Evaluating genetic status and management tradeoffs for conservation of cutthroat trout (\u3ci\u3eoncorhynchus clarkii\u3c/i\u3e)

Habitat fragmentation and invasive species are two of the primary threats to global biodiversity, yet biologists have tested few guidelines for protecting species under these conditions. These threats are particularly relevant to conservation of freshwater species like the Cutthroat Trout (Oncorhynchus clarkii). Hybridization with introduced Rainbow Trout (O. mykiss) has already caused extinction of one subspecies and threatens extant populations. Additionally, Cutthroat populations have lost genetic diversity across their range due to habitat destruction and fragmentation. These threats create a catch-22 for managers, wherein treating one problem (connecting populations) may lead to the other (interactions with invasive species). Furthermore, little is known about requirements for persistence of populations isolated to protection against invasive species. I assessed tradeoffs in conservation strategies for Westslope Cutthroat Trout (O. c. lewisi). In connected populations, steeper streams had smaller hybrid zones and less introgressive hybridization. I found that geomorphology (slope) limited hybridization between Rainbow and Cutthroat Trout and provided a natural refuge for native fish in connected systems. Isolated Cutthroat populations residing in under 5km of habitat above anthropogenic barriers (\u3c80yrs) suffered loss of genetic diversity independent of habitat size, quality, and time since isolation. Geologically isolated populations in larger fragments (up to 18km) also experienced loss of genetic diversity, likely from stochastic events causing population bottlenecks. Significant loss of genetic diversity compared to connected populations occurred despite exceeding habitat size and population recommendations derived from genetic theory for maintaining diversity. Thus over the long-term, isolated populations may not retain genetic diversity even if they meet suggested conservation thresholds. In these anthropogenically isolated populations, population growth rate (lambda) was positively associated with water volume during summer base flow and declined with increasing land use in the watershed. Lambda was most sensitive to probability of maturity, and increased as size of maturity decreased. Populations with low adult survival had rapid somatic growth rates, thus reaching maturity sooner. This highlighted the potential for local adaption under isolation as populations adjust to shifting environmental conditions and life history tradeoffs. Although isolated population may have reduced genetic diversity, actions such as genetic rescue should be considered with caution

Testing an eDNA marker for Common Snapping Turtles

Common snapping turtles (Chelydra serpentina) are a species of concern in southeastern Montana and some southern states; however, they are invasive to the Crown of the Continent ecosystem. Although raccoons and foxes destroy over 90% of the eggs, the few remaining survivors that reach adulthood are enough to raise serious concern as they prey upon many native species and have no natural predators. According to the Montana Natural Heritage Program, there have been only three documented reports of snapping turtles in the Flathead Valley, yet we have observed an additional 19 unreported individuals. We tested a previously developed environmental DNA (eDNA) marker for common snapping turtles to help determine their distribution in the Flathead Valley. We extracted DNA from snapping turtle tissue samples collected in the Flathead Valley to verify marker effectiveness. We hypothesized McGilvray Lake and a nearby small pond would be positive for snapping turtle DNA, while Spencer Lake would be negative. Painted turtles (Chrysemys picta belli) were visually detected in all of the waterbodies while snapping turtles have not been observed in Spencer Lake. We collected eDNA samples via water filtration in December 2016. All of the eDNA samples were negative for snapping turtle DNA. We believe our analysis produced negative results because during the winter the turtles bury themselves in the mud and the DNA can degrade or that we did not capture enough DNA. We plan to sample in the summer when the turtles are more active to increase our probability of detection

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

Does Whirling Disease Mediate Hybridization between a Native and Nonnative Trout?

<div><p></p><p>The spread of nonnative species over the last century has profoundly altered freshwater ecosystems, resulting in novel species assemblages. Interactions between nonnative species may alter their impacts on native species, yet few studies have addressed multispecies interactions. The spread of whirling disease, caused by the nonnative parasite <i>Myxobolus cerebralis</i>, has generated declines in wild trout populations across western North America. Westslope Cutthroat Trout <i>Oncorhynchus clarkii lewisi</i> in the northern Rocky Mountains are threatened by hybridization with introduced Rainbow Trout <i>O. mykiss</i>. Rainbow Trout are more susceptible to whirling disease than Cutthroat Trout and may be more vulnerable due to differences in spawning location. We hypothesized that the presence of whirling disease in a stream would (1) reduce levels of introgressive hybridization at the site scale and (2) limit the size of the hybrid zone at the whole-stream scale. We measured levels of introgression and the spatial extent of hybridization between Rainbow Trout and Westslope Cutthroat Trout in four disease-positive streams and six disease-negative streams within the Blackfoot River basin of Montana. In addition to disease status, we considered habitat quality, stream slope, distance from the confluence, temperature, and elevation. Whirling disease presence was not associated with either the level of introgression at a site or the size of the hybrid zone. Temperature, elevation, and stream slope were all influential in determining levels of introgression at the site scale. Stream slope was the most influential factor determining the size of the hybrid zone, as longer, steeper streams contained smaller hybrid zones. Stream slope is a driver of many habitat characteristics that may provide refuge from invasive species in the coming decades. Although the multispecies interactions examined in this study did not alter the impacts of invasion on native species, community assemblages will continue to change with the spread of nonnative species, requiring continued assessment to determine their impacts on native species.</p><p>Received May 15, 2014; accepted January 7, 2015</p></div

Life history, population viability, and the potential for local adaptation in isolated trout populations

Habitat loss and fragmentation have caused population decline across taxa through impacts on life history diversity, dispersal patterns, and gene flow. Yet, intentional isolation of native fish populations is a frequently used management strategy to protect against negative interactions with invasive fish species. We evaluated the population viability and genetic diversity of 12 isolated populations of Oncorhynchus clarkii lewisi located on the Flathead Indian Reservation in Montana, USA. Length-structured integral projection models (IPMs) were used to project population growth rate (lambda) and its sensitivity to underlying vital rates and parameters. We examined relationships between lambda, genetic diversity, and habitat size and quality. Lambda ranged from 0.68 to 1.1 with 10 of 12 populations projected to be in decline. A sensitivity analysis of lambda with respect to projection matrix elements indicated that lambda was generally sensitive to changes in early life history stages (survival/growth), but patterns differed among populations. Another sensitivity analysis with respect to underlying model parameters showed highly consistent pattern across populations, with lambda being most sensitive to the slope of probability of maturity (estimated from published literature), generally followed by adult survival, and the slope of somatic growth rate (directly measured from each population). Lambda was not correlated with genetic diversity. For populations residing in small isolated streams (≤5 km of occupied habitat), lambda significantly increased with base flow discharge (r2=0.50, p<0.02). Our results highlight the potential importance of local adaptation for persistence of small, isolated populations. Specifically we saw evidence for higher probability of maturity at smaller sizes in the smallest, coldest isolated systems, increasing probability of persistence for these populations. Climate change threatens to further fragment populations of aquatic organisms and reduce summertime base flows in much of western North America. Insights from studies such as ours will inform management strategies for long-term persistence of species facing these challenges

A Noninvasive Tool to Assess the Distribution of Pacific Lamprey (Entosphenus tridentatus) in the Columbia River Basin.

The Pacific lamprey (Entosphenus tridentatus) is an anadromous fish once abundant throughout coastal basins of western North America that has suffered dramatic declines in the last century due primarily to human activities. Here, we describe the development of an environmental DNA (eDNA) assay to detect Pacific lamprey in the Columbia River basin. The eDNA assay successfully amplified tissue derived DNA of Pacific lamprey collected from 12 locations throughout the Columbia River basin. The assay amplifies DNA from other Entosphenus species found outside of the Columbia River basin, but is species-specific within this basin. As a result, the assay presented here may be useful for detecting Entosphenus spp. in geographic range beyond the Columbia River Basin. The assay did not amplify tissue or synthetically derived DNA of 14 commonly sympatric non-target species, including lampreys of the genus Lampetra, which are morphologically similar to Pacific lamprey in the freshwater larval stage

Environmental DNA assays for the sister taxa sauger (Sander canadensis) and walleye (Sander vitreus).

Sauger (Sander canadensis) and walleye (S. vitreus) are percid fishes that naturally co-occur throughout much of the eastern United States. The native range of sauger extends into the upper Missouri River drainage where walleye did not historically occur, but have been stocked as a sport fish. Sauger populations have been declining due to habitat loss, fragmentation, and competition with non-native species, such as walleye. To effectively manage sauger populations, it is necessary to identify areas where sauger occur, and particularly where they co-occur with walleye. We developed quantitative PCR assays that can detect sauger and walleye DNA in filtered water samples. Each assay efficiently detected low quantities of target DNA and failed to detect DNA of non-target species with which they commonly co-occur

Quantitative PCR Assays for Detecting Loach Minnow (Rhinichthys cobitis) and Spikedace (Meda fulgida) in the Southwestern United States.

Loach minnow (Rhinichthys cobitis) and spikedace (Meda fulgida) are legally protected with the status of Endangered under the U.S. Endangered Species Act and are endemic to the Gila River basin of Arizona and New Mexico. Efficient and sensitive methods for monitoring these species' distributions are critical for prioritizing conservation efforts. We developed quantitative PCR assays for detecting loach minnow and spikedace DNA in environmental samples. Each assay reliably detected low concentrations of target DNA without detection of non-target species, including other cyprinid fishes with which they co-occur