Genetic Structure across Broad Spatial and Temporal Scales: Rocky Mountain Tailed Frogs (Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate Rainforest

Hydroclimatic Conditions, Wildfire, and Species Assemblages Influence Co-Occurrence of Bull Trout and Tailed Frogs in Northern Rocky Mountain Streams

Although bull trout (Salvelinus confluentus) and tailed frogs (Ascaphus montanus) have co-existed in forested Pacific Northwest streams for millennia, these iconic cold-water specialists are experiencing rapid environmental change caused by a warming climate and enhanced wildfire activity. Our goal was to inform future conservation by examining the habitat associations of each species and conditions that facilitate co-occupancy. We repurposed data from previous studies in the northern Rocky Mountains to assess the efficacy of bull trout electrofishing surveys for determining the occurrence of tailed frogs and the predictive capacity of habitat covariates derived from in-stream measurements and geospatial sources to model distributions of both species. Electrofishing reliably detected frog presence (89.2% rate). Both species were strongly associated with stream temperature and flow regime characteristics, and less responsive to riparian canopy cover, slope, and other salmonids. Tailed frogs were also sensitive to wildfire, with occupancy probability peaking around 80 years after a fire. Co-occupancy was most probable in locations with low-to-moderate frequencies of high winter flow events, few other salmonids, a low base-flow index, and intermediate years since fire. The distributions of these species appear to be sensitive to environmental conditions that are changing this century in forests of the northern Rocky Mountains. The amplification of climate-driven effects after wildfire may prove to be particularly problematic in the future. Habitat differences between these two species, considered to be headwater specialists, suggest that conservation measures designed for one may not fully protect the other. Additional studies involving future climate and wildfire scenarios are needed to assess broader conservation strategies and the potential to identify refuge streams where both species are likely to persist, or complementary streams where each could exist separately into the future.

Comparative phylogeography of two Northern Rocky Mountain endemics: the widespread Anguispira kochi occidentalis and the narrow-range Anguispira nimapuna (Gastropoda: Discidae)

The Northern Rocky Mountain ecosystem supports rich biological diversity with many endemic and rare species. Extant endemics display two biogeographic patterns: widespread species with fragmented populations, and narrow-range endemics. These distributions are shown by the congeneric snails Anguispira kochi occidentalis and Anguispira nimapuna. These two taxa are disjunct from the remaining species of the genus, which achieves its greatest diversity in eastern North America. Given the disjunct nature of A. k. occidentalis and A. nimapuna, we here present a mtDNA phylogeny of the genus that includes both eastern and western species to assess the phylogenetic position of A. k. occidentalis and A. nimapuna. We then reconstruct the demographic history of A. k. occidentalis and A. nimapuna by analysing current patterns of genetic variation and interpreting the results considering the historical biogeography of the region. Both A. k. occidentalis and A. nimapuna represent unique taxa that are genetically and geographically distinct from their congeners. The current distribution and genetic structure of A. k. occidentalis has been shaped by both historical isolation in refugia and more recent northward shifts, whereas A. nimapuna is represented by two populations with shallow divergence in an area of long-term habitat stability.

Circuitscape in Julia: Empowering Dynamic Approaches to Connectivity Assessment

The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.

Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.

Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections

Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches-allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in phrapl. We then expand this model selection framework by including an assessment of absolute fit of the models to the data. For this, we utilize DNA isolated from existing natural history collections that span the distribution of red alder (Alnus rubra) in the Pacific Northwest of North America to generate genomic data for the evaluation of 13 demographic scenarios. The quality of DNA recovered from herbarium specimen leaf tissue was assessed for its utility and effectiveness in demographic model selection, specifically in the two approaches mentioned. We present strong support for the use of herbarium tissue in the generation of genomic DNA, albeit with the inclusion of additional quality control checks prior to library preparation and analyses with multiple approaches that incorporate various data. Analyses with allele frequency spectra and gene trees predominantly support A. rubra having experienced an ancient vicariance event with intermittent and frequent gene flow between the disjunct populations. Additionally, the data consistently fit the most frequently selected model, corroborating the model selection techniques. Finally, these results suggest that the A. rubra disjunct populations do not represent separate species.

High genetic diversity of common toad (Bufo bufo) populations under strong natural fragmentation on a Northern archipelago

The last decades have shown a surge in studies focusing on the interplay between fragmented habitats, genetic variation, and conservation. In the present study, we consider the case of a temperate pond-breeding anuran (the common toad Bufo bufo) inhabiting a naturally strongly fragmented habitat at the Northern fringe of the species' range: islands offshore the Norwegian coast. A total of 475 individuals from 19 populations (three mainland populations and 16 populations on seven adjacent islands) were genetically characterized using nine microsatellite markers. As expected for a highly fragmented habitat, genetic distances between populations were high (pairwise F st values ranging between 0.06 and 0.33), with however little differences between populations separated by ocean and populations separated by terrestrial habitat (mainland and on islands). Despite a distinct cline in genetic variation from mainland populations to peripheral islands, the study populations were characterized by overall high genetic variation, in line with effective population sizes derived from single-sample estimators which were on average about 20 individuals. Taken together, our results reinforce the notion that spatial and temporal scales of fragmentation need to be considered when studying the interplay between landscape fragmentation and genetic erosion.