an area-related sampling artifact at higher abundances. The implications for habitat management are that the size and connectivity of existing habitat networks should be maintained whenever possible. In situations where habitat restoration is occurring, expansion of existing areas or creation of new habitats in key areas that increase connectivity may be beneficial. Information about habitat size and connectivity also could be used to strategically prioritize areas for improvement of local habitat quality, with areas not meeting minimum thresholds being deemed inappropriate for pursuit of restoration activities.

Macroscale hydrologic modeling of ecologically relevant flow metrics

Stream hydrology strongly affects the structure of aquatic communities. Changes to air temperature and precipitation driven by increased greenhouse gas concentrations are shifting timing and volume of streamflows potentially affecting these communities. The variable infiltration capacity (VIC) macroscale hydrologic model has been employed at regional scales to describe and forecast hydrologic changes but has been calibrated and applied mainly to large rivers. An important question is how well VIC runoff simulations serve to answer questions about hydrologic changes in smaller streams, which are important habitat for many fish species. To answer this question, we aggregated gridded VIC outputs within the drainage basins of 55 streamflow gages in the Pacific Northwest United States and compared modeled hydrographs and summary metrics to observations. For most streams, several ecologically relevant aspects of the hydrologic regime were accurately modeled, including center of flow timing, mean annual and summer flows and frequency of winter floods. Frequencies of high and low flows in the summer were not well predicted, however. Predictions were worse for sites with strong groundwater influence, and some sites showed errors that may result from limitations in the forcing climate data. Higher resolution (1/16th degree) modeling provided small improvements over lower resolution (1/8th degree). Despite some limitations, the VIC model appears capable of representing several ecologically relevant hydrologic characteristics in streams, making it a useful tool for understanding the effects of hydrology in delimiting species distributions and predicting the potential effects of climate shifts on aquatic organisms.Related website: Western US Stream Flow Metric Dataset

Fine-scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: Insights from spatial autocorrelation analysis of individual genotypes

Natal homing is a hallmark of the life history of salmonid fishes, but the spatial scale of homing within local, naturally reproducing salmon populations is still poorly understood. Accurate homing (paired with restricted movement) should lead to the existence of fine‐scale genetic structuring due to the spatial clustering of related individuals on spawning grounds. Thus, we explored the spatial resolution of natal homing using genetic associations among individual Chinook salmon (Oncorhynchus tshawytscha) in an interconnected stream network. We also investigated the relationship between genetic patterns and two factors hypothesized to influence natal homing and localized movements at finer scales in this species, localized patterns in the distribution of spawning gravels and sex. Spatial autocorrelation analyses showed that spawning locations in both sub‐basins of our study site were spatially clumped, but the upper sub‐basin generally had a larger spatial extent and continuity of redd locations than the lower sub‐basin, where the distribution of redds and associated habitat conditions were more patchy. Male genotypes were not autocorrelated at any spatial scale in either sub‐basin. Female genotypes showed significant spatial autocorrelation and genetic patterns for females varied in the direction predicted between the two sub‐basins, with much stronger autocorrelation in the sub‐basin with less continuity in spawning gravels. The patterns observed here support predictions about differential constraints and breeding tactics between the two sexes and the potential for fine‐scale habitat structure to influence the precision of natal homing and localized movements of individual Chinook salmon on their breeding grounds.

Slow climate velocities of mountain streams portend their role as refugia for cold-water biodiversity

Significance Many studies predict climate change will cause widespread extinctions of flora and fauna in mountain environments because of temperature increases, enhanced environmental variability, and invasions by nonnative species. Cold-water organisms are thought to be at particularly high risk, but most predictions are based on small datasets and imprecise surrogates for water temperature trends. Using large stream temperature and biological databases, we show that thermal habitat in mountain streams is highly resistant to temperature increases and that many populations of cold-water species exist where they are well-buffered from climate change. As a result, there is hope that many native species dependent on cold water can persist this century and mountain landscapes will play an important role in that preservation. The imminent demise of montane species is a recurrent theme in the climate change literature, particularly for aquatic species that are constrained to networks and elevational rather than latitudinal retreat as temperatures increase. Predictions of widespread species losses, however, have yet to be fulfilled despite decades of climate change, suggesting that trends are much weaker than anticipated and may be too subtle for detection given the widespread use of sparse water temperature datasets or imprecise surrogates like elevation and air temperature. Through application of large water-temperature databases evaluated for sensitivity to historical air-temperature variability and computationally interpolated to provide high-resolution thermal habitat information for a 222,000-km network, we estimate a less dire thermal plight for cold-water species within mountains of the northwestern United States. Stream warming rates and climate velocities were both relatively low for 1968–2011 (average warming rate = 0.101 °C/decade; median velocity = 1.07 km/decade) when air temperatures warmed at 0.21 °C/decade. Many cold-water vertebrate species occurred in a subset of the network characterized by low climate velocities, and three native species of conservation concern occurred in extremely cold, slow velocity environments (0.33–0.48 km/decade). Examination of aggressive warming scenarios indicated that although network climate velocities could increase, they remain low in headwaters because of strong local temperature gradients associated with topographic controls. Better information about changing hydrology and disturbance regimes is needed to complement these results, but rather than being climatic cul-de-sacs, many mountain streams appear poised to be redoubts for cold-water biodiversity this century.

The past as prelude to the future for understanding 21st-Century climate effects on Rocky Mountain trout

ABSTRACT Bioclimatic models predict large reductions in native trout across the Rocky Mountains in the 21st century but lack details about how changes will occur. Through five case histories across the region, we explore how a changing climate has been affecting streams and the potential consequences for trout. Monitoring records show trends in temperature and hydrographs consistent with a warming climate in recent decades. Biological implications include upstream shifts in thermal habitats, risk of egg scour, increased wildfire disturbances, and declining summer habitat volumes. The importance of these factors depends on the context, but temperature increases are most relevant where population boundaries are mediated by thermal constraints. Summer flow declines and wildfires will be important where trout populations are fragmented and constrained to small refugia. A critical information gap is evidence documenting how populations are adjusting to long-term habitat trends, so biological monitoring is a pr...

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

Linking Climate Change and Fish Conservation Efforts Using Spatially Explicit Decision Support Tools

Fisheries professionals are increasingly tasked with incorporating climate change projections into their deci- sions. Here we demonstrate how a structured decision frame- work, coupled with analytical tools and spatial data sets, can help integrate climate and biological information to evaluate management alternatives. We present examples that link down- scaled climate change scenarios to fish populations for two common types of problems: (1) strategic spatial prioritization of limited conservation resources and (2) deciding whether removing migration barriers would benefit a native fish also threatened with invasion by a nonnative competitor. We used Bayesian networks (BNs) to translate each decision problem into a quantitative tool and implemented these models under historical and future climate projections. The spatial prioriti- zation BN predicted a substantial loss of habitat for the target species by the 2080s and provided a means to map habitats and populations most likely to persist under future climate projec- tions. The barrier BN applied to three streams predicted that barrier removal decisions—previously made assuming a sta- tionary climate—were likely robust under the climate scenario considered. The examples demonstrate the benefit of structuring the decision-making process to clarify management objectives, formalize assumptions, synthesize current understanding about climate effects on fish populations, and identify key uncertain- ties requiring further investigation.