UNDERSTANDING DISTRIBUTION AND CONNECTIVITY OF SPECIES IN CHANGING LANDSCAPES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: TERMINATED
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1003409
• Project No.: WYO-536-14
• Project Start Date: Oct 1, 2014
• Project End Date: Sep 30, 2019

Project Director
Murphy, ME.

Recipient Organization
UNIVERSITY OF WYOMING
1000 E UNIVERSITY AVE DEPARTMENT 3434
LARAMIE,WY 82071-2000

Performing Department
Ecosystem Science and Management

Non Technical Summary
A central need in making land-management decisions is knowing how to optimize the position management activities accross a landscape to best meet management goals. My research program addresses this need by: 1) understanding where animals of management concern are and how they are connected, 2) assessing the effects of landscape change (e.g., development, climate change) on ecosystems services (e.g., water availability, forage production), and 3) developing analytical tools to be able to address these issues effectively. Agriculture and rural life are inherently tied to the land and its management. Pressures on rural agricultural landscapes are changing due to multiple forces including energy development and climate change. My research will provide tools for evaluating land use planning strategies (for grazing, energy development, and other land-use regimes) in relation to multiple species of concern and ecosystems. The selected focal species, such as Greater Sage Grouse, are of particular importance for both Wyoming and other semi-arid rangelands across the United States.I will develop new methodology for using genetically-based measures of connectivity and network function for informing land use decisions. I will also address how landscape change, due to both development and climate change, may alter biodiversity (e.g., distribution and connectivity of species of concern) and ecosystem services (e.g., water availability). I will address water availability, how water availability is likely to be altered by climate change and how this will impact both people and biological diversity using remotely sensed approaches.This research will build basic ecological understanding for semi-arid systems that is directly applicable to management in rural and agricultural landscapes. For example, restoration efforts are often legally required after development activities. Identifying which areas are most important for meeting Greater Sage Grouse management goals will make those efforts more cost-effective and productive. Addressing connectivity of species, such as Greater Sage Grouse, may have benefit to multiple species dependent on connected ecological systems for persistence. Semi-arid rangelands are water limited. Information on potential water availability under alternative climate-change scenarios is critically important for both biological diversity and human land use.

Animal Health Component

0%

Research Effort Categories

Basic

20%

Applied

50%

Developmental

30%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
121	0330	1070	25%
135	0330	1070	20%
136	0830	1080	25%
121	7310	2090	20%
121	0850	1070	10%

Knowledge Area
135 - Aquatic and Terrestrial Wildlife; 136 - Conservation of Biological Diversity; 121 - Management of Range Resources;

Subject Of Investigation
0850 - Wildlife habitats; 7310 - Experimental design and statistical methods; 0830 - Wild animals; 0330 - Wetland and riparian systems;

Field Of Science
2090 - Statistics, econometrics, and biometrics; 1070 - Ecology; 1080 - Genetics;

Keywords

landscape change

ecosystem services

environmental dna

climate change

species of concern

Goals / Objectives
Objectives: I have three primary interrelated areas of research:Assess distribution & functional connectivity of species in changing landscapes.Maintaining biodiversity and ecosystem function are central land management goals. To address these needs, I am developing and applying landscape genetic approaches to estimate current species' distribution and functional connectivity (the degree of movement or flow of organisms through their distribution on the landscape, necessary for maintaining biodiversity and ecosystem function). I am then applying this framework to estimate functional connectivity under potential land-use scenarios and assess risk of functional connectivity loss for a variety of species. Currently projects include: Greater Sage-grouse in NE Wyoming in relation to oil and gas development; Swift fox in Wyoming, Colorado and Texas (collaborating with Donnelle Schwalm, Texas Technical University/Oregon State University and Sam Cushman, USDA Forest Service RMRS) and Boreal chorus frogs in Northern Colorado in relation to land acquisition priorities (collaborating with W. Chris Funk, Colorado State University and Erin Muths, USGS).Evaluate water availability and ecosystem services under climate change scenarios. Climate change will affect not only temperature and moisture but timing. The timing of the water's presence is the critical factor affecting water availability for both biodiversity and anthropogenic use. Semi-permanent wetlands, those that retain water seasonally, may be an indicator of water availability. My aim is to assess surface water availability for both biodiversity and anthropogenic use by linking wetland hydroperiod (length of time water is available in a wetland) to climatic variation in a semi-arid environment. In this context, I am also investigating ecosystem services provided by beaver in the context of wetland dynamics (water quality and biodiversity). In addition, I am developing eDNA methods to identify wetland dependent species as a way to measure biodiversity while reducing observer bias.Develop and test analytical tools for landscape genetics. Reliable estimates of functional connectivity may require decades of field data, information not generally available when addressing pressing management concerns. In response to the challenge of quantifying functional connectivity, the emerging field of landscape genetics combines landscape ecology and population genetics. Landscape genetics applies molecular markers to estimate average functional connectivity using genetic distance in a shorter sampling period than demographic studies (~1-2 sampling efforts). However, the field of landscape genetics is still fairly new and methodological approaches are currently insufficient to answer many research and management questions.

Project Methods
Assess distribution & functional connectivity of species in changing landscapes.Greater Sage Grouse exampleDistribution. I am quantifying lek occupancy of Greater Sage Grouse in the Powder River and Bighorn basins, Wyoming during the breeding/rearing season (April-July). My research group will build models of occurrence using field occupancy data and a non-parametric model selection approach using Random Forests (Murphy et al. in prep). Potential covariates of occurrence (habitat characteristics, topography, disturbance (Murphy and Evans 2011)) will be collected through remotely-sensed data so that resulting models can be extrapolated to predict probability of occurrence across the landscape (e.g., Murphy et al. in prep). These explanatory data will be chosen based on underlying ecological importance and those likely to be altered under alternative development and reclamation scenarios (e.g., Murphy and Evans 2011).Connectivity. In coordination with existing field efforts, shed feathers are being collected at lek sites for DNA analysis using established methods for sterile collection and silica preservation (Bayard de Volo et al. 2008). The protocol will include collection of 10-20 feathers per lek using a sampling grid to limit the number of feathers collected from a single individual. We will aim for ~50 leks per basin for a total of ~1500 samples, sample size exceeding minimum requirements to detect landscape genetic relationships (Murphy 2008). Multi-locus genotypes will be used to estimate functional connectivity by calculating genetic distance (Dieringer and Schlötterer 2003; Raymond and Rousset 1995; Murphy et al. 2010b) from 12-20 microsatellite loci (Murphy 2008; Taylor et al. 2003). We will then model functional connectivity (measured by genetic distance; (Murphy and Evans 2011)) as a function of environmental (temperature, moisture, topography) and anthropogenic (oil and gas development, roads, housing) landscape characteristics (Murphy et al. 2010a). Using gravity models (Murphy et al. 2010a), we will evaluate multiple candidate models with an information theoretic approach applying appropriate correction for autocorrelation of genetic distances (Murphy et al. 2010a). Gravity models are a network approach that model flow (e.g., gene flow) through a network of locations (leks) where that flow is restricted by landscape resistance (Murphy et al. 2010a). Areas of high functional connectivity will have high flow rates, while areas of low functional connectivity will have low flow rates (Murphy et al. 2010b). This approach allows for generating surfaces of functional connectivity across the current landscape as well as using the model relationships to predict connectivity under alternative development/reclamation scenarios.Management scenarios. We will evaluate sustainability of Greater Sage Grouse networks under alternative scenarios of development and reclamation by using the relationships among probability of occupancy, functional connectivity and development. Based on these models, we will be able to identify spatially explicit locations critical for maintaining functional connectivity (conservation priorities) and developed sites that would mostly likely have high return on investment, in relation to long-term sustainability of Greater Sage Grouse populations, if reclaimed (Murphy & Evans 2011; Murphy et al. 2010a). The results will then be used to map relative importance of Greater Sage Grouse sites for avoidance, mitigation, and/or reclamation. Evaluate water availability and ecosystem services under climate change scenarios. My lab group has initiated this objective in the Plains and Prairie Potholes Landscape Conservation Cooperative (PPP LCC; consisting of the short and tall grass prairie - E MT, NE WY, ND, SD, W MN, W IA). In order to build the relationship between climatic variation and hydroperiod, it is critically important that we have field data from across the temperature-moisture conditions. Therefore, we stratified the PPP LCC by current climate (precipitation and temperature) and tillage. For each stratum (9 strata total), we will select 3 replicate Landsat scenes (27 scenes). In each replicate, we are performing a complete survey of all wetlands.Quantify Wetland Hydroperiod. We will measure wetland hydroperiod in the field by: 1) ice free date, 2) wetland size (area, depth) across the season, and 3) dry (or freeze) date. Wetlands have high intra- and inter-annual variation in size, have broad ecological diversity, and ecologically important wetland may be small in size. These factors make mapping wetlands, especially small wetlands, challenging. To circumvent these issues, new methodologies employing a suite of remotely sensed data could be adapted to classify wetlands and their hydroperiod (Bourgeau-Chavez et al. 2009).We will synthesize RADAR (Rosenqvist et al. 2007), optical (e.g., tasseled cap, spectral unmixing (Settle and Drake 1993)) and topographically derived metrics (Murphy et al. 2010b) to provide a novel framework for robust prediction of wetlands in a Radom Forests framework (Evans et al. 2011). RADAR is extremely effective for quantifying soil moisture, a defining characteristic of wetland habitat (short wavelength is best for low-lying vegetation; longer wavelengths are for habitat with tall vegetation (Kasischke et al. 1997; Whitcomb et al. 2009)). Optical data will include Landsat-derived indices measuring wetness and cover (e.g., tassel capped, fractional cover maps via spectral unmixing (Settle and Drake 1993)). Water holding capacity can be estimated using topographically derived metrics (Murphy et al. 2010b) and will be calculated using the National Elevation Dataset (NED).Link Hydroperiod to Climate Stochasticity. Once we have built the relationship between remotely sensed data and hydroperiod, we will link wetland hydroperiod to annual climatic variation through a time series analysis. Annual differences in temperature and moisture result in hydroperiod variation. We will use climate records, archived spectral data (Landsat) and RADAR data collected across the season to establish a hydroperiod for a given climatic conditions. We will collate this temporal series for a range of years (dry to wet, cold to hot) to build the relationship between wetland hydroperiod (response variable) and climate stochasticity.Predict Future Hydroperiod. We will apply the relationship between wetland hydroperiod and climate to predict hydroperiod under climate change scenarios in a Random Forests framework (e.g., Evans et al. 2011). A range of potential future climates will be estimated by GCMs (Global Circulation Models) representing minimum, maximum and median future climate (2030, 2060, & 2090).We will test that these future climates exceed the variation in contemporary climates and address change where future climates are outside the range of contemporary variation. These predictions of future hydroperiod can be used by the PPP LCC partners to assess impacts to biodiversity (e.g., waterfowl, amphibians) and water availability.Development and testing of analytical tools for landscape genetics. eDNA. Fast, reliable, and simple methods are needed for effective management. I am developing environmental DNA tests for monitoring amphibian presence (in collaboration with Dr. Caren Goldberg, University of Idaho) and presence of microbial species groups as a measure of water quality. Environmental DNA, in this case, uses DNA from the target species extracted from the water in (potentially) occupied habitats (Ficetola et al. 2008). Once methods are developed, all species present could be established from a few water samples collected at one sampling point, reducing both field effort and error (Ficetola et al. 2008).

Progress 10/01/14 to 09/30/19

Outputs
Target Audience:• US Fish and Wildlife Service • USDA Forest Service • Wyoming Department of Game and Fish • University of Wyoming - Undergraduates in Rangeland Ecology and Watershed Management • University of Wyoming - Program in Ecology (graduate program) •University of Georgia - Athens (Odem School of Ecology)• Community of Laramie Wyoming• Professional organizations: Wyoming chapter of The Wildlife Society, Wyoming/Colorado chapter of the American Fisheries Society, US section of the International Association for Landscape Ecology Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Assess distribution & functional connectivity of species in changing landscapes: One PhD student near completion and one in her thirdyear; one undergraduate researcher under this project in summer 2019. Evaluate water availability and ecosystem services under climate change scenarios: started one new PhD student. Develop and test analytical tools for landscape genetics: mentoring graduate student group on project comparing methods; also mentoring MS student from CSU - Northridge adapting gravity models for genomics data from horned lizards. How have the results been disseminated to communities of interest?We have presented at local, regional, national and international scientific meetings. I co-chaired an invited symposium at the US-IALE meetings in spring 2019 on landscape genetics featuring multiple projects from my research group. The work has also been covered in the local press and presented to community groups including at Wyoming Toad release day. We have been publishing in the peer reviewed literature. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Assess distribution and connectivity of species - Spatial distribution of biodiversity The habitat heterogeneity hypothesis postulates that species richness is positively related to variation in habitat in both space and time. Semi-permanent wetlands, those that retain water seasonally, are highly tied to both primary productivity and biodiversity particularly in semi-arid ecosystems. Climate change will affect not only temperature and moisture but timing, potentially drastically impacting wetland dynamics, primary productivity, water availability and biodiversity. My research group identified support for the habitat heterogeneity hypothesis across space, time and taxonomic groups. I investigated ecosystem services provided by beaver in the context of amphibian occupancy (water quality and biodiversity) with my master's student Victoria Zero where we found Northern leopard frogs require beaver ponds across a gradient of ages (funded by NSF-GRFP; Zero & Murphy 2016, Ecosphere). We were able to use upscaling of remotely sensed data to predict wetland ephemerality across time in the plains and prairie potholes (PPP) region with my PhD student Charlotte Gabrielsen (completed 2017; Gabrielsen, Murphy & Evans, 2016, RSE). We found support for the habitat heterogeneity hypothesis using an environmental DNA (eDNA) based index of species richness to link habitat heterogeneity across space (wetland vs. landscape context) and time (wetland vs. variation in wetland ephemerality across time; Gabrielsen, Murphy & Evans, submitted to Nature Communications). Combining multiple sources of citizen science data including eBird, we found that bird species richness is positively associated with habitat heterogeneity across both space and time (Harter & Murphy, Landscape Ecology, in prep). The Wyoming toad, a critically endangered local endemic, is extinct in the wild. Changes in habitat, hydrology, water quality and disease may have led to this decline. Understanding why Wyoming toads became rare and lack of recovery thus far, is critical for informing recovery team management decisions. With my MS student Julie Polasik, we tested these limits to species recovery (Polasik et. al, 2016 JWM) and used historic data to predict habitat suitability under current conditions across the species range (Murphy & Polasik, in prep Landscape Ecology). In part due to soft release methods employed as part of this research, the largest number of Wyoming toads were seen at the primary recovery site in 2015 with subsequent breeding the past two years. With my MS student James Vance, we tested the effects of fire and grazing on Wyoming toad survival, growth and habitat while accounting for spatial structure of the environment (Vance, Murphy & Abbot in revision, J Herp). Next, we are using radio tracking of adult toads to link individual behavior, habitat heterogeneity, disease and genetics (new ~$235K grant from Fish and Wildlife Service with collaborators Anna Chalfoun and Annika Walters, work initiated in 2019). I recruited a new PhD student, Rachel Arrick, who led the first year of field work in 2019. Assess distribution and connectivity of species - Functional connectivity in the context of landscape change. Functional connectivity, the degree of movement or flow of organisms through the landscape, is necessary for preserving biodiversity and is a measure of ecosystem function. To test alternate hypotheses of factors driving current functional connectivity, I developed and am applying novel landscape genetic/genomic approaches (Storfer, Murphy et al., 2007 Heredity; Storfer, Murphy et al., 2010 Molecular Ecology). I am applying this framework to estimate functional connectivity under potential land-use scenarios and/or assess risk of functional connectivity loss for a variety of species (Murphy et al. 2010, Ecology). Examples include: functional connectivity of two spotted frog species across 6 regions (Robertson, Murphy et. al 2018 Molecular Ecology), comparing limits to functional connectivity for two sister ground squirrel species (Zero et. al, 2017 Frontiers in Genetics), Boreal chorus frogs in the Northern Front-Range (Watts et. al, 2016 Frontiers in Genetics; Billerman et. al, 2020 Canadian Journal of Zoology), and Greater Sage-grouse in NE Wyoming in relation to oil and gas development (funded through Wyoming Restoration and Reclamation Center (WRRC),Wyoming NE sage-grouse working group, Christie Stevens Wildlife Award, awarded in 2018; publications in prep for Landscape Ecology and Molecular Ecology). As part of my sabbatical activities in fall 2019, I did a two-week intensive analysis of landscape genomic data on horned lizards (MS student Sarah Wenner, PI - Dr. Jeanne Robertson; California State University - Northridge). This is a species of conservation concern in highly human-modified landscapes with strong-hold populations in national parks. This collaboration will help move my own lab to using next-generation genomics techniques to address landscape genetics questions. Water, climate change and ecosystem services - importance of understanding species rarity Common species are alike; rare species are rare in their own way. Rabinowitz identified 7 types of rarity using the axes of geographic range (small vs. large), habitat specificity (specialist vs. generalist) and local abundance (sparse vs. dense). Species' rarity form may have consequences for niche, dispersal ability and local adaptation. Rarity can be described by three dimensions: geographic distribution, habitat specificity and local abundance. With my current PhD Student Melanie Torres (URDM fellow), we are assessing the impacts of rarity of species distribution, abundance and functional connectivity for the amphibian suite using eDNA and landscape genomics. Fundamental to understanding rarity is reliable estimates of site occupancy. However, visual detection surveys are known to underestimate presence for many species. I am developing eDNA methods to identify wetland dependent species as a way to measure biodiversity while reducing observer bias. With my MS student Andrew Gygli and Wendy Estes-Zumpf (Wyoming Natural Diversity Database (WyNDD)), we evaluated the efficacy of visual vs. eDNA surveys for long-term amphibian monitoring (Gygli, Murphy et. al in prep, Methods in Ecology and Evolution). In addition to meeting a critical state and federal wildlife management need, we will be able to assess ecological factors driving species rarity for the species suite within the study area. I have multiple collaborations to apply eDNA methods for biodiversity assessment and monitoring wide variety taxa including fish, microbes (such as E. coli), and arthropods. In addition, I just secured seed funding for a pilot project in Gabon to ask if intact forest of the Congo support higher species richness than disturbed forest by combing acoustic and eDNA. As part of my fall 2019 sabbatical, I continued to build relationships in Baja Sur, Mexico to initiate a study that will address questions of species occurrence and rarity of oasis dependent amphibians. Develop and test analytical tools for landscape genetics.I have developed new landscape genetics approaches to increase the technical capacity to address landscape genetic questions. Products include: R statistical package for Random Forests rfUtilities), R package for gravity models (GenNetIt; publication in prep forMethods in Ecology and Evolution), and development and dissemination of multiple statistical approaches for analysis of landscape genetic data (e.g., Murphy et. al 2010,Molecular Ecology; Murphy et. al 2008,Ecography). In addition, I am completing a project comparing analytical approaches in landscape genetics (isolation by environment, gravity models, linear mixed effects models) using simulated data in collaboration with 3 graduate students.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Alexander N, Remford R, Gantz C, Murphy M. (2019) Assessing the efficacy of genetic distance metrics in gravity and general mixed effects models. April 2019. US-IALE. Fort Collins, CO.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Parsley M, Torres# M, Banergee S, Tobias Z, Goldberg C, Murphy MA, Mims MC (2020) Local and landscape factors influence functional connectivity in an amphibian metapopulation: evidence from multiple lines of genetic inquiry. Landscape Ecology
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Billerman S, Jesmer J, Watts A, Schlichting P, Micheletti S, Bergamini R, Fortin M-J, Funk WC, Hapeman P, Muths E, Murphy (2019) Testing theoretical metapopulation conditions with genotypic data: an amphibian case study. Canadian Journal of Zoology. 97:1042-1053.
• Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Gabrielsen CG, Murphy MA, Evans JS (submitted) Dynamic landscapes promote species diversity across spatiotemporal scales. Nature Communications
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Arrick# R, Murphy MA, Keineth D. (2019) Wyoming toad research update. October 2019. Wyoming Toad Recovery Team. Laramie, WY.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Arrick# R, Murphy MA, Keineth D. (2019) Wyoming toad research update. October 2019. Wyoming toad Species Survival Plan annual meeting. Centenial, WY.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Murphy MA (2019) Wyoming toad research update. April 2019. Wyoming Toad Recovery Team. Laramie, WY.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Gabrielsen# C, Murphy MA, Evans JE. (2019) Diversity begets diversity: assessing the influence of wetland permanence and stochasticity on amphibian richness and abundance. April 2019. US-IALE. Fort Collins, CO.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Parsley M, Torres# M, Banergee S, Tobias Z, Goldberg C, Murphy MA, Mims MC (2020) Local and landscape factors influence functional connectivity in an amphibian metapopulation: evidence from multiple lines of genetic inquiry. April 2019. US-IALE. Fort Collins, CO.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience: US Fish and Wildlife Service USDA Forest Service Wyoming Department of Game and Fish Girl Scouts of America University of Wyoming - Undergraduates in Rangeland Ecology and Watershed Management University of Wyoming - Program in Ecology (graduate program) Professional organizations: Wyoming chapter of The Wildlife Society, Wyoming/Colorado chapter of the American Fisheries Society, US section of the International Association for Landscape Ecology Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Assess distribution & functional connectivity of species in changing landscapes. One PhD student near completion and one in her second year. Evaluate water availability and ecosystem services under climate change scenarios. Graduated one PhD student. Develop and test analytical tools for landscape genetics. Graduated one MS student. How have the results been disseminated to communities of interest?We have presented at local, regional, national and international scientific meetings. The work has also been covered in the local press and presented to community groups including the Laramie Audubon Society. We have been publishing in the peer reviewed literature. What do you plan to do during the next reporting period to accomplish the goals?Assess distribution & functional connectivity of species in changing landscapes. Complete 1 PhD Student and submit 2 papers. Submit at least two large funding proposals. Take on one PhD student (funding for a minority student). Evaluate water availability and ecosystem services under climate change scenarios. Submit 2 papers and graduate 1 MS student. Develop and test analytical tools for landscape genetics. Submit 2 papers and take on one PhD student.

Impacts
What was accomplished under these goals? Assess distribution & functional connectivity of species in changing landscapes. Have one PhD student near completion and another student in the second year of her program. 3 presentations at regional meetings in 2018. We have multiple national-level grants under review and 3 manuscripts in review. Evaluate water availability and ecosystem services under climate change scenarios. We are in the final stages of preparation for two manuscripts. One to be submitted to Nature and the other for Global Change Biology. I graduated a PhD student in 2017 who is now a post-doc at University of Alaska-Fairbanks. Develop and test analytical tools for landscape genetics. I have developed environmental DNA tests for 2 mussel species and have assays for multiple amphibian species working in the lab. We have applied these to assess use of eDNA compared to visual surveys for amphibian monitoring. We have 3 manuscripts in preparation.

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Robertson J, Murphy MA, Pearl C, Adams M, Paex-Vacas M, Haig S, Pilliod D, Storfer A, Funk WC (2018) Region variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the U.S. Pacific Northwest. Molecular Ecology. 27:3242-3256.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Vanbianchi C, Gains WL, Murphy MA, Pither J, Hodges KE (2018) Navigating fragmented landscapes: Canada lynx brave poor habitats while traveling. Ecology and Evolution DOI: 10.1002/ece3.4605
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Cushman SA, Shirk AJ, Howe GT, Murphy MA, Dyer RJ, Joost S (2018) The Least Cost Path from Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context. Frontiers in Genetics 9 10.3389/fgene.2018.00215
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Zero� V, Barocas A#, Jochimsen D#, Pelletier A, Giroux-Bougard X, Trumbo DR, Castillo J, Evans Mack D, Linnell MA, Pigg RM, Hoisington-Lopez J, Spear SF, Murphy MA, Waits LP (2017) Complementary network-based approaches for exploring genetic structure and functional connectivity in two vulnerable, endemic ground squirrels. Frontiers in Genetics 8:81. 10.3389/fgene.2017.00081
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Vanbianchi C, Gains WL, Murphy MA, Pither J, Hodges KE (2017) Habitat selection by Canada lynx: making do in heavily fragmented landscapes. Biodiversity and Conservation. 26:3343-3361.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Vanbianchi C, Murphy MA, Hodges KE (2017) Canada lynx use of burned areas: Conservation implications of changing fire regimes. Ecology and Evolution dio:10.1002/ece3.2824
• Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Billerman S, Jesmer J, Watts A, Schlichting P, Micheletti S, Bergamini R, Fortin M-J, Funk WC, Hapeman P, Muths E, Murphy (in review) Testing theoretical metapopulation conditions with genotypic data: an amphibian case study. Canadian Journal of Zoology. Resubmitted 2/14/2019. 2018 .
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Dibner R, Doak D, Murphy MA (2017) Discrepancies in occupancy and abundance approaches to identifying and protecting habitat for at-risk species. Ecology and Evolution. dio: 10.1002/ece3.3131
• Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Kipnis E, Murphy MA, Klatt A, Miller S, Williams D (in review) Terrain and land cover affect seasonal snowpack accumulation in Rocky Mountain headwater catchments affected by bark-beetle induced tree mortality. Ecohydrology. In revisions. 2018 .
• Type: Journal Articles Status: Submitted Year Published: 2019 Citation: Local and landscape factors influence functional connectivity in an amphibian metapopulation: evidence from multiple lines of genetic inquiry (in review) Meghan B Parsley, M.S.; Melanie L. Torres; Shreya Banerjee; Zachary Tobias; Caren S. Goldberg; Melanie A. Murphy; Meryl C. Mims.
• Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Wuenschel, A, Hild AL, Paige GB, Holleran MJ, Murphy MA (in revisions) Structural patterns in habitat revealed upon a fine-scale, spatially explicit investigation. Ecology and Evolution. In revisions. 2019 .
• Type: Journal Articles Status: Other Year Published: 2019 Citation: Gabrielsen CG, Murphy MA, Evans JS (in prep) Spatial and temporal environmental variability drives species diversity: assessing the influence of wetland permanence and stochasticity on amphibian richness and abundance. Target: Nature (to be submitted Feb 2019).
• Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Schlichting P, Murphy MA, Mayer JJ, Gipson PS, Dabbert CB. (in review) Delineation of wild pig management units across an arid ecoregion. Journal of Wildlife Management. Resubmitted October, 2018. In revisions. 2018 .
• Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Melanie Torres and Melanie Murphy. 2018 THE MORE, THE MERRIER? ASSESSING EDNA SAMPLING METHODS TO IMPROVE DETECTION RESULTS AMONG WY AMPHIBIANS OF VARYING RARITY Laramie, Wy. WYTWS..
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Murphy MA, Gabrielsen# C, Evans JE. (2018). 2018 Spatial and temporal environmental variability drives species diversity: assessing the influence of wetland permanence and stochasticity on amphibian richness and abundance. November 2018. Wyoming Chapter of The Wildlife Society Laramie, Wyoming
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Murphy MA, Gabrielsen# C, Evans JE. 2018 Spatial and temporal environmental variability drives species diversity: assessing the influence of wetland permanence and stochasticity on amphibian richness. Colorado/Wyoming Chapter of the American Fisheries Society. Laramie, Wyoming.
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Wimlot O, Tronstad L, Murphy MA, Fitzpatrick# B . 2018 Using eDNA to investigate native mussel distribution in eastern Wyoming. Colorado/Wyoming Chapter of the American Fisheries Society. Laramie, Wyoming.
• Type: Conference Papers and Presentations Status: Other Year Published: 2018 Citation: Harter# J, Murphy MA, Evans JS. 2018 Effects of wetland ephemerality on bird diversity in the Plains and Prairie Potholes Region. Society for Wetland Science.
• Type: Other Status: Published Year Published: 2018 Citation: Melanie Murphy, Doug Keinath. 2018 Wyoming toad population dynamics report. Laramie, Wy. April 2018..
• Type: Other Status: Published Year Published: 2018 Citation: Melanie Murphy, Tessa Wittman. eDNA assay for the Wyoming toa. Laramie Wy.

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:Federal Agencies - US Fish and Wildlife Service, US Forest Service. Testing impacts of vegetation management (grazing and fire) on Wyoming toad populations in collaboration with US Fish and Wildlife Service. Testing efficacy of environmental DNA for monitoring amphibian populations on national forest lands. State Agencies - Wyoming Game and Fish Department Scientific Community - Presentations at multiple regional, national and international scientific meetings (SRM, TWS, IALE). Publication of paper in peer-reviewed journals. Citizen organizations - Laramie Audubon Society Undergraduate students - Use of research (Wyoming toad recovery plan, eDNA monitoring, sage grouse connectivity) in REWM 2000 and REWM 4900 courses. Professional organizations - Society for Range Management, The Wildlife Society - presentations. Full day workshop on using genetic data for rangeland management at SRM 2016 meeting. General Public - Video produced by National Geographic, Coverage in Ag News, coverage in local newspapers. Changes/Problems:I was on family medical leave for spring semester 2017. What opportunities for training and professional development has the project provided?Training of 7 graduate students (2 PhD and 5 MS), training of 5undergraduate researchers. Full day workshop at Society for Rangeland Management: Application of molecular methods for rangeland management. Society for Rangeland Management. February 4, 2016. Graduated 1 PhD student and 1 MS student in reporting year. How have the results been disseminated to communities of interest?Results have been disseminated this reporting period through journal articles and conference presenations as noted in the products section. In addition, communities of interest were reached through coverage in the popular press and various internet venues. What do you plan to do during the next reporting period to accomplish the goals?Publish thesis work (J Vance (two papers in review), A Gygli) Submit dissertation work (B Fitzpatrick, C Gabrielsen (one paper out, 2 in prep)) Mentor undergraduate researcher in the lab Submit NSF proposal (Winter 2018) Continue outreach efforts (Beth Fitzpatrick (PhD student) participating in sage grouse workshop, outreach presentations to local citizen groups, etc). Fund Wyoming toad disease, habitat, behavior interaction study (building on work of 2 MS students)

Impacts
What was accomplished under these goals? The goal of my research is to understand species distribution, persistence and connectivity in changing landscapes. I have three primary interrelated areas of research: 1 - Functional connectivity in the context of landscape change. Functional connectivity, the degree of movement or flow of organisms through the landscape, is necessary for preserving biodiversity and is a measure of ecosystem function. To test alternate hypotheses of factors driving current functional connectivity, I develop and apply landscape genetic approaches (Storfer, Murphy et al. 2007, Heredity). I then estimate functional connectivity under potential land-use scenarios and assess potential consequences to a variety of species. Current projects include: Greater sage-grouse in NE Wyoming in relation to oil and gas development (funded through Wyoming Restoration and Reclamation Center (WRRC) and Wyoming NE sage-grouse working group); Feral pig connectivity in Texas (collaborating with Peter Schlichting and Brad Dabbert, Texas Tech University), Columbia spotted frogs in the Bighorn mountains (in collaboration with Anna Chalfoun, University of Wyoming), Swift fox in Wyoming, Colorado and Texas (collaborating with Donnelle Schwalm, Texas Tech University/Oregon State University and Sam Cushman, USDA Forest Service RMRS), Boreal chorus frogs in Northern Colorado in relation to land acquisition priorities (collaborating with W. Chris Funk, Colorado State University and Erin Muths, USGS), and the amphibian suite of the northern Front Range. This research program (with 15 grants totaling ~$490K) currently supports a PhD student and has resulted in 14 peer-reviewed publications (including a chapter in a landscape genetics book), 4 manuscripts in progress and 25 presentations at scientific meetings (peer-reviewed abstracts) since 2010. In addition, I have developed new approaches to address landscape genetic questions: R statistical package for Random Forests (rfUtilities, published on CRAN), R statistical package for analyzing landscape genetic networks (GenNetIt, currently in beta testing), and 3 new statistical approaches for analysis of landscape genetic data. The next development is to incorporate genomics methods to disentangle connectivity (gene flow) and local adaptation (supported by Wyoming NASA space grant). 2 - Water, ecosystem services, and climate change. Climate change will affect temperature, moisture and its timing. The timing of the water's presence with the landscape is critical to water availability for both biodiversity and anthropogenic use. Semi-permanent wetlands, those that retain water seasonally, may be an indicator of water availability. My research assesses surface water availability for both biodiversity and anthropogenic use by linking wetland hydroperiod (length of time water is available in a wetland) to climatic variation. In this context, I investigated ecosystem services provided by beaver resulting in amphibian occupancy (water quality and biodiversity) with my master's student Victoria Zero (funded by NSF-GRFP; Zero & Murphy in press, Ecosphere). I link hydroperiod to climate to predict impacts to ecosystem services across the plains and prairie potholes (PPP) region with my PhD student Charlotte Gabrielsen (funded through US Fish and Wildlife Service; Gabrielsen, Murphy & Evans, 2016, RSE). PhD student Charlotte Gabrielsen and undergraduate Elise Sulser, are using environmental DNA (eDNA) methods to inventory biodiversity (amphibians, microbes, fish) in relation to wetland ephemerality. Products from this research include grants from Fish and Wildlife Service (FWS; ~$65K) and Wyoming EPSCoR ($35K), 2 graduate student publications, additional manuscript in revision, a major report to FWS and 14 presentations at scientific meetings. As my research program continues, I will link wetland ephemerality with functional connectivity of wetland-dependent species. 3 - Understanding species rarity Report Date 03/02/2018 Page 2 of 7 United States Department of Agriculture Progress Report Accession No. 1003409 Project No. WYO-536-14 Species rarity is a critical issue for state and federal wildlife management. It may influence three components central to my overall research program: niche, connectivity and local adaptation. Rarity can be described by three dimensions: geographic distribution, habitat specificity and local abundance. Fundamental to understanding rarity is reliable estimates of site occupancy. Because visual detection surveys are known to underestimate presence for many species, I am developing eDNA methods to identify wetland-dependent species as a way to measure biodiversity and reduce observer bias. MS student Andrew Gygli, Wendy Estes-Zumpf (Wyoming Natural Diversity Database (WyNDD) and I are evaluating the efficacy of visual vs. eDNA surveys for long-term amphibian monitoring (~$140K, US Forest Service and WGFD). Using eDNA to establish amphibian presence could: increase accuracy and decrease costs of surveys, increase the number of sites sampled per unit effort, refine distribution and extinction records, and provide early detection of invasive species, without any risk to the local ecosystem. In addition to meeting these critical state and federal wildlife management needs, we will be able to assess ecological factors driving species rarity. eDNA methods are also useful for establishing presence of a wide variety taxa including fish, microbes (such as E. coli), and arthropods. For example, I am collaborating with Amy Pocewicz to develop eDNA methods to assess presence of macroinvertebrate species to monitor water quality indicators. The Wyoming toad, a critically endangered local endemic, is extinct in the wild and an example of the most extreme form of rarity. Changes in habitat, hydrology, water quality and disease may have led to this decline. Understanding why Wyoming toads became rare and lack of recovery thus far, is critical for informing recovery team management decisions. Julie Polasik (MS student) and I tested the limits to species recovery (Polasik et al., 2016 JWM). In part due to our soft release methods, the largest number of Wyoming toads were recorded at the recovery site in 2015. In the next stage, MS student James Vance tested the effects of fire and grazing on Wyoming toad survival and growth. The species rarity research aim has supported 3 MS students and partially funded a PhD student. Funding includes: Fish and Wildlife Service (>$400K), USDA Forest Service ($100K), Wyoming Game and Fish Department (~$180K), The Nature Conservancy ($4k), and Biodiversity Institute ($10K, Charlotte Gabrielsen). The research has been presented in three invited talks at international scientific meetings including a symposia that will result in a best practices paper (lead by Caren Goldberg) Results and protocols have also been presented at state (WY-TWS, WY-SRM) and regional meetings. What opportunities for training and profession

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: Vanbianchi C, Gains WL, Murphy MA, Pither J, Hodges KE (2017) Habitat selection by Canada lynx: making do in heavily fragmented landscapes. Biodiversity and Conservation. 26:3343-3361.
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Vanbianchi C, Murphy MA, Hodges KE (2017) Canada lynx use of burned areas: Conservation implications of changing fire regimes. Ecology and Evolution dio:10.1002/ece3.2824
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Zero� V, Barocas A#, Jochimsen D#, Pelletier A, Giroux-Bougard X, Trumbo DR, Castillo J, Evans Mack D, Linnell MA, Pigg RM, Hoisington-Lopez J, Spear SF, Murphy MA, Waits LP (2017) Complementary network-based approaches for exploring genetic structure and functional connectivity in two vulnerable, endemic ground squirrels. Frontiers in Genetics 8:81. 10.3389/fgene.2017.00081 This paper is a product of the Landscape Genetics Distributed Graduate Course 2012,
• Type: Journal Articles Status: Published Year Published: 2017 Citation: Dibner R, Doak D, Murphy MA (2017) Discrepancies in occupancy and abundance approaches to identifying and protecting habitat for at-risk species. Ecology and Evolution. dio: 10.1002/ece3.3131
• Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Murphy MA, Funk WC, Gabrielsen# C, Gygli# A. (2017) Amphibian distribution and connectivity as a function of rarity using eDNA and NGS. Invited symposium. July 2017. International Congress for Conservation Biology. Cartagena, Colombia. Invited symposium. Symposium chair.
• Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Fitzpatrick# B, Murphy MA. (2017) Does greater sage-grouse habitat quality increase likelihood of lek extirpation? Invited symposium. July 2017. International Congress for Conservation Biology. Cartagena, Colombia. Accepted symposium.
• Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Evans JS, Doherty K, MacKenzie D, Murphy MA (2017) The importance of incorportatin regional variation into conservation planning and species management. July 2017. International Congress for Conservation Biology. Cartagena, Colombia.
• Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Murphy, MA, Vance J#, Polasik J#, Abbott T. Fire, grazing and toads: vegetation management and Wyoming toads (Anaxyrus baxteri) recovery efforts. November, 2016. Wyoming chapter of The Wildlife Society. Cody, Wy.
• Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Gygli#, A Murphy MA, Estes-Zumpf W, Henderson R. (2016) Enhancing detection of native Wyoming amphibians through environmental DNA and visual surveys. November, 2016. Wyoming chapter of The Wildlife Society. Cody, Wy.
• Type: Other Status: Other Year Published: 2017 Citation: Invited seminar: From genes to landscapes  distribution and connectivity of species in a changing world (Department of Fish and Wildlife Sciences 75th Anniversary Alumni Seminar Series, University of Idaho, Moscow, Idaho)
• Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Harter, J.C. and Melanie A. Murphy. The influence of wetland ephemerality on bird diversity in the Plains and Prairie Potholes Region. 12 April 2017. Society of Wetland Scientists Rocky Mountain Chapter Annual Meeting. Golden, CO.
• Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Colorado/Wyoming/Utah American Fisheries Society February 23, 2017 in Grand Junction, CO Enhancing detection of native Wyoming and Colorado amphibians through environmental DNA and visual surveys Andrew Gygli, Melanie A. Murphy, Wendy Estes-Zumpf, Rick Henderson
• Type: Conference Papers and Presentations Status: Other Year Published: 2017 Citation: Rocky Mountain Society of Wetland Scientists April 12, 2017 in Golden, CO Enhancing detection of native Wyoming and Colorado amphibians through environmental DNA and visual surveys Andrew Gygli, Melanie A. Murphy, Wendy Estes-Zumpf, Rick Henderson

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Federal Agencies - US Fish and Wildlife Service, US Forest Service. Testing impacts of vegetation management (grazing and fire) on Wyoming toad populations in collaboration with US Fish and Wildlife Service. Testing efficacy of environmental DNA for monitoring amphibian populations on national forest lands. State Agencies - Wyoming Game and Fish Department Scientific Community - Presentations at multiple regional, national and international scientific meetings (SRM, TWS, IALE). Publication of paper in peer-reviewed journals. Citizen organizations - Laramie Audubon Society Undergraduate students - Use of research (Wyoming toad recovery plan, eDNA monitoring, sage grouse connectivity) in REWM 2000 and REWM 4900 courses. Professional organizations - Society for Range Management, The Wildlife Society - presentations. Full day workshop on using genetic data for rangeland management at SRM 2016 meeting. General Public - Video produced by National Geographic, Coverage in Ag News. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training of 7 graduate students (2 PhD and 5 MS), training of 4 undergraduate researchers. Full day workshop at Society for Rangeland Management: Application of molecular methods for rangeland management. Society for Rangeland Management. February 4, 2016. How have the results been disseminated to communities of interest?Results have been disseminated this reporting period through journal articles and conference presenations as noted in the products section. In addition, communities of interest were reached through coverage in the popular press and various internet venues: Coverage in the popular press Toad trials - https://issuu.com/uw_extension/docs/toad_trials Newman, E. (2015) Researcher looking at ways to protect genetic diversity in sage grouse. Boomerang Jan. 24, 2015. http://www.laramieboomerang.com/news/outdoors/article_c05ca717-c163-5843-9843-16158c61555f.html Nixon L. (2013) Climate change study includes Fort Pierre National Grassland. http://m.capjournal.com/news/climate-change-study-includes-fort-pierre-national-grassland/article_8a07d278-6092-11e3-b924-0019bb2963f4.html?mode=jqm#.UqZsA5GsftU.facebook Bowlby J. (2013) Wyoming toad: rarest amphibian in North American is in our own backyard. Boomerang. November 8, 2013. http://www.laramieboomerang.com/articles /2013/11/08/outdoors/doc527c78ee3d944171924612.txt Bowlby J. (2013) Recovery efforts in place for Wyoming toad. Wyoming Tribune Eagle. http://www.wyomingnews.com/articles/2001/12/16/news/import-2073.txt Tippin C. (2013) Fishing for frogs on Pole Mountain. Laramie Boomerang. July 11.2013. Keim, B. (2011) The Design of Science: 10 Great Research Graphics. Wired Press. December 13, 2011. Link Coverage of Murphy et al. 2010 Molecular Ecology paper. Coverage of research on the internet Can We Save These Rare Toads from Extinction? http://video.nationalgeographic.com/video/news/151112-rare-wyoming-toad-extinction-save-vin How to Find a Frog: https://www.youtube.com/watch?v=k_SlX_nMWBM Focus Wyoming: https://www.youtube.com/watch?v=cCPsPAZIJB8 What do you plan to do during the next reporting period to accomplish the goals?• Submit thesis work (J Vance, A Gygli), Submit dissertation work (B Fitzpatrick, C Gabrielsen) • Submit wetland emphemerality/climate change modeling work (part of Charlotte Gabrielsen's PhD) • Mentor undergraduate researcher in the lab • Submit NSF proposal (Winter 2017) • Continue outreach efforts (Beth Fitzpatrick (PhD student) participating in sage grouse workshop, outreach presentations to local citizen groups, etc).

Impacts
What was accomplished under these goals? The goal of my research is to understand species distribution, persistence and connectivity in changing landscapes. I have three primary interrelated areas of research: 1 - Functional connectivity in the context of landscape change. Functional connectivity, the degree of movement or flow of organisms through the landscape, is necessary for preserving biodiversity and is a measure of ecosystem function. To test alternate hypotheses of factors driving current functional connectivity, I develop and apply landscape genetic approaches (Storfer, Murphy et al. 2007, Heredity). I then estimate functional connectivity under potential land-use scenarios and assess potential consequences to a variety of species. Current projects include: Greater sage-grouse in NE Wyoming in relation to oil and gas development (funded through Wyoming Restoration and Reclamation Center (WRRC) and Wyoming NE sage-grouse working group); Feral pig connectivity in Texas (collaborating with Peter Schlichting and Brad Dabbert, Texas Tech University), Columbia spotted frogs in the Bighorn mountains (in collaboration with Anna Chalfoun, University of Wyoming), Swift fox in Wyoming, Colorado and Texas (collaborating with Donnelle Schwalm, Texas Tech University/Oregon State University and Sam Cushman, USDA Forest Service RMRS), Boreal chorus frogs in Northern Colorado in relation to land acquisition priorities (collaborating with W. Chris Funk, Colorado State University and Erin Muths, USGS), and the amphibian suite of the northern Front Range. This research program (with 15 grants totaling ~$490K) currently supports a PhD student and has resulted in 14 peer-reviewed publications (including a chapter in a landscape genetics book), 4 manuscripts in progress and 25 presentations at scientific meetings (peer-reviewed abstracts) since 2010. In addition, I have developed new approaches to address landscape genetic questions: R statistical package for Random Forests (rfUtilities, published on CRAN), R statistical package for analyzing landscape genetic networks (GenNetIt, currently in beta testing), and 3 new statistical approaches for analysis of landscape genetic data. The next development is to incorporate genomics methods to disentangle connectivity (gene flow) and local adaptation (supported by Wyoming NASA space grant). 2 - Water, ecosystem services, and climate change. Climate change will affect temperature, moisture and its timing. The timing of the water's presence with the landscape is critical to water availability for both biodiversity and anthropogenic use. Semi-permanent wetlands, those that retain water seasonally, may be an indicator of water availability. My research assesses surface water availability for both biodiversity and anthropogenic use by linking wetland hydroperiod (length of time water is available in a wetland) to climatic variation. In this context, I investigated ecosystem services provided by beaver resulting in amphibian occupancy (water quality and biodiversity) with my master's student Victoria Zero (funded by NSF-GRFP; Zero & Murphy in press, Ecosphere). I link hydroperiod to climate to predict impacts to ecosystem services across the plains and prairie potholes (PPP) region with my PhD student Charlotte Gabrielsen (funded through US Fish and Wildlife Service; Gabrielsen, Murphy & Evans, 2016, RSE). PhD student Charlotte Gabrielsen and undergraduate Elise Sulser, are using environmental DNA (eDNA) methods to inventory biodiversity (amphibians, microbes, fish) in relation to wetland ephemerality. Products from this research include grants from Fish and Wildlife Service (FWS; ~$65K) and Wyoming EPSCoR ($35K), 2 graduate student publications, additional manuscript in revision, a major report to FWS and 14 presentations at scientific meetings. As my research program continues, I will link wetland ephemerality with functional connectivity of wetland-dependent species. 3 - Understanding species rarity Species rarity is a critical issue for state and federal wildlife management. It may influence three components central to my overall research program: niche, connectivity and local adaptation. Rarity can be described by three dimensions: geographic distribution, habitat specificity and local abundance. Fundamental to understanding rarity is reliable estimates of site occupancy. Because visual detection surveys are known to underestimate presence for many species, I am developing eDNA methods to identify wetland-dependent species as a way to measure biodiversity and reduce observer bias. MS student Andrew Gygli, Wendy Estes-Zumpf (Wyoming Natural Diversity Database (WyNDD) and I are evaluating the efficacy of visual vs. eDNA surveys for long-term amphibian monitoring (~$140K, US Forest Service and WGFD). Using eDNA to establish amphibian presence could: increase accuracy and decrease costs of surveys, increase the number of sites sampled per unit effort, refine distribution and extinction records, and provide early detection of invasive species, without any risk to the local ecosystem. In addition to meeting these critical state and federal wildlife management needs, we will be able to assess ecological factors driving species rarity. eDNA methods are also useful for establishing presence of a wide variety taxa including fish, microbes (such as E. coli), and arthropods. For example, I am collaborating with Amy Pocewicz to develop eDNA methods to assess presence of macroinvertebrate species to monitor water quality indicators. The Wyoming toad, a critically endangered local endemic, is extinct in the wild and an example of the most extreme form of rarity. Changes in habitat, hydrology, water quality and disease may have led to this decline. Understanding why Wyoming toads became rare and lack of recovery thus far, is critical for informing recovery team management decisions. Julie Polasik (MS student) and I tested the limits to species recovery (Polasik et al., 2016 JWM). In part due to our soft release methods, the largest number of Wyoming toads were recorded at the recovery site in 2015. In the next stage, MS student James Vance tested the effects of fire and grazing on Wyoming toad survival and growth. The species rarity research aim has supported 3 MS students and partially funded a PhD student. Funding includes: Fish and Wildlife Service (>$400K), USDA Forest Service ($100K), Wyoming Game and Fish Department (~$180K), The Nature Conservancy ($4k), and Biodiversity Institute ($10K, Charlotte Gabrielsen). The research has been presented in three invited talks at international scientific meetings including a symposia that will result in a best practices paper (lead by Caren Goldberg) Results and protocols have also been presented at state (WY-TWS, WY-SRM) and regional meetings.

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: Zero V, Murphy MA (2016) An amphibian species of concern prefers breeding in active beaver ponds. Ecosphere 7:e01330. 10.1002/ecs2.1330
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Polasik JS, Murphy MA, Abbott T, Vincent K (2016). Factors limiting early life stage survival and growth during endangered Wyoming toad reintroductions. Journal of Wildlife Management. 80:540-552.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Funk, WC, Murphy MA, Hoke K, Muths E, Amburgey S, Lemmon E, Lemmon A (2016). Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient. Journal of Evolutionary Biology. 29: 241252. doi: 10.1111/jeb.12760
• Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Gabrielsen#, CG, Murphy MA, Evans JS. (2016) Wavering water in the West: Predicting the effects of climate change on wetlands and amphibian diversity" March 3, 2016 UW Ecology Student Symposium. Laramie, Wy.
• Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Murphy MA, Gabrielsen# G, Sulser* AE, Zero# V, Gygli# A, Estes-Zumpf W, Henderson R, Pocewicz A, Tibbits T (2016) Applications of eDNA for Biodiversity Monitoring. Colorado-Wyoming Chapter of the American Fisheries Society. Laramie, WY March 2, 2016.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Billerman, S. M., Murphy, M. A. and Carling, M. D. (2016), Changing climate mediates sapsucker (Aves: Sphyrapicus) hybrid zone movement. Ecology and Evolution, 6: 79767990. doi: 10.1002/ece3.2507
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Gabrielsen C, Murphy MA, Evans JS. (2016) Using a multiscale, probabilistic approach to identify spatial-temporal wetland gradients. Remote Sensing of Environment. 184:522-538.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Goldberg, C. S., Turner, C. R., Deiner, K., Klymus, K. E., Thomsen, P. F., Murphy, M. A., Spear, S. F., McKee, A., Oyler-McCance, S. J., Cornman, R. S., Laramie, M. B., Mahon, A. R., Lance, R. F., Pilliod, D. S., Strickler, K. M., Waits, L. P., Fremier, A. K., Takahara, T., Herder, J. E. and Taberlet, P. (2016), Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods Ecol Evol, 7: 12991307. doi:10.1111/2041-210X.12595
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Amburgey, S. M., M. Murphy, and W. C. Funk. 2016. Phenotypic plasticity in developmental rate is insufficient to offset high tadpole mortality in rapidly drying ponds. Ecosphere 7(7): e01386. 10.1002/ecs2.1386
• Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Gabrielsen, CG, Evans JS, Murphy MA. (2016) Predicting wetlands in drylands: Influence of climate change on wetland drying and amphibian diversity Front Range Student Symposium. February 24, 2016.
• Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Gabrielsen, CG, Murphy MA, Evans JS. (2016) Modeling wetland ephemerality under climate change: Implications for amphibian diversity and gene flow. Society of Range Management. February 2, 2016.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Murphy MA, Gabrielsen# G, Sulser* AE, Zero# V, Gygli# A, Estes-Zumpf W, Henderson R, Pocewicz A, Tibbits T (2015) Applications of eDNA for Biodiversity Monitoring. Wyoming Chapter of The Wildlife Society. Lander, WY December 2015. (regional)
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Harter, J, Murphy MA. (2015) The Effect of Wetland Ephemerality on Bird Species Richness of the Prairie. Research Across Disciplines Seminar. University of Wyoming, Laramie, WY. November 13, 2015.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Murphy MA (2015) Influence of wetland ephemerality on biodiversity in the context of climate change Douglas, WY November 2015.

Progress 10/01/14 to 09/30/15

Outputs
Target Audience:Federal Agencies - US Fish and Wildlife Service, US Forest Service. Testing impacts of vegetation management (grazing and fire) on Wyoming toad populations in collabration with US Fish and Wildlife Service. Testing efficacy of environmental DNA for monitoring amphibian populations on national forest lands. State Agencies - Wyoming Game and Fish Department Scientific Community - Presentations at multiple regional, national and international scientific meetings (SRM, TWS, IALE). Publication of paper in peer-reviewed journals. Citizen organizations - Laramie Audubon Society Undergraduate students - Use of research (Wyoming toad recovery plan, eDNA monitoring, sage grouse connectivity) in REWM 2000 and REWM 4900 courses. Professional organizations - Society for Range Management, The Wildlife Society - presentations. Full day workshop on using genetic data for rangland management at SRM 2016 meeting. General Public - Video produced by National Geographic Changes/Problems:The eDNA componant has grown. Reliably establishing amphibian occupancy is of critical importance for meeting current management goals of Wyoming Game and Fish Department (WGFD), US Forest Service, and other agencies in Wyoming. Many species are state Species of Greatest Conservation Need (SGCN), with lack of information a major contributing factor to species status. In 2011 the Medicine Bow-Routt National Forest implemented a forest wide occupancy-based amphibian monitoring program. The program was designed by the Wyoming Natural Diversity Database (WYNDD) and has been implemented as a partnership between WYNDD, Colorado Natural Heritage Program, and the Forest Service (Fig 1). The program goal was to design and implement a long-term program to monitor trends in amphibian occupancy (proportion of wetlands that contain a species) for all local species. The program uses multiple independent visual surveys at each site to estimate detection rates (how often do you see them if they are actually there) and then corrects occupancy estimates for bias due to imperfect detection of species. Visual detection surveys are known to underestimate amphibian presence (MacKenzie et al. 2006). Environmental DNA (eDNA), an innovative new technique where species presence can be determined from DNA in the environment, can increase detection rates (Hunter et al. 2015, Zero et al. in prep) (Fig 1). To augment our current visual based surveying, we will apply eDNA techniques from shed DNA extracted from water samples (Ficetola et al. 2008, Goldberg et al. 2012, Pilliod et al. 2013). Using eDNA to establish amphibian presence could: increase accuracy and decrease costs of surveys, increase the number of sites sampled per unit effort, refine distribution and extinction records, and provide early detection of invasive species without any risk to the species (Goldberg et al. 2012, Wilcox et al. 2013, Zero et al. in prep). Previous work found that eDNA detection rates were higher than visual detection rates for tiger salamanders (Fig 2a), leopard frogs (Fig 2b) and chorus frogs (Fig 2c) on Pole Mountain, Wyoming (Zero et al. in prep). In addition, visual observation data resulted in an overestimate of the probability of detection for all species compared to eDNA alone or estimates based on combining both data types (Fig 2). This is because low densities of individuals are rarely detected visually, resulting in overconfidence that a species is not present at a site due to repeated non-detections. These results suggest that eDNA may benefit amphibian monitoring programs under some circumstances. Objectives: The goal is to determine the efficacy of eDNA for long-term amphibian monitoring in the Medicine Bow-Routt National Forest (MBR). The objectives are to: Objective 1: Complete development of eDNA markers for all five amphibian species on the MBR. Objective 2: Compare and contrast estimates of occupancy and detection of visual, eDNA and combined data by species to determine which approach(es) can most efficiently meet management goals in a long-term monitoring framework. Objective 3: Ascertain if breeding sites can be identified with eDNA. Methods: Study area. We stratified MBR catchments with suitable amphibian habitat by elevation and observed species (Fig 2; Estes-Zumpf et al. 2012, Estes-Zumpf 2015). In each catchment, all wetlands ("sites") will be surveyed, both visually and with eDNA, at two timepoints during the breeding/rearing season (June - July). At surveyed sites, all amphibian life stages are detected by visual encounter methods. Twenty catchments were surveyed in 2015 across the MBR (Fig 1); 20 additional catchments will be surveyed in 2016. Our budget only request funds to support the Wyoming portion of the study area. We will collect visual and eDNA for the entire amphibian species suite. This includes two SGCN (Boreal toads Anaxyrus boreas boreas (ANBO); Wood frogs (Lithobates sylvatica, LISY)), boreal chorus frog (Pseudacris maculata; PSMA, "chorus frog"), barred tiger salamanders (Ambystoma mavortium; AMMA, "tiger salamander") and northern leopard frogs (Lithobates pipiens; LIPI, "leopard frog"). The ecological characteristics of these species will likely lead to differences in visual and eDNA detections rates; we do not expect that one method will have the highest efficacy across all species. eDNA collection. All sites will be surveyed twice during the season to estimate detection rates, filtering 1-L sample filled from three points around the wetland. DNA will be extracted from water filtered at each selected site plus bottled water to act as a negative control to monitor for field contamination (Goldberg et al. 2015). All extractions and quantitative PCRs will have at least one negative control to monitor for contamination. In addition, all PCRs will have a series of known samples with all species present in at least one sample to monitor for failed amplifications plus the addition of an internal control in each reaction (Goldberg et al. in prep). Objective 1 - test development. We will use known mitochondrial DNA sequences from previous studies of each species to develop a polymerase chain reaction (PCR) test that will produce a species-specific fragment for each amphibian species (Wilcox et al. 2013). We will apply or develop species-specific quantitative PCR primer-probe combinations (Wilcox et al. 2013). Species-specific primers have been developed for tiger salamanders (C. Goldberg), boreal chorus frogs (Zero et al. in prep), boreal toad, and northern leopard frog (Zero et al. in prep). We will develop species-specific markers for Wood frog. We will perform quantitative PCR in triplicate (Ficetola et al. 2008, Goldberg et al. 2012, Goldberg et al. 2015) and test for cross-amplification by using markers developed for one species on all others and check for "false positive" reactions. Once all markers are developed and tested, we will then formulate 2 multiplex quantitative PCR reactions (3-4 species/reaction, 2 reactions). We currently have tiger salamander, chorus frog and leopard frog operating as a multiplex reaction (Gabrielsen and Murphy, unpublished data). Objective 2 - visual vs. eDNA. We will then compare visual surveys to eDNA to determine: efficacy of each method by species' rarity, detection probability, number of eDNA sampling events required for detection, and optimal timing of surveys. We will treat each eDNA sample as a sampling occasion in a multi-model occupancy framework (MacKenzie et al. 2002, Mackenzie and Royle 2005, Zero et al. in prep). Potential covariates of detection probability--canopy cover over wetland, water temperature, pH (Strickler et al. 2015), amount of water filtered (Goldberg et al. in prep)--will be collected at each site. We will compare the cost-effectiveness of the two detection methods based on the above factors. Objective 3 - identification of breeding sites. Using positive eDNA results, we will use qtPCR values to model probability of breeding by relating quantity of target DNA to observed breeding activity by site. We then will assess the reliability of using quantity of eDNA in determining presence of breeding. Expected results and benefits: 1) Development of eDNA tests and protocols for multiple amphibian species, including the complete species suite in the study area, that can be applied for long-term monitoring and other amphibian management activities. 2) Established protocols and estimates of sensitivity for using eDNA as a long-term, multi-species monitoring method. 3) Technological development to assess breeding status of amphibian species by estimating probability of breeding for each species at each wetland using eDNA sampling. 4) Education of a University of Wyoming graduate student (Andrew Gygli, MS student). 5) Presentation of results at regional and national scientific meetings. Submission of at least one manuscript for peer-reviewed publication What opportunities for training and professional development has the project provided?Training of 7 graduate students (2 PhD and 5 MS), training of 4 undergraduate researchers. Full day workshop at Society for Rangeland Management: Application of molecular methods for rangeland management. Society for Rangeland Management. February 4, 2016. How have the results been disseminated to communities of interest?Amburgey# SM, Murphy MA, Funk WC (in press). Phenotypic plasticity in developmental rate insufficient to offset high tadpole morality in rapidly drying ponds. Ecosphere. Accepted March 7, 2016. Zero± V, Murphy MA (in press) An amphibian species of concern prefers breeding in active beaver ponds. Ecosphere Final acceptance Nov. 3, 2015. Polasik± JS, Murphy MA, Abbott T, Vincent K (2016). Factors limiting early life stage survival and growth during endangered Wyoming toad reintroductions. Journal of Wildlife Management. 80:540-552. Funk, WC, Murphy MA, Hoke K, Muths E, Amburgey S, Lemmon E, Lemmon A (2016). Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient. Journal of Evolutionary Biology. Murphy MA, Dyer R, Cushman S. (2015) Graph theory and network models in landscape genetics. Peer-reviewed book chapter in: Landscape genetics: Concepts, methods applications Ed: Balkenhol N, Cushman C, Storfer A, Waits L. Wiley. Watts A#, Schlichting P#, Billerman S#, Jesmer B#, Micheletti S#, Fortin M-J, Funk WC, Hapeman P, Muths E, Murphy MA (2015) How spatio-temporal habitat connectivity affects amphibian genetic structure. Frontiers in Genetics 6:275. doi: 10.3389/fgene.2015.00275. Pilliod DS, Arkle RA, Robertson JM, Murphy MA, Funk WC (2015). Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape. Evolution and Ecology doi:10.1002/ece3.1634 Amburgey S#, Bailey L, Murphy M, Muths E, Funk C. (2014). The effects of hydropattern and predator communities on amphibian occupancy. Canadian Journal of Zoology. 92: 927-937 Murphy M, Fitzpatrick B (2015). Identifying habitat restoration and land-use priorities for sage-grouse. July 21, 2015. Vance J, Murphy M (2015). 2015 Field Season Report. USFWS. Oct. 12, 2015. Polasik± J, Murphy M (2014). Factors limiting survival, growth and reestablishment of the critically endangered Wyoming Toad. 2014 Field Season Report. USFWS Murphy M, Fitzpatrick± B (2014). Identifying habitat restoration and land-use priorities for sage-grouse - 2014 report. Report to Wyoming game and Fish. Polasik± J, Murphy M (2014). Factors limiting survival, growth and reestablishment of the critically endangered Wyoming Toad. 2013 Field Season Report. USFWS Gabrielsen, CG, Murphy MA, Evans JS. (2015) All in the timing: Wetlands, climate, and drought in rangelands. University of WyomingResearch Across Disciplines Seminar. October 30, 2015 Vance# J, Murphy MA (2015) Impact of fire and grazing on Wyoming toad metamorph growth: 2015 field season report. Wyoming Toad Recovery Team Meeting. Cheyenne, WY. October 22, 2015. Murphy MA, Scherer R, Muths E, Noon B, Oyler-McCance (2015) Multi-scale network analysis of wood frog connectivity. International Association of Landscape Ecology - World Congress. Portland, Oregon. Invited speaker - Seascape Genetics symposium. Murphy MA (2015) Networks in landscape genetics. International Association of Landscape Ecology - World Congress. Portland, Oregon. Invited speaker - Landscape Genetics symposium. Gabrielsen# C, Murphy MA, Evans JS (2015). Evaluating species diversity under climate change: eDNA analysis in a semi-arid wetland ecosystem. Portland, Oregon. Invited speaker - Seascape Genetics symposium. Murphy MA (2015) Testing soft-release methods across reintroduction sites: proposal for 2015 field season. Wyoming Toad Recovery Team Meeting. Cheyenne, WY. April 2015. Vance# J, Murphy MA (2015) Impact of fire and grazing on Wyoming toad metamorph growth: current status and proposal for 2015 field season. Wyoming Toad Recovery Team Meeting. Cheyenne, WY. April 2015. Fitzpatrick# B, Murphy MA (2015). Using Science to Problem Solve: Planning Future Restoration for Long Term Persistence of a Species. WRRC Sage Grouse Habitat Restoration Workshop. March 24-25, 2015. Casper, Wyoming. Fitzpatrick# B, Murphy MA (2015). Using Science to Problem Solve: Planning Future Restoration for Long Term Persistence of a Species. Reclamation and Restoration Seminar, University of Wyoming. February 6, 2015. Fitzpatrick# B, Murphy M (2015) Using Science to Problem Solve: Planning Future Restoration for Long Term Persistence of a Species.Isaack Walton League. Laramie, Wyoming. January. Invited Speaker Fitzpatrick# B, Murphy M (2014) Using Science to Problem Solve: Planning Future Restoration for Long Term Persistence of a Species.Meadowlark Audubon SocietyMeeting. Cody, Wyoming. November 2014. Invited Speaker Fitzpatrick# B, Murphy M (2014) Identifyinghabitat restoration and land-use priorities for GreaterSage-Grouse in Northern Wyoming 3-6 Nov 2014. Sustainable Management of Rangeland Resources Extension Educator's Conference. Laramie, WY. Presentation. Gabrielsen# C, Murphy M (2014) Wetlands, ephemerality, and climate change. 3-6 Nov 2014. Sustainable Management of Rangeland Resources Extension Educator's Conference. Laramie, WY. Presentation. Zero# V, Murphy M (2014) Using lab methods to help us find frogs. 3-6 Nov 2014. Sustainable Management of Rangeland Resources Extension Educator's Conference. Laramie, WY. Presentation. Fitzpatrick# B, Murphy M (2014) Using Science to Problem Solve: Planning FutureRestoration forLong Term Persistence of a Species.Laramie Audubon Society Meeting.Laramie, Wyoming. October 2014. Invited Speaker. Gabrielsen# C, Murphy M, Evans J (2014) Climate change effects on amphibian persistence in the Plains and Prairie Pothole Region. 24 September 2014. Laramie Audubon Society/Isaak Walton League Lecture Series. Laramie, WY. Public presentation Polasik# J, Murphy M (2014) Factors limiting survival, growth and reestablishment of the critically endangered Wyoming toad, phase II testing habitat improvements using disturbance - 2014 field season summary. Wyoming Toad Recovery Team Meeting. Cheyenne, WY. October 2014. Presentation. Gabrielsen# C, Murphy M, Evans J (2014) Implication of wetland ephemerality for amphibian diversity and gene flow. 26-28 August, 2014. WY-TWS and CMPS Joint Annual Meeting. Sheridan, WY. Best poster award. Poster. Polasik# J, Murphy M (2014) Habitat factors limiting Wyoming toad (Anaxyrus baxteri) survival and growth at a reintroduction site in the Laramie Basin of Wyoming. North American Congress for Conservation Biology Meeting, Missoula, MT. July 2014 Presentation. Murphy M, Funk WC (2014) Mulit-scale assessment of chorus frog distribution and connectivity. North American Congress for Conservation Biology Meeting, Missoula, MT. July 2014. Presentation. Zero# V, Murphy M (2014) Beaver as ecosystem engineers.Research Across Disciplines (RAD) seminar April 2014. Presentation. Polasik# J, Murphy M (2014) Habitat factors limiting Wyoming toad (Anaxyrus baxteri) survival and growth at a reintroduction site in the Laramie Basin of Wyoming. Annual Meeting of the Colorado Chapter of the Wildlife Society, Fort Collins, CO. Poster Gabrielsen# C, Murphy M, Evans J (2014) Modeling wetland ephemerality under climate change:Implications for amphibian biodiversity and gene flow. 27 May-1 June 2014. Landscape Genetics Synthesis Meeting. Coeur d'Alene, ID. Poster Polasik# J, Murphy M (2014) Factors limiting survival, growth and reestablishment of the criticallyendangered Wyoming toad - 2013 field season summary. Wyoming Toad Recovery Team Meeting, Cheyenne, WY. April 2014. Presentation. Gabrielsen# C, Murphy M, Evans J (2014) Understanding wetland ephemerality in the context of climate change. 21 February 2014. UW Ecology Student Symposium. Laramie, WY. Presentation. Zero# V, Murphy M (2014) Ecosystem engineers, wetlands, and amphibian diversity. Laramie Audubon Society. Laramie, WY. Zero# V, Murphy M (2014) Ecosystem engineers, wetlands, and amphibian diversity. Isaak Walton League. Laramie, WY. What do you plan to do during the next reporting period to accomplish the goals? Submit thesis work (V Zero and J Polasi) Submit wetland emphemerality/climate change modeling work (part of Charlotte Gabrielsen's PhD) Mentor undergraduate researcher in the lab Submit NSF proposal (Fall 2016) Continue outreach efforts (Beth Fitzpatrick (PhD student) participating in sage grouse workshop, publication of Wyoming toad work in Reflections, outreach presentations to local citizen groups, etc).

Impacts
What was accomplished under these goals? The goal of my research is to understand species distribution, persistence and connectivity in changing landscapes. I have three primary interrelated areas of research: 1 - Functional connectivity in the context of landscape change. Functional connectivity, the degree of movement or flow of organisms through the landscape, is necessary for preserving biodiversity and is a measure of ecosystem function. To test alternate hypotheses of factors driving current functional connectivity, I develop and apply landscape genetic approaches (Storfer, Murphy et al. 2007, Heredity). I then estimate functional connectivity under potential land-use scenarios and assess potential consequences to a variety of species. Current projects include: Greater Sage-grouse in NE Wyoming in relation to oil and gas development (funded through Wyoming Restoration and Reclamation Center (WRRC) and Wyoming NE sage-grouse working group); Feral pig connectivity in Texas (collaborating with Peter Schlichting and Brad Dabbert, Texas Tech University), Columbia spotted frogs in the Bighorn mountains (in collaboration with Anna Chalfoun, University of Wyoming), Swift fox in Wyoming, Colorado and Texas (collaborating with Donnelle Schwalm, Texas Tech University/Oregon State University and Sam Cushman, USDA Forest Service RMRS), Boreal chorus frogs in Northern Colorado in relation to land acquisition priorities (collaborating with W. Chris Funk, Colorado State University and Erin Muths, USGS), and the amphibian suite of the northern Front Range. This research program (with 15 grants totaling ~$490K) currently supports a PhD student and has resulted in 14 peer-reviewed publications (including a chapter in the new landscape genetics book), 2 manuscripts in progress and 25 presentations at scientific meetings (peer-reviewed abstracts) since 2010. In addition, I have developed new approaches to address landscape genetic questions: R statistical package for Random Forests (rfUtilities, published on CRAN), R statistical package for analyzing landscape genetic networks (GenNetIt, currently in beta testing), and 3 new statistical approaches for analysis of landscape genetic data. The next development is to incorporate genomics methods to disentangle connectivity (gene flow) and local adaptation (NSF-CAREER grant pending). 2 - Water, ecosystem services, and climate change. Climate change will affect temperature, moisture and its timing. The timing of the water's presence with the landscape is critical to water availability for both biodiversity and anthropogenic use. Semi-permanent wetlands, those that retain water seasonally, may be an indicator of water availability. My research assesses surface water availability for both biodiversity and anthropogenic use by linking wetland hydroperiod (length of time water is available in a wetland) to climatic variation. In this context, I investigated ecosystem services provided by beaver resulting in amphibian occupancy (water quality and biodiversity) with my master's student Victoria Zero (funded by NSF-GRFP; Zero & Murphy in press, Ecosphere). I link hydroperiod to climate to predict impacts to ecosystem services across the plains and prairie potholes (PPP) region with my PhD student Charlotte Gabrielsen (funded through US Fish and Wildlife Service; Gabrielsen, Murphy & Evans, in revision, RSE). PhD student Charlotte Gabrielsen and undergraduate Elise Sulser, are using environmental DNA (eDNA) methods to inventory biodiversity (amphibians, microbes, fish) in relation to wetland ephemerality. Products from this research include grants from Fish and Wildlife Service (FWS; ~$65K) and Wyoming EPSCoR ($35K), 2 graduate student publications, additional manuscript in revision, a major report to FWS and 10 presentations as scientific meetings. As my research program continues, I will link wetland ephemerality with functional connectivity of wetland-dependent species. 3 - Understanding species rarity Species rarity is an issue a critical state and federal wildlife management concern. It may influence three components central to my overall research program: niche, connectivity and local adaptation. Rarity can be described by three dimensions: geographic distribution, habitat specificity and local abundance. Fundamental to understanding rarity is reliable estimates of site occupancy. Because visual detection surveys are known to underestimate presence for many species, I am developing eDNA methods to identify wetland -dependent species as a way to measure biodiversity and reduce observer bias. MS student Andrew Gygli, Wendy Estes-Zumpf (Wyoming Natural Diversity Database (WyNDD) and I are evaluating the efficacy of visual vs. eDNA surveys for long-term amphibian monitoring ($56K, US Forest Service). Using eDNA to establish amphibian presence could: increase accuracy and decrease costs of surveys, increase the number of sites sampled per unit effort, refine distribution and extinction records, and provide early detection of invasive species, without any risk to the local ecosystem. In addition to meeting these critical state and federal wildlife management needs, we will be able to assess ecological factors driving species rarity. eDNA methods are also useful for establishing presence of a wide variety taxa including fish, microbes (such as E. coli), and arthropods. For example, I am collaborating with Amy Pocewicz to develop eDNA methods to assess presence of macroinvertebrate species to monitor water quality indicators. The Wyoming toad, a critically endangered local endemic, is extinct in the wild and an example of the most extreme form of rarity. Changes in habitat, hydrology, water quality and disease may have led to this decline. Understanding why Wyoming toads became rare and lack of recovery thus far, is critical for informing recovery team management decisions. Julie Polasik (MS student) and I tested the limits to species recovery (Polasik et al., in revision JWM). In part due to our soft release methods, the largest number of Wyoming toads were recorded at the recovery site in 2015. In the next stage, MS student James Vance will testing the effects of fire and grazing on Wyoming toad survival and growth. The species rarity research aim has supported 3 MS students and partially funded a PhD student. Funding includes: Fish and Wildlife Service (>$300K), USDA Forest Service ($60K), Wyoming Game and Fish Department (~$160K), The Nature Conservancy ($4k), and Biodiversity Institute ($10K, Charlotte Gabrielsen). The research has been presented in three invited talks at international scientific meetings including a symposia that will result in a best practices paper (lead by Caren Goldberg).

Publications

• Type: Journal Articles Status: Published Year Published: 2014 Citation: Hayes M, Miller S, Murphy M. (2014) High-resolution landcover classification using Random Forests. Remote Sensing Letters. 5: 112-121
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Amburgey S, Bailey L, Murphy M, Muths E, Funk C. (2014). The effects of hydropattern and predator communities on amphibian occupancy. Canadian Journal of Zoology. 92: 927-937
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Pilliod DS, Arkle RA, Robertson JM, Murphy MA, Funk WC (2015). Effects of changing climate on aquatic habitat and connectivity for remnant populations of a wide-ranging frog species in an arid landscape. Evolution and Ecology doi: 10.1002/ece3.1634
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Watts A, Schlichting P, Billerman S, Jesmer B, Micheletti S, Fortin M-J, Funk WC, Hapeman P, Muths E, Murphy MA (2015) How spatio-temporal habitat connectivity affects amphibian genetic structure. Frontiers in Genetics 6:275. doi: 10.3389/fgene.2015.00275.
• Type: Journal Articles Status: Published Year Published: 2015 Citation: Murphy MA, Dyer R, Cushman S. (2015) Graph theory and network models in landscape genetics. Peer-reviewed book chapter in: Landscape genetics: Concepts, methods applications Ed: Balkenhol N, Cushman C, Storfer A, Waits L. Wiley.