A Snow-tracking Protocol Used to Delineate Local Lynx, Lynx canadensis, Distributions

Determining Canada Lynx (Lynx canadensis) distribution is an important management need, especially at the southern extent of the species range where it is listed as threatened under the U. S. Endangered Species Act. We describe a systematic snowtrack based sampling framework that provides reliable distribution data for Canada Lynx. We used computer simulations to evaluate protocol efficacy. Based on these simulations, the probability of detecting lynx tracks during a single visit (8 km transect) to a survey unit ranged from approximately 0.23 for surveys conducted only one day after snowfall, to 0.78 for surveys conducted 7 days after a snowfall. If the survey effort was increased to three visits, then detection probabilities increased substantially from 0.58 for one day after snowfall to about 0.95 for surveys conducted 7 days after a snowfall. We tested the protocol in the Garnet Range, Montana, where most lynx were radio-collared. We documented a total of 189 lynx tracks during two winters (2001-2003). Lynx distribution based on snow-track surveys was coincident with the area defined through radio telemetry. Additionally, we conducted snow-track surveys in areas of western Wyoming where lynx were believed present but scarce. We detected a total of six lynx tracks during three winters (1999-2002). In Wyoming , where lynx presence was inferred from a few tracks, we verified species identification by securing genetic samples (hairs from daybeds) along track-lines

Broad-Scale Genetic And Compositional Monitoring Of Aquatic Vertebrate Populations: A Proof Of Concept In The Interior Columbia River And Upper Misouri River Basins

Monitoring fish and amphibian populations is essential for evaluating conservation efforts and the status and trends of individual species, but measuring abundance is time-consuming and problematic at large scales. Also, relations between fish populations and their surrogates, such as habitat characteristics, are often obscure. As an alternative, genetic assessment and monitoring offers promise as an indicator of population status and trends by providing information on genetic diversity, connectivity among populations, and the prevalence of hybridization with non-native species. We have undertaken intensive sampling of native and nonnative fishes and amphibians in streams monitored by the Pacfish/Infish Biological Opinion Monitoring Program, which includes a spatially comprehensive, random sample of subbasins in the interior Columbia River Basin and upper Missouri River Basin. We have also developed a panel of ~100 single nucleotide polymorphism markers for cutthroat trout, redband trout, and rainbow trout to describe patterns of hybridization and landscape genetic structure. If fully realized, analyses of tissues sampled from over 1500 streams in Montana, Idaho, eastern Oregon, and eastern Washington on federal lands should permit broad-scale evaluations of the status and distribution of much of the aquatic vertebrate fauna and enable detection of responses to climate change. Preliminary results of sampling at nearly 700 sites on almost 300 western Montana and northern Idaho streams indicate that westslope cutthroat trout occupy headwater sites in most of their historical range except in the Kootenai and Missouri River basins, brook trout are more widely distributed than previously recognized, and the taxonomic complexity of sculpins is underappreciated

Genetic Sampling of Palmer\u27s Chipmunks in the Spring Mountains, Nevada

Palmer\u27s chipmunk (Neotamias palmeri) is a medium-sized chipmunk whose range is limited to the higherelevation areas of the Spring Mountain Range, Nevada. A second chipmunk species, the Panamint chipmunk (Neotamias panamintinus), is more broadly distributed and lives in lower-elevation, primarily pinyon-juniper (Pinus monophylla-Juniperus osteosperma) habitat types. Panamint chipmunks are not closely related to Palmer\u27s, but field identification of the 2 species is unreliable. Palmer\u27s chipmunk is a species of concern in the state of Nevada and is listed by the International Union for Conservation of Nature (IUCN) as endangered. As such, conservation of Palmer\u27s chipmunks is a priority in the Spring Mountains National Recreation Area. We sampled putative Palmer\u27s chipmunks from 13 sites distributed across the Spring Mountains during 2010–2011. We removed Panamint chipmunks by using DNA-based identifications and then analyzed the genetic population structure of Palmer\u27s chipmunks by using a panel of 9 microsatellites. Of the 228 samples that were genotyped, 186 were Palmer\u27s; there was no evidence of hybridization between species. Four sites had exclusively Panamint chipmunks, 5 had exclusively Palmer\u27s chipmunks, and 3 had a mixture of the 2 species. In this study, Palmer\u27s chipmunks were exclusively captured at sites above 2400 m elevation, and Panamint chipmunks were exclusively captured at sites below 2200 m. Panamint chipmunks were trapped in areas typed as pinyon-juniper, but they were also trapped at sites typed as ponderosa pine (Pinus ponderosa) and mixed conifer. Both species were trapped at 3 sites; at all 3 sites, the lowerelevation traps contained Panamint chipmunks and the higher ones Palmer\u27s chipmunks. Population structure within Palmer\u27s chipmunks was minimal: heterozygosity was relatively high, and the populations displayed no signs of recent bottlenecks. Indications are that the distribution of Palmer\u27s chipmunk is limited to higher-elevation areas in the Spring Mountains, but within this area, Palmer\u27s chipmunk occurs as a single, large, well-connected, and stable population

Grizzly Bear Population Trend Estimated Using Genetic Detection

We use genetic detection data from natural bear rub sites to estimate annual rate of change for a threatened grizzly bear (Ursus arctos) population in the 33,300 km2 Northern Continental Divide Ecosystem (NCDE) in northwestern Montana, USA). Bear rubs were surveyed twice annually in 2004, 2009-2012 (3,580 – 4,805 rubs).  We detected approximately 1/3 of the grizzly bear population annually. Using spatially explicit capturerecapture (SCR) models in a maximum likelihood framework, we estimate growth rate from the slope of a linear regression fit to the log of density estimates.  To evaluate the usefulness of our estimates, we compare them to estimates of ? made using independent data from known-fate telemetry monitoring for our population.  Total annual population rate of change was 1.056 (95% CI = 1.033-1.079). The large sample sizes generated by genetic detection provided information on variation in density and trend within the NCDE useful for designing monitoring and management strategies tailored to area-specific needs and priorities.  Local rates of change within the NCDE were higher in areas of lower density and population expansion than in Glacier NP, the area with highest density.  As density increased, the amount of space used by bears estimated by the SCR models, ?, decreased. Hair collection from natural bear rub sites was an efficient sampling approach able to generate precise estimates of annual growth rate from 2 years of data

Something’s Fishy: A Genetic Investigations Of Sculpin Species In Western Montana

Sculpin (Cottus spp.) are small, cryptic, bottom-dwelling fish native to cool and coldwater systems throughout North America. Although three species of primarily streamdwelling sculpin are thought to occur in Montana (one of which is a species of concern), their taxonomy, distribution, and origin are not well understood. In western Montana, the present distribution of sculpin species may have been shaped by both historical events, e.g., the Columbian Ice Sheet, and contemporary landscape changes (passage barriers, climate change, pollution, etc.). To evaluate sculpin presence, and species diversity, we analyzed sculpins from river drainages throughout western Montana—the Clark Fork, Blackfoot, Flathead, Bitterroot, Kootenai, Gallatin, Madison, and Missouri—east and west of the Continental Divide. We analyzed 135 samples at the mitochondrial DNA COXI gene and at 11 microsatellite DNA loci. Preliminary results of genetic analysis suggest the presence of four distinct species with hybridization among three of the species in some locations. Hybridization led to uncertainty in species designations based on morphology, but even genetically pure fish were occasionally misidentified. One species may represent an undescribed taxon that is limited in its distribution to the St. Regis drainage, although its relation to sculpin in Idaho is unknown. A second species, previously thought to be Cottus bairdii, is distinct from that taxon and is distributed on both sides of the Continental Divide

When Reintroductions are Augmentations: The Genetic Legacy of Fishers (Martes Pennanti) in Montana

Fishers (Martes pennanti) were purportedly extirpated from Montana by 1930 and extant populations are assumed to be descended from translocated fishers. To determine the lineage of fisher populations, we sequenced 2 regions of the mitochondrial DNA genome from 207 tissue samples from British Columbia, Minnesota, Wisconsin, and Montana. In northwestern Montana, fishers share haplotypes with samples from the upper Midwest and British Columbia; in west-central Montana, we detected haplotypes found in British Columbia samples, but also detected a control region and cytochrome-b haplotype not found in source populations. Based on the unique haplotypes found in west-central Montana, we propose that individuals with these haplotypes are descended from a relic population. Fishers in northwestern Montana are likely descended from fishers from the Midwest and British Columbia

Robust Detection of Rare Species Using Environmental DNA: the Importance of Primer Specificity

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method\u27s sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. In this study we test factors that influence the specificity and sensitivity of TaqMan MGB assays using co-occurring, closely related brook trout (Salvelinus fontinalis) and bull trout (S. confluentus) as a case study. We found qPCR to be substantially more sensitive than traditional PCR, with a high probability of detection at concentrations as low as 0.5 target copies/ml. We also found that number and placement of base pair mismatches between the Taqman MGB assay and non-target templates was important to target specificity, and that specificity was most influenced by base pair mismatches in the primers, rather than in the probe. We found that insufficient specificity can result in both false positive and false negative results, particularly in the presence of abundant related species. Our results highlight the utility of qPCR as a highly sensitive eDNA tool, and underscore the importance of careful assay design

Climate Change Predicted to Shift Wolverine Distributions, Connectivity, and Dispersal Corridors

Boreal species sensitive to the timing and duration of snow cover are particularly vulnerable to global climate change. Recent work has shown a link between wolverine (Gulo gulo) habitat and persistent spring snow cover through 15 May, the approximate end of the wolverine’s reproductive denning period. We modeled the distribution of snow cover within the Columbia, Upper Missouri, and Upper Colorado River Basins using a downscaled ensemble climate model. The ensemble model was based on the arithmetic mean of 10 global climate models (GCMs) that best fit historical climate trends and patterns within these three basins. Snow cover was estimated from resulting downscaled temperature and precipitation patterns using a hydrologic model. We bracketed our ensemble model predictions by analyzing warm (miroc 3.2) and cool (pcm1) downscaled GCMs. Because Moderate-Resolution Imaging Spectroradiometer (MODIS)-based snow cover relationships were analyzed at much finer grain than downscaled GCM output, we conducted a second analysis based on MODIS-based snow cover that persisted through 29 May, simulating the onset of spring two weeks earlier in the year. Based on the downscaled ensemble model, 67% of predicted spring snow cover will persist within the study area through 2030–2059, and 37% through 2070–2099. Estimated snow cover for the ensemble model during the period 2070– 2099 was similar to persistent MODIS snow cover through 29 May. Losses in snow cover were greatest at the southern periphery of the study area (Oregon, Utah, and New Mexico, USA) and least in British Columbia, Canada. Contiguous areas of spring snow cover become smaller and more isolated over time, but large (.1000 km2) contiguous areas of wolverine habitat are predicted to persist within the study area throughout the 21st century for all projections. Areas that retain snow cover throughout the 21st century are British Columbia, north-central Washington, northwestern Montana, and the Greater Yellowstone Area. By the late 21st century, dispersal modeling indicates that habitat isolation at or above levels associated with genetic isolation of wolverine populations becomes widespread. Overall, we expect wolverine habitat to persist throughout the species range at least for the first half of the 21st century, but populations will likely become smaller and more isolated

Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Information on the distribution of multiple species in a common landscape is fundamental to effective conservation and management. However, distribution data are expensive to obtain and often limited to high-profile species in a system. A recently developed technique, environmental DNA (eDNA) sampling, has been shown to be more sensitive than traditional detection methods for many aquatic species. A second and perhaps underappreciated benefit of eDNA sampling is that a sample originally collected to determine the presence of one species can be re-analyzed to detect additional taxa without additional field effort. We developed an eDNA assay for the western pearlshell mussel (Margaritifera falcata) and evaluated its effectiveness by analyzing previously collected eDNA samples that were annotated with information including sample location and deposited in a central repository. The eDNA samples were initially collected to determine habitat occupancy by nonbenthic fish species at sites that were in the vicinity of locations recently occupied by western pearlshell. These repurposed eDNA samples produced results congruent with historical western pearlshell surveys and permitted a more precise delineation of the extent of local populations. That a sampling protocol designed to detect fish was also successful for detecting a freshwater mussel suggests that rapidly accumulating collections of eDNA samples can be repurposed to enhance the efficiency and cost-effectiveness of aquatic biodiversity monitoring

Recovery of Wolverines in the Western United States: Recent Extirpation and Recolonization or Range Retraction and Expansion?

Wolverines were greatly reduced in number and possibly extirpated from the contiguous United States (U.S.) by the early 1900s. Wolverines currently occupy much of their historical range in Washington, Idaho, Montana, and Wyoming, but are absent from Utah and only single individuals are known to occur in California and Colorado. In response, the translocation of wolverines to California and Colorado is being considered. If wolverines are to be reintroduced, managers must identify appropriate source populations based on the genetic affinities of historical and modern wolverine populations. We amplified the mitochondrial control region of 13 museum specimens dating from the late 1800s to early 1900s and 209 wolverines from modern populations in the contiguous U.S. and Canada and combined results with previously published haplotypes. Collectively, these data indicated that historical wolverine populations in the contiguous U.S. were extirpated by the early 20th century, and that modern populations in the contiguous U.S. are likely the descendants of recent immigrants from the north. The Cali1 haplotype previously identified in California museum specimens was also common in historical samples from the southern Rocky Mountains, and likely evolved in isolation in the southern ice-free refugium that encompassed most of the contiguous U.S. during the last glaciation. However, when southern populations were extirpated, these matrilines were eliminated. Several of the other haplotypes found in historical specimens from the contiguous U.S. also occur in modern North American populations, and belong to a group of haplotypes that are associated with the rapid expansion of northern wolverine populations after the last glacial retreat. Modern wolverines in the contiguous U.S. are primarily haplotype A, which is the most common and widespread haplotype in Canada and Alaska. For the translocation of wolverines to California, Colorado, and other areas in the western U.S., potential source populations in the Canadian Rocky Mountains may provide the best mix of genetic diversity and appropriate learned behavior