SSN2: The next generation of spatial stream network modeling in R.

The SSN2 package provides tools for spatial statistical modeling, parameter estimation, and prediction on stream (river) networks. SSN2 is the successor to the SSN package (Ver Hoef, Peterson, Clifford, & Shah, 2014), which was archived alongside broader changes in the -spatial ecosystem (Nowosad, 2023) that included 1) the retirement of rgdal (Bivand, Keitt, & Rowlingson, 2021), rgeos (Bivand & Rundel, 2020), and maptools (Bivand & Lewin-Koh, 2021) and 2) the lack of active development of sp (Bivand, Pebesma, & Gómez-Rubio, 2013). SSN2 maintains compatibility with the input data file structures used by the SSN package but leverages modern -spatial tools like sf (Pebesma, 2018).

Indexing and partitioning the spatial linear model for large data sets.

We consider four main goals when fitting spatial linear models: 1) estimating covariance parameters, 2) estimating fixed effects, 3) kriging (making point predictions), and 4) block-kriging (predicting the average value over a region). Each of these goals can present different challenges when analyzing large spatial data sets. Current research uses a variety of methods, including spatial basis functions (reduced rank), covariance tapering, etc, to achieve these goals.

Riparian vegetation shade restoration and loss effects on recent and future stream temperatures.

River temperatures are expected to increase this century harming species requiring cold-water habitat unless restoration activities protect or improve habitat availability. Local shading by riparian vegetation can cool water temperatures, but uncertainty exists over the scaling of this local effect to larger spatial extents. We evaluate this issue using a regional spatial stream network temperature model with covariates representing shade effects to predict mean August stream temperatures across 78,195 km of tributaries flowing into the Columbia River in the northwestern US.

Broad-scale eDNA sampling for describing aquatic species distributions in running waters: Pacific lamprey Entosphenus tridentatus in the upper Snake River, USA.

One of the most fundamental yet challenging tasks for aquatic ecologists is to precisely delineate the range of species, particularly those that are broadly distributed, require specialized sampling methods, and may be simultaneously declining and increasing in different portions of their range. An exemplar is the Pacific lamprey Entosphenus tridentatus, a jawless anadromous fish of conservation concern that is actively managed in many coastal basins in western North America. To efficiently determine its distribution across the accessible 56,168 km of the upper Snake River basin in the north-western United States, we first delimited potential habitat by using predictions from a species distribution model based on conventionally collected historical data and from the distribution of a potential surrogate, Chinook salmon Oncorhynchus tshawytscha, which yielded a potential habitat network of 10,615 km.

Do metapopulations and management matter for relict headwater bull trout populations in a warming climate?

Mountain headwater streams have emerged as important climate refuges for native cold-water species due to their slow climate velocities and extreme physical conditions that inhibit non-native invasions. Species persisting in refuges often do so as fragmented, relict populations from broader historical distributions that are subject to ongoing habitat reductions and increasing isolation as climate change progresses. Key for conservation planning is determining where remaining populations will persist and how habitat restoration strategies can improve biological resilience to enhance the long-term prospects for species of concern.

Application of multiple-population viability analysis to evaluate species recovery alternatives.

Population viability analysis (PVA) is a powerful conservation tool, but it remains impractical for many species, particularly species with multiple, broadly distributed populations for which collecting suitable data can be challenging. A recently developed method of multiple-population viability analysis (MPVA), however, addresses many limitations of traditional PVA. We built on previous development of MPVA for Lahontan cutthroat trout (LCT) (Oncorhynchus clarkii henshawi), a species listed under the U.

Hierarchical multi-population viability analysis.

Population viability analysis (PVA) uses concepts from theoretical ecology to provide a powerful tool for quantitative estimates of population dynamics and extinction risks. However, conventional statistical PVA requires long-term data from every population of interest, whereas many species of concern exist in multiple isolated populations that are only monitored occasionally. We present a hierarchical multi-population viability analysis model that increases inference power from sparse data by sharing information among populations to assess extinction risks while accounting for incomplete detection and sampling biases with explicit observation and sampling sub-models.

Ecological segregation moderates a climactic conclusion to trout hybridization.

For decades, it has been assumed that introgressive hybridization between introduced rainbow trout and native cutthroat trout in western North America will lead to genomic extinction of the latter. A broad-scale re-examination of their interaction indicates that ecological differences between these species and demographic processes are dictating the location and extent of their hybrid zones, and that runaway introgression between these taxa is unlikely.

Big biology meets microclimatology: defining thermal niches of ectotherms at landscape scales for conservation planning.

Temperature profoundly affects ecology, a fact ever more evident as the ability to measure thermal environments increases and global changes alter these environments. The spatial structure of thermalscapes is especially relevant to the distribution and abundance of ectothermic organisms, but the ability to describe biothermal relationships at extents and grains relevant to conservation planning has been limited by small or sparse data sets. Here, we combine a large occurrence database of >23 000 aquatic species surveys with stream microclimate scenarios supported by an equally large temperature database for a 149 000-km mountain stream network to describe thermal relationships for 14 fish and amphibian species.

Climate, Demography, and Zoogeography Predict Introgression Thresholds in Salmonid Hybrid Zones in Rocky Mountain Streams.

Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream databases and from 12 published studies of hybridization to assess whether environmental covariates could explain levels of introgression between westslope cutthroat trout and rainbow trout in the U.

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

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.

The cold-water climate shield: delineating refugia for preserving salmonid fishes through the 21st century.

The distribution and future fate of ectothermic organisms in a warming world will be dictated by thermalscapes across landscapes. That is particularly true for stream fishes and cold-water species like trout, salmon, and char that are already constrained to high elevations and latitudes. The extreme climates in those environments also preclude invasions by most non-native species, so identifying especially cold habitats capable of absorbing future climate change while still supporting native populations would highlight important refugia.

Probabilistic accounting of uncertainty in forecasts of species distributions under climate change.

Forecasts of species distributions under future climates are inherently uncertain, but there have been few attempts to describe this uncertainty comprehensively in a probabilistic manner. We developed a Monte Carlo approach that accounts for uncertainty within generalized linear regression models (parameter uncertainty and residual error), uncertainty among competing models (model uncertainty), and uncertainty in future climate conditions (climate uncertainty) to produce site-specific frequency distributions of occurrence probabilities across a species' range. We illustrated the method by forecasting suitable habitat for bull trout (Salvelinus confluentus) in the Interior Columbia River Basin, USA, under recent and projected 2040s and 2080s climate conditions.

Stream isotherm shifts from climate change and implications for distributions of ectothermic organisms.

Stream ecosystems are especially vulnerable to climate warming because most aquatic organisms are ectothermic and live in dendritic networks that are easily fragmented. Many bioclimatic models predict significant range contractions in stream biotas, but subsequent biological assessments have rarely been done to determine the accuracy of these predictions. Assessments are difficult because model predictions are either untestable or so imprecise that definitive answers may not be obtained within timespans relevant for effective conservation.

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 km(2)), based on empirical statistical models built from fish surveys at 9,890 sites.

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.

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.