The importance of warm habitat to the growth regime of cold-water fishes.

A common goal of biological adaptation planning is to identify and prioritize locations that remain suitably cool during summer. This implicitly devalues areas that are ephemerally warm, even if they are suitable most of the year for mobile animals. Here we develop an alternative conceptual framework, the growth regime, which considers seasonal and landscape variation in physiological performance, focusing on riverine fish. Using temperature models for 14 river basins, we show that growth opportunities propagate up and down river networks on a seasonal basis, and that downstream habitats that are suboptimally warm in summer may actually provide the majority of growth potential expressed annually. We demonstrate with an agent-based simulation that shoulder-season use of warmer downstream habitats can fuel annual fish production. Our work reveals a synergy between cold and warm habitats that could be fundamental for supporting coldwater fisheries, highlighting the risk in conservation strategies that underappreciate warm habitats.

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem.

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Corrigendum: Ecosystem experiment reveals benefits of natural and simulated beaver dams to a threatened population of steelhead (Oncorhynchus mykiss).

This corrects the article DOI: 10.1038/srep28581.

Alteration of stream temperature by natural and artificial beaver dams.

Beaver are an integral component of hydrologic, geomorphic, and biotic processes within North American stream systems, and their propensity to build dams alters stream and riparian structure and function to the benefit of many aquatic and terrestrial species. Recognizing this, beaver relocation efforts and/or application of structures designed to mimic the function of beaver dams are increasingly being utilized as effective and cost-efficient stream and riparian restoration approaches. Despite these verities, the notion that beaver dams negatively impact stream habitat remains common, specifically the assumption that beaver dams increase stream temperatures during summer to the detriment of sensitive biota such as salmonids. In this study, we tracked beaver dam distributions and monitored water temperature throughout 34 km of stream for an eight-year period between 2007 and 2014. During this time the number of natural beaver dams within the study area increased by an order of magnitude, and an additional 4 km of stream were subject to a restoration manipulation that included installing a high-density of Beaver Dam Analog (BDA) structures designed to mimic the function of natural beaver dams. Our observations reveal several mechanisms by which beaver dam development may influence stream temperature regimes; including longitudinal buffering of diel summer temperature extrema at the reach scale due to increased surface water storage, and creation of cool-water channel scale temperature refugia through enhanced groundwater-surface water connectivity. Our results suggest that creation of natural and/or artificial beaver dams could be used to mitigate the impact of human induced thermal degradation that may threaten sensitive species.

Ecosystem experiment reveals benefits of natural and simulated beaver dams to a threatened population of steelhead (Oncorhynchus mykiss).

Beaver have been referred to as ecosystem engineers because of the large impacts their dam building activities have on the landscape; however, the benefits they may provide to fluvial fish species has been debated. We conducted a watershed-scale experiment to test how increasing beaver dam and colony persistence in a highly degraded incised stream affects the freshwater production of steelhead (Oncorhynchus mykiss). Following the installation of beaver dam analogs (BDAs), we observed significant increases in the density, survival, and production of juvenile steelhead without impacting upstream and downstream migrations. The steelhead response occurred as the quantity and complexity of their habitat increased. This study is the first large-scale experiment to quantify the benefits of beavers and BDAs to a fish population and its habitat. Beaver mediated restoration may be a viable and efficient strategy to recover ecosystem function of previously incised streams and to increase the production of imperiled fish populations.

Using Inverse Probability Bootstrap Sampling to Eliminate Sample Induced Bias in Model Based Analysis of Unequal Probability Samples.

In ecology, as in other research fields, efficient sampling for population estimation often drives sample designs toward unequal probability sampling, such as in stratified sampling. Design based statistical analysis tools are appropriate for seamless integration of sample design into the statistical analysis. However, it is also common and necessary, after a sampling design has been implemented, to use datasets to address questions that, in many cases, were not considered during the sampling design phase. Questions may arise requiring the use of model based statistical tools such as multiple regression, quantile regression, or regression tree analysis. However, such model based tools may require, for ensuring unbiased estimation, data from simple random samples, which can be problematic when analyzing data from unequal probability designs. Despite numerous method specific tools available to properly account for sampling design, too often in the analysis of ecological data, sample design is ignored and consequences are not properly considered. We demonstrate here that violation of this assumption can lead to biased parameter estimates in ecological research. In addition, to the set of tools available for researchers to properly account for sampling design in model based analysis, we introduce inverse probability bootstrapping (IPB). Inverse probability bootstrapping is an easily implemented method for obtaining equal probability re-samples from a probability sample, from which unbiased model based estimates can be made. We demonstrate the potential for bias in model-based analyses that ignore sample inclusion probabilities, and the effectiveness of IPB sampling in eliminating this bias, using both simulated and actual ecological data. For illustration, we considered three model based analysis tools--linear regression, quantile regression, and boosted regression tree analysis. In all models, using both simulated and actual ecological data, we found inferences to be biased, sometimes severely, when sample inclusion probabilities were ignored, while IPB sampling effectively produced unbiased parameter estimates.

Modelling dendritic ecological networks in space: an integrated network perspective.

Dendritic ecological networks (DENs) are a unique form of ecological networks that exhibit a dendritic network topology (e.g. stream and cave networks or plant architecture). DENs have a dual spatial representation; as points within the network and as points in geographical space. Consequently, some analytical methods used to quantify relationships in other types of ecological networks, or in 2-D space, may be inadequate for studying the influence of structure and connectivity on ecological processes within DENs. We propose a conceptual taxonomy of network analysis methods that account for DEN characteristics to varying degrees and provide a synthesis of the different approaches within the context of stream ecology. Within this context, we summarise the key innovations of a new family of spatial statistical models that describe spatial relationships in DENs. Finally, we discuss how different network analyses may be combined to address more complex and novel research questions. While our main focus is streams, the taxonomy of network analyses is also relevant anywhere spatial patterns in both network and 2-D space can be used to explore the influence of multi-scale processes on biota and their habitat (e.g. plant morphology and pest infestation, or preferential migration along stream or road corridors).