Muhlfeld and Hauer GNLCC Proposal 2012 1

Predicting Effects of Climate Change on Aquatic Ecosystems in the Crown of the Continent Ecosystem: Combining Vulnerability Assessments, Landscape Connectivity, and Modeling for Conservation and Adaptation

Principal Investigators: Dr. Clint Muhlfeld, USGS - Northern Rocky Mountain Science Center (NOROCK), Glacier National Park, MT, phone: 406.888.7926, cmuhlfeld@usgs.gov; Dr. Richard Hauer, Flathead Lake Biological Station, The University of Montana, Polson, MT, phone: 406.982.3301 x232, ric.hauer@flbs.umt.edu. Participants: Robert Al-Chokhachy1, Matthew Boyer2, Vincent D’Angelo3, Zack Holden6, Joe Giersch3, Leslie Jones3, Kevin M. Kappenman5, Erin Landguth6, Mark Lorang6, Gordon Luikart6, Gregory Pederson1, Erin Sexton6, Maury Valett6, and Molly Webb5

1 USGS-NOROCK, Bozeman, MT; 2 Montana Fish, Wildlife & Parks, Kalispell, MT; 3 USGS-NOROCK, West Glacier, MT; 4 U.S. Forest Service, Missoula, MT; 5 USFWS, Bozeman Fish Technology Center, Bozeman, MT; 6 The University of Montana, Missoula, MT; 7 Flathead Lake Biological Station, The University of Montana, Polson, MT.

Thematic Categories: Habitat connectivity, aquatic integrity (primary), data integration, climate, and partnerships. Agency Partners: Crown Mangers Partnership, U.S. Geological Survey, The University of Montana, Flathead Basin Commission, Glacier National Park, U.S. Forest Service, U.S. Fish & Wildlife Service, Montana Fish, Wildlife & Parks, Confederated Salish and Kootenai Tribes, Montana State University. Project Summary: Global climate change is likely to dramatically impact the structure and function of freshwater systems, yet no studies have comprehensively assessed the potential effects of climate change on aquatic ecosystems in the Great Northern Landscape. The continued research described herein aims to build on an existing climate change and transboundary research program to assess the potential hydrologic, geomorphic, and thermal effects on foodwebs (rare and endemic macroinvertebrates), native salmonids (threatened bull trout and westslope cutthroat trout), and lotic habitats in the transboundary (US and Canada) Flathead River system. The project will apply new and existing techniques for combining downscaled and regionalized climate models linked with specific spatial data, fine-scale aquatic species vulnerability assessments (invertebrates→fish),

population genetic data, and remotely sensed riparian and aquatic habitat analysis. This information will be used to begin development of an aquatics adaptation plan. Results may be used to identify populations and habitats most susceptible to the impacts of climate change; develop monitoring and evaluation programs; inform future research needs; and develop conservation delivery options (e.g.,

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adaptation strategies) in response to or in anticipation of climate change and other important cumulative stressors (e.g., habitat loss and invasive species). Need for Project: Climate change poses a serious threat to natural resources, biodiversity, and ecosystem services in the United States (Botkin et al. 2007) and especially in the Rocky Mountain Ecoregion (Hauer et al. 1997; Hauer et al. 2007). Increasingly, natural resource managers require scientifically robust and regionally relevant information on climate change and associated variability to assess key impacts and species sensitivities to future climate conditions. Global climate change is expected to dramatically impact the structure and function of freshwater aquatic ecosystems. Regional climate change in the interior West has already manifested in warmer winters, changes in snowpack, fires, and has increased stream temperatures, modified hydrologic regimes, and increased the amount and frequency of disturbance events (Pederson et al. 2010). Changes in known ecological drivers related directly to climate change combined with species-specific tolerances to regime extremes (e.g., critical temperature thresholds) will likely result in significant changes in the distribution, abundance, phenology, and genetic diversity of many aquatic species (Hall et al. 1992; Parmesan and Yohe 2003), particularly inland salmonids (Rahel et al. 1996, Rieman et al. 2007; Haak et al. 2010). Therefore, understanding the potential impacts of climate change on aquatic ecosystems is needed to develop and implement pro-active conservation, recovery, and management programs at regional and watershed scales in the Great Northern Landscape Conservation Cooperative (GNLCC). The Crown of the Continent Ecosystem (CCE) is considered one of the largest, most pristine, and biodiverse ecosystems in North America (UNESCO 2010). The CCE is located at the narrowest point in the Rocky Mountain cordillera where four main climatic zones converge – Arctic/boreal, Alpine, Pacific temperate, and Eastern grasslands (Figure 1). There are reported to be more than 1,200 species of vascular plants, 70 species of mammals (including all North America’s native carnivores), 270 species of birds, 25 species of fish, and 400-600 species of aquatic insects (many of which are

endemic and rare) – an aquatic life richer than any place in the Rockies between the Yukon and Mexico. On the western boundary of the CCE, is the Transboundary Flathead Watershed, a significant portion of which forms Waterton-Glacier International Peace Park, a World Heritage Site and Biosphere Reserve (Figure 2). The Transboundary Flathead River (North Fork) originates in British Columbia and flows into Montana and is considered one of America's wildest and most biodiverse river systems. Its water quality is pristine, it harbors abundant and diverse

aquatic life, and it has long been recognized as a range-wide stronghold for two hallmark native fish species, the bull trout Salvelinus confluentus, listed as a threatened species under the Endangered Species Act, and the westslope cutthroat trout Oncorhynchus clarkii lewisi, a species of special concern.

Figure 1. The Crown of the Continent Ecosystem – located at the convergence of four bioclimatic zones in North America.

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Since the mid 1970’s, however, this globally unique ecosystem has been continuously threatened by British Columbia plans of strip mining for coal and industrial development. In 2007, British Petroleum announced plans for coal-bed methane development in the basin. The swift and successful response included three elements: a careful scientific analysis, a fact-finding mission that respected the scientific input, and a productive diplomatic relationship that resulted in policy changes (Hauer and Muhlfeld 2010). In September 2009, a joint United Nations Educational, Scientific, and Cultural Organization (UNESCO)/International Union for Conservation of Nature fact-finding mission visited the Flathead in Montana and British Columbia and their report concluded that mining in the Flathead would be “incompatible” with Waterton-Glacier as a World Heritage Site (UNESCO 2010). Furthermore, the report stated that future research and conservation should focus on addressing the compounding issues associated with global climate change: “The Flathead is regarded as one of the last of America’s remaining wild rivers and of global ecological significance….and recognizing the clear evidence for ecological and environmental stress under changing climatic regimes, specific programs of management and associated monitoring and research should be developed to combat climate change impacts. Adaptive management strategies should give emphasis to enhancing the resilience and capacity of wildlife and plants in adjusting to changing environmental conditions”. Salmonids and aquatic invertebrates provide an excellent early warning indicator of climate warming because their body temperature is dependent on the temperature of their surroundings, and they have characteristically narrow tolerances to thermal fluctuations (Williams et al. 2009; Muhlfeld et al. 2011, In-press). Bull and cutthroat trout require the coldest water temperatures of any native northwest salmonid, and clean stream bottoms for spawning and rearing. Many aquatic insects have very narrow thermal tolerances and are highly habitat-specific in their distributions. Among the salmonids, complex habitats built from the connections between river, lake, and headwater streams support annual spawning and feeding migrations- unique behaviors that maintain genetic diversity and adaptive potential. As the CCE (and indeed all of the Great Northern Landscape) undergoes rapid change as the regional climate continues to modulate with strong trends toward a warmer-drier regime, understanding how climate change will influence habitat for various sensitive aquatic species is critical for pro-active conservation and recovery programs for “at risk” populations and critical habitats in the GNLCC. There is an urgent need to collect and assimilate historical and contemporary climate and aquatic species information and conduct vulnerability assessments for fish and invertebrate populations and habitats most susceptible to the potential impacts of climate

Figure 2. The Transboundary Flathead system – The Heart of the Crown.

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change in the GNLCC. Further, there is a need to develop population and habitat models to enhance conservation and responses to climate change and other existing stressors (e.g., land-use and invasive species). Additionally, there is a need to identify biologically meaningful physiological thresholds (e.g., temperature and flow) to inform vulnerability assessments. Current climate change, habitat, and invasive species research in the Flathead system presents an ideal opportunity to build on this framework to include vulnerability assessments on trends and connectivity of native salmonids and rare and sensitive invertebrate species in this heterogenous watershed. Results may be used to identify populations and habitats most susceptible to the impacts of climate change; develop monitoring and evaluation programs; inform future research needs; and develop conservation delivery options in response to climate change and other stressors (habitat loss and invasive species) with broad application that reaches beyond the Flathead system in the GNLCC. Indeed, the Transboundary Flathead and the ongoing research, policy applications, and political complexities has many of the elements specifically coherent with the goals and objectives of the GNLCC; thus, the proposed activities described herein can be viewed as a unique opportunity to set a strong pace for future GNLCC development. Overarching Goals: The project described herein is part of ongoing research to assess aquatic integrity in the Transboundary Flathead Basin and Crown of the Continent Ecosystem, Canada and USA. We propose to continue our regional assessment of aquatic ecosystem processes, population vulnerabilities, and the modeling of potential responses to both climate change and human-induced change as the basis for adaptive management of aquatic ecosystems in the GNLCC, using the Transboundary Flathead Ecosystem as a case example. This region encompasses a complex mix of federal, state, tribal, and private lands in the US and federal, provincial and private lands in Canada. Current first nation land claims from the Ktunaxa tribe have yet to be resolved in Canada. The complex suite of ownerships, international relations, and agency objectives establish their own set of challenges; however, all will experience a similar range of climatic (e.g., long-term drought and declining snow pack) and non-climatic (e.g., habitat fragmentation, shifting land- and water use patterns, and invasive species) changes requiring coordinated management and planning. Objectives: Through this project we propose to build on our existing research projects (see next section) through the following specific objectives:

(1) Develop vulnerability assessments for native salmonids (bull trout and westslope cutthroat trout) and stream macroinvertebrates in the Transboundary Flathead and CCE, which will produce spatially explicit distribution and abundance models coupled with climate projections and response variables of aquatic biota at multiple trophic levels in the food web;

(2) Apply new and existing techniques for combining downscaled, regionalized climate models to spatially explicit habitat data. These will be coupled to population and genetic data to monitor and predict effects of climate change on connectivity, distributional shifts, gene flow, demographics and persistence for bull trout, westslope cutthroat trout, and rare macroinvertebrate populations;

(3) Develop detailed, spatially explicit hydrogeomorphic, thermal and habitat models of critical stream and riparian habitats of the North Fork river corridor using airborne remote sensing tools. These products, from headwater tributaries to the valley-bottom corridor and floodplains where much of the connectivity and response to variation in thermal and hydrologic regimes will be played out, will couple directly to the vulnerability assessments of Objective 1, the connectivity models of Objective 2 and the thermal and flow tolerance assessments of Objective 3.

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(4) Develop an adaptation plan for the Transboundary Flathead Aquatic Ecosystem (Canada and USA) to identify conservation delivery options in response to climate change and other important cumulative stressors (e.g., habitat degradation and fragmentation, and invasive species).

Role of Existing Climate Change-Related Projects - Global climate change in the GNLCC region is likely to increase air and water temperatures, increase the risk of catastrophic fire, change the timing and quantity of water available from snowpack, and contribute to the invasion of nonnative species. To better understand and assess potential effects of climate change on aquatic ecosystems, habitat, foodwebs, and native salmonids in the Northern Rocky Mountains, we will build the research agenda for this project on a platform of collaborative and ongoing supporting research. Aquatic Foodwebs – Aquatic invertebrates are excellent biological indicators of climate and human-induced change in aquatic ecosystems because they are integral components of aquatic food webs and their distributions and abundances are strongly influenced by temperature and stream flow gradients. We recently completed a freshwater invertebrate analysis of stream and river sites that were particularly at risk to the effects of the proposed coal mining in the headwaters of the Tranboundary Flathead in Canada (Environmental Assessment of Baseline Conditions and Evaluation: Glacier National Park and the Flathead Basin Threatened by Coal Mine and Coalbed Methane Development, R. Hauer, PI). Additionally, we will continue to evaluate the current status and distribution (occurrence, abundance, and genetic diversity) of rare and sensitive alpine aquatic invertebrates and communities in Waterton-Glacier International Peace Park (WGIPP). Our GNLCC-funded research showed that one species that may be particularly vulnerable to climate change is the meltwater stonefly (Lednia tumana) - a species endemic to glacial and snowmelt-driven alpine streams in WGIPP and has been petitioned for listing under the ESA due to climate-change-induced glacier loss. We found that L. tumana inhabits a narrow distribution, restricted to short sections (~500 m) of cold, alpine streams directly below glaciers, permanent snowfields, and springs (Muhlfeld et al. 2011). Our simulation models suggest that climate change threatens the future distribution and stability of these sensitive habitats and the persistence of L. tumana through the loss of glaciers and snowfields (Figure 3). Data and analysis from these efforts will be linked directly with the sampling protocols of the fish component of the project (given below). This is particularly important as we develop spatially explicit temperature and hydrologic and geomorphic models of stream response to climate change from the alpine areas of WGIPP to the valley-bottoms where bull and cutthroat trout occupy the full extent of the interconnected aquatic system to complete their life cycle.

Lednia tumana (J. Giersch)

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Fish - We will use and build upon existing methodologies and climate change outputs from a USGS fine-scale modeling project in the upper Flathead River system (The Potential Influence of Changing Climate on the Persistence of Native Salmonids at Risk, C. Muhlfeld, Co-PI). The fine-scale submodels use high resolution, site-specific data in a spatially explicit geographic information system (GIS) framework to examine risk associated with increasing temperatures, modified hydrologic regimes, and disturbance events for threatened bull trout and westslope cutthroat trout. The objectives of this ongoing research are to: (1) synthesize current data on the distribution and temperature requirements of native bull and cutthroat trout; (2) compile all current and historic data for water and air temperature, flow and precipitation, and their relationships to biotic and abiotic covariates; (3) assess the relationship of these factors and the distribution of each focal species; (4) map the current fish distributions, temperatures and habitats in a GIS framework; (5) explore the distributions of thermally and hydrologically suitable habitat for each species and life history type under various climate change scenarios; and (6) identify populations and species that are at greater risk of extirpation in the face of climate change. Aquatic and Riparian Habitat – We have developed advanced techniques for the analysis of riparian habitat, river hydraulics, potential for geomorphic change, aquatic habitat, and thermal imaging. Using high resolution (5 – 10cm) airborne remote sensing imagery and tools developed specifically for the CCE during NSF-funded research and development, we will integrate specific climate-change outputs for this project across a representative suite of river reaches from alpine to floodplains on the valley floor. The objectives of the on-going research are to 1) acquire the remote sensing imagery for the North Fork corridor from headwaters to the confluence of the Middle Fork., 2) integrate the imagery into a GIS framework, and 3) develop riparian and hydraulic habitat maps along the North Fork Corridor. Collaboration with the Crown Managers Partnership - In February 2001, government representatives from over twenty federal, aboriginal, provincial and state agencies gathered in Cranbrook, B.C. to explore ecosystem-based ways of collaborating in the transboundary Crown of the Continent.

The Crown Managers Partnership (CMP) seeks to involve a blend of senior and middle managers that have a role in management at the ecosystem scale (e.g., conservation biologists, land use planners, etc.) to address the environmental management challenges in the Crown region. The voluntary partnership seeks to build common awareness and adopt transboundary collaborative approaches to environmental management. Our collaboration with the CMP has a long history and

Figure 3. Occurrence (a), and predicted current (b) and future (c) distribution of L.

tumana.

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is well developed. We will share our data, decision-support tools and results with the CMP and their collaborators in order to assist the CMP in meeting their management objectives at the scale of the CCE. In addition to directly collaborating with the CMP on data-sharing, we will utilize the Annual Forum to reach a broad audience around the Crown of agency managers and citizen stakeholders. In 2010, the CMP shared geospatial data assembled for the CMP Landscapes Analysis project, and this will continue in 2011. The Montana Transboundary Coordinator, Erin Sexton, is a member of the CMP, is a Research Scientist at Flathead Lake Biological Station of the University of Montana, and is supervised by project co-PI Hauer. Muhlfeld, Hauer, and Sexton will work collaboratively on the Transboundary Adaptation Plan (see Objective 4). All products from this project are and will continue to be made available to the agencies involved in the CMP, and will also be as we expand the project, increasing scope and dimension to the entire CCE. The Transboundary MOU- The Memorandum of Understanding (MOU) and Cooperation on Environmental Protection, Climate Action and Energy signed by British Columbia and Montana in February of 2010 outlines a framework by which the signatories can work together with Federal, State, Provincial, Tribal and First Nations partners on 1) Environmental protection, 2) Climate action, and 3) Renewable and low carbon energy in the Transboundary Flathead River Basin. The GNLCC is facilitating implementation of the BC-MT MOU provisions specifically related to Cooperating on Fish and Wildlife Management (MOU Section I. Paragraph B) and Facilitation Climate Change Adaptation (MOU Section II. Paragraph A). The framework provided in the MOU of the Transboundary Flathead provides a unique opportunity to embrace a watershed-wide approach to developing a climate change adaptation strategy for the transboundary watershed. Additionally, the Transboundary Flathead provides an excellent case study for development of an adaptation strategy in a watershed that is both jurisdictionally complex and biologically diverse. We propose to synthesize existing biological, physical, and climate data in order to develop a suite of possible management strategies, based on a regional assessment of aquatic species vulnerabilities and responses to climate change in the Transboundary Flathead. The final synthesis will be used to prioritize conservation and management options that are consistent with the MOU. Objective 1: Vulnerability assessments of native salmonids and stream invertebrates - Vulnerability assessments are a key tool to assess the potential impacts of environmental change on species and ecosystems to inform adaptation planning and management decisions. Understanding the interactions between climate shifts and existing stressors is key to identifying which species and ecosystems are likely to be affected by projected changes and why they are likely to be vulnerable. This component of our research will provide a better understanding of how climate change will influence native salmonids and aquatic invertebrate populations, their persistence and vulnerability to climate change, and the adaptability of species to thermal and hydrologic change. Maintaining native species and ecosystems requires conservation and preservation of specific habitats that will be under threat from expected changes in climate. While it is likely that the most abundant of stream habitats will persist, the habitats that are relatively rare and sustained by snowpack and slow hydrologic regime release are at great risk. A landscape level assessment is, therefore, needed that combines existing data with newly acquired data over the spatial extent of the Crown from the BC headwaters, across the WGIPP, and additional lands on the west side of the Transboundary North Fork to resolve regional sustainability of a biodiverse foodweb.

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We are developing fine-scale submodels using high resolution (22 meter cells) data in a spatially explicit framework to examine risk associated with increasing temperatures, modified hydrologic regimes, and disturbance events for aquatic species in the CCE. We have established a stream temperature monitoring network (>300 sites) throughout the CCE, which will be expanded to the Swan and BC portions of the system in 2012. Spatially explicit stream temperature models have been developed to predict water temperatures in streams throughout Glacier National Park and the upper Flathead River system, with applications to threatened bull trout (Jones et al. In-review). Models are being used to assess thermal exceedences for aquatic species under climate change scenarios. Our objective is to develop and apply novel techniques for linking regionally downscaled and spatially explicit climate data to the specific distributions of key-indicator species. Outputs from both the high-resolution GCMs that have been regionalized to the GNLCC will be linked with the habitat remote sensing data to derive distribution analysis and spatially explicit forecastings of fish and invertebrate community responses to projected climate change. Objective 2: Landscape connectivity - Understanding how climate change will influence population persistence, connectivity (both demographic and genetic connectivity), and invasive

species is increasingly urgent for management and restoration of interior species of native salmonids. Maintaining populations and their adaptive potential requires preservation of life history variation, connectivity corridors among populations, and genetic variation within and among populations. Genetic connectivity (gene flow) can now be assessed with great precision for both ‘neutral’ and adaptive gene markers. This genetic variation can subsequently be associated with physical and environmental features at increasingly fine spatial scales to model and predict spread of neutral and adaptive alleles across landscapes and river networks (Luikart et al. 2003).

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Here, our objective is to develop and apply novel techniques for combining downscaled spatial climate data with population genetic data to monitor and predict effects of climate change on connectivity and persistence for bull trout and westslope cutthroat trout populations in the Flathead system and CCE that are sensitive to climate change (Figure 3). Outputs from high-resolution GCM data (S. Hostetler, USGS) and fine-scale climate models will be used with novel genetic markers (in adaptive genes) in populations of native trout in the Flathead River system.

Recently we developed a spatially explicit landscape genetics simulator for aquatic species in complex riverscapes that tracks movements of individuals as functions of water temperature, flow, habitat complexity, physical barriers, and other variables (Landguth et al. 2011). This novel approach allows researchers and managers to assess the impacts of stressors (e.g., climate change, invasive species, habitat loss) on the genetic diversity and demography of populations through time. This product and others will help produce vulnerability maps to guide restoration strategies for protection of the most threatened stream segments and populations at risk in the CCE.

We will apply our new demogenetic riverscape simulator (Landguth et al. 2001) to derive spatially explicit estimates of connectivity (movement and life history), demography (population abundance), and genetic diversity in the Transboundary Flathead and CCE. This information will be immediately useful to managers and adaptation planning (see Objective 4) to understand where barriers (thermal and hydrological) and disturbances (wildfire, debris flows) are likely to arise and fragment populations and possibly facilitate the invasion of nonnative aquatic species. These models, tools, and information are crucially needed to predict and prevent population extirpations, introgressive hybridization, and replacement of native trout populations with invasive trout. This research will inform restoration programs in the context of both climate change and human-induced landscape change, including the control/suppression of nonnative fish species, protection of aboriginal populations, and by improving habitat conditions to improve the survival and the long-term persistence of critical populations.

Objective 3: Remote Sensing of Habitat - Fundamental to understanding the distribution and abundance of species and their potential response to climate change is quantifying biophysical space (habitat) used by species or in different life stages that promotes successful growth and reproduction. Conservation biologists sometimes refer to locally adapted populations with habitat-specific distributions or life cycles as ecologically significant units. However, habitats are constantly changing as units within a changing landscape. Physical and biological attributes of riverscapes and landscapes vary in time and space and interact to determine the quantity and quality of specific habitat. Sufficient habitat and complexity of habitats are not only required for species-specific persistence, but also broad biodiversity in a landscape. And, of course, a given landscape is composed of multiple gradients and species responses. Often feedback mechanisms

Figure 4. Map of a spatially explicit demogentic riverscape simulator for the Transboundary Flathead system

(Landguth et al. 2011)

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are complex and nonlinear, making habitat for each species in the landscape very difficult to define. Nonetheless, quantifying habitat for species in very specific spatial and temporal terms is fundamental to conservation of biodiversity. The objectives in this component of the proposed project are to: 1) quantify, in a spatially explicit way, stream channel habitats (e.g., riffles, runs, pools), various riparian habitats (e.g., forest, shrub and wetland complexes), and potential sites of subsurface habitats of low and high hydraulic conductance of ground water (e.g., the hyporheic zone); 2) habitat specific thermal regimes, especially linked to summer thermal refugia and winter ice cover; 3)link these physical, biological and thermal habitat markers to the distribution and productivity of foodweb species and the distribution of critical life histories of bull and cutthroat trout (especially within the context of their genomic variation); and 4) link trajectories of habitat change (persistence or spatial change) with the regionally downscaled climate models. Understanding the processes and the habitat structure associated with critical habitats of the Transboundary Flathead will be crucial in any long-term diagnosis of effects due to climate change. Objective 4: Develop an adaptation plan of aquatic integrity for the Transboundary Flathead Adaptation planning has emerged as a powerful management tool to help people and natural systems prepare for and cope with the current and projected impacts of climate change and other important cumulative stressors (e.g., habitat loss and invasive species). Climate change requires altering traditional approaches to conservation and natural resource management, which are focused on short term response variables, to conservation and restoration goals focused toward longer time periods (e.g., several decades) and larger scales (e.g., landscapes and biogeographical areas). This includes adaptation analyses that account for an increasingly unknown future. Adaption planning may include conservation measures to reduce deleterious effects or to take preventative measures to slow the impact and rate of climate change. As such, climate change adaptation planning is rapidly becoming the primary lens for conservation and natural resource planning and management to develop approaches that minimize risk for increasingly different and uncertain future changes. Adaptation science and planning are in nascent development stages, yet are evolving rapidly (Heller and Zavaleta 2009). However, most adaptation strategies to date have focused on three adaptation principles: (1) building resistance to climate-related stressors; (3) enhancing resilience to change; and (3) anticipating and facilitating ecological transitions that reflect the changing environmental conditions (Glick et al. 2011). In the context of adaptation, resistance refers to the ability of a system to endure environmental disturbance or change without significant loss of ecological structure or function (Heller and Zavaleta 2009). For aquatic systems, resistance means that the species or ecosystem can tolerate or avoid changes in physical variables that structure the ecosystem (e.g., water temperatures, hydrologic regimes, and disturbance events). Resilience, on the other hand, refers to the ability of a system to recover from disturbances, or short-term departures from normative conditions or that change to a given ecological state without significant loss of ecosystem structure or function (Gunderson 2000; Hauer et al. 2003). To conserve native aquatic species and ecosystems in the Transboundary Flathead, CCE and GNLCC, adaptation planning requires proactively responding to the cumulative impacts of climate change, invasive species, and habitat loss/degradation. Developing comprehensive and effective adaptation strategies, therefore, requires understanding the potential impacts and uncertainties associated with climate change, and assessing the vulnerability of populations, species, and ecosystems to climate change and existing stressors. Results may be used to: a) develop pro-active, on-the-ground conservation programs to reduce existing stressors; b) manage ecosystem function and diversity; c)

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provide refugia and improve habitat connectivity and complexity; d) monitor populations and habitats (physical, biological – including invasives); and e) implement management and restoration programs to build resistance and resiliency for adaptation. We propose to use our vulnerability assessments and spatially explicit tools (described in Objectives 1-3) to develop a strategic adaptation plan for the Transboundary Flathead Aquatic Ecosystem over the next two years (FY2012-13). Specifically, we propose to apply a climate change adaptation framework (Glick et al. 2011), which involves four elements: (1) identifying conservation targets (2012); (2) assessing vulnerability to climate change (2012); (3) identifying management options (2013); (4) and implementing management options (2013 and beyond).

Figure 5. A framework for developing climate change adaptation strategies for aquatic ecosystems in the Transboundary Flathead (adapted from Glick et al., 2011). The plan will be used to identify which species and systems are most likely to be impacted by ongoing and projected climate change and why they are likely vulnerable. This information can be used to prioritize and implement effective conservation strategies for the entire aquatic ecosystem (Year 1). Year 2 (2013) will involve completing component 3, which will involve other technical, financial, and policy-level considerations (including chance of success) and will require obtaining input from multiple stakeholders and resource management agencies in the Transboundary Flathead system (e.g., CMP). Methods: Overview of Objective Linkages and Approaches - We will structure this project to dovetail with our previous GNLCC funding, as well as currently funded National Park Service, Flathead National Forest, and USGS projects. These projects have been underway in the Transboundary Flathead Basin, and while not duplicating the effort, these projects strongly couple with the above objectives, thus leveraging the efforts into a more comprehensive mission. We will use the outputs of regional

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climate models (e.g., RegCM3) that simulate climate resolutions of 50 and ~12 km using existing statistically downscaled data of some subset of the AR4 IPCC global model output (S. Hostetler, USGS). We have also developed hydrologic, thermal, and geomorphic models to downscale climate effects to specific stream reaches throughout the Transboundary Flathead, and have developed biological models that predict trout population attributes from stream habitat. When coupled with our proposed stream corridor/hydraulics habitat analysis and thermal imagery data, we will have direct linkage between the downscaled climate models, the habitats that lead to specific thermal and hydrologic regimes, and the geospatial analysis of the distribution and abundance of those habitats. We will also use these climate models to predict changes in habitat distributions and risks posed to trout and key-indicator invertebrate populations throughout stream networks of the Transboundary Flathead Basin for a range of plausible climate scenarios. These data will be combined with new genetic data of the two fish species using spatially explicit ‘landscape genomic’ modeling approaches (Manel et al. 2003; Kalinowski et al. 2008; Allendorf and Luikart 2008) to project effects of climate change on trout and develop a Transboundary Flathead Adaptation Plan for aquatic species. Approach of Objective 1: Salmonid and invertebrate vulnerability assessments- Our research will 1) link species distributions with climate and habitat model output, 2) identify spatially explicit temperature and flow models that lead to habitat change, and 3) provide future casting scenarios that allow analysis and synthesis of management actions that may enhance sustainability of stream foodwebs. We propose to integrate our salmonid (bull trout and westslope cutthroat trout) and invertebrate distribution data by incorporating biological information on key-indicator, rare and sensitive species with both the downscaled climate models and the remote sensing habitat analysis. We will also incorporate the invertebrate data from the NPS Vital Signs project in GNP (Schweiger and Hauer In-prep). Over 300 species of macroinvertebrates from the three aquatic insect orders Plecoptera (stoneflies), Trichoptera (caddisflies), and Ephemeroptera (mayflies) occur in the Flathead system. This extremely high aquatic biodiversity is unparalleled anywhere in the Rocky Mountains from New Mexico to the Yukon. Many of these species are endemic to the CCE. Climate change posses are real threat to the biodiversity of the aquatic foodweb in streams as thermal, hydrologic and riparian habitat changes in response to fundamental drivers. Approach of Objective 2: Landscape connectivity - Our research will 1) develop novel standardized DNA markers in important functional genes genome-wide using SNPs, 2) using existing DNA samples to genotype bull trout, westslope cutthroat trout, and L. tumana, 3) identify spatially explicit temperature and flow models that best correlate with connectivity and hybridization, and finally (4) predict where future barriers and corridors are likely to exist by simulating movement of individuals across forecasted future stream networks using movement rules validated from current and past connectivity models (Landguth et al. 2011). We will develop DNA markers in neutral and adaptive genes using 1000s of SNPs (single nucleotide polymorphisms) for population genetics and species identification. This development is feasible because collaborators are currently conducting large-scale SNP discovery using genomics technologies. Enormous advantages of SNP data over microsatellite data (which are currently widely used) is that SNP data can be easily compared and standardized among laboratories (microsatellites cannot), and can be found in adaptive genes and genotyped at far lower cost. Next, we will genotype 100-200 SNPs from fish from existing contemporary samples. Samples will be relatively evenly-distributed across the stream networks so that novel individual-based genetic analyses can be conducted along with traditional population-based landscape. Third, we will identify models best explaining connectivity and hybridization. To identify stream and climate features that influence genetic variation, gene flow, and hybridization, we will calculate correlations between genetic variables (e.g., variation, genetic distances) and the stream cost-distances between

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all pairs of individuals for each of many alternative stream movement/resistance hypotheses (i.e. models). Finally, we will project effects of climate change on connectivity, hybridization and persistence. To forecast how future stream and climate changes will alter connectivity, hybridization, and persistence, we will use available projections of future stream characteristics (flow, temperature etc.) to parameterize resistance surfaces on which individual fish will move according to the movement costs identified in models from Task 3. Specifically, we will apply an agent-based gene flow model for salmonids and invertebrates in complex and non-equilibrium stream environments. Approach of Objective 3: Remote Sensing of Riparian and Aquatic Habitat - We have developed over the past 5 years the technology of collecting and processing airborne remotely sensed data (ARS) for the purpose of habitat evaluation and analysis. Airborne remotely sensed data are collected with ultra-high resolution multispectral imagery system (Princeton Instruments EC16000 CCD interline imager) and a thermal imagery system (Electrophysics PV 320), both deployed from the FLBS/UM research aircraft Cessna 185. We will collect multispectral imagery in mid-summer for riparian and water cover classification. A combination of supervised and unsupervised classifications will be used to produce a cover map for each study reach (Figure 4). An unsupervised classification will be used to discriminate between vegetative cover and non- vegetative cover (i.e. vegetation vs cobble and water). To help discriminate among different vegetation types, homogeneous stands of the varying cover types (e.g., cottonwood, willow, water, cobble, dry grass) are identified and associated with specific spectral signatures. These specific imagery signatures are used as “training areas” to classify the image into the different land cover types. Mean spectral signatures are calculated for each cover type and subsequently used in a supervised classification. Using the spectral signatures, the Mixed Tune Matched Filtering (MTMF) algorithm in ENVI (RSI 2000) is then applied to the vegetative component of the imagery to discriminate the varying vegetation types. For each reach, a final riparian cover map is produced consisting of dominant cover types (i.e., water, cobble, deciduous – predominately cottonwood, willow, mixed grasses, dry grasses, and shadows; See Figure 4, Panel A). Stream and river aquatic habitats are classified using an unsupervised approach to differentiate spectral reflectance categories of different habitats within the main channel and then within the off-channel. Remote sensing data are calibrated with Accoustic Doppler Profiler data co-located with a Trimble AgGPS 132 v1.73 GPS receiver with sub-meter accuracy. An unsupervised clustering approach (ISODATA, Iterative Self-Ordering Data Analysis) is used to enumerate similar clusters of spectral reflectances. The clusters are aggregated into velocity categories (0-0.5, 0.5–1.0, 1.0–1.5, > 1.5 m/s). A subset of the ADP data is then used to calibrate the classification relationship to spectral reflectance and assign the appropriate depth and velocity categories (See Figure 4, Panel B). The remaining ADP data are used to validate the relationship and assess the accuracy of the classification. This methodology followed the approach developed by Whited et al. (2002, 2003), Hauer and Lorang (2004), and Lorang et al. (2005). Simultaneously, we deploy an Electrophysics EC600 thermal imager that collects thermal emission data from land and water surfaces (+ 0.5Co; See Figure 4, Panel C). This method of classifying vegetation and stream and river hydraulics is a significant departure from approaches involving digitizing and photo-interpretation. We are able to take this approach to conduct an integrated supervised and unsupervised classification because of the application of the spectral imagery allowing water surface and vegetation specific differentiation. We are also then able to conduct various analyses on the spatially explicit habitat coverages of the riparian/stream/river corridor that would not otherwise be feasible using traditional photo-interpretation methods. All ARS data will be processed at FLBS GIS lab.

Muhlfeld and Hauer GNLCC Proposal 2012 14

Approach of Objective 4: Develop an aquatic integrity adaptation plan for the Transboundary Flathead We propose to use our vulnerability assessments and spatially explicit tools (described in Objectives 1-3) to develop an aquatic integrity adaptation plan for Transboundary Flathead system over the next two years. The framework consists of four main components (see Figure 5). Our vulnerability assessments will be used to identify which species and systems are most likely to be impacted by projected changes, and why they are likely vulnerable (Components 1-2, Year 1 FY2012). Year 2 (FY2013) will involve completing Component 3 and beginning Component 4 (see Figure 5), both of which will involve other technical, financial, and policy-level considerations and input from multiple stakeholders and resource management agencies in the Transboundary Flathead system (e.g., CMP).

1. Identify conservation targets: The conservation foci will include native bull trout and westslope cutthroat trout populations in the Transboundary Flathead system. We have studied these “keystone” salmonids for over thirty years in the Flathead and thus have an excellent understanding of their distribution, abundance, genetic diversity, and life history strategies (Shepard 1984; Fraley and Shepard 1989; Muhlfeld et al. 2003; Muhlfeld and Marotz 2005; Muhlfeld et al. 2009; Hauer and Muhlfeld 2010; Muhlfeld et al. 2011; Muhlfeld et al. In-press). These data will be incorporated in a spatially explicit framework to assess vulnerability of populations, species and life histories.

2. Assess vulnerability to climate change: We propose to develop and apply a novel interdisciplinary modeling framework to predict how climate change will influence riverscape connectivity, population vulnerability, and adaptive potential of ecologically important species and riverscapes. We will combine species’ distributions, population genomic data, landscape genetic spatial models, and climate change models of habitat quality and connectivity (water flow, temperature, and spawning and nursery habitat availability) to predict vulnerability of stream reaches (22 m scale) and salmonid populations to climate change (see Objectives 1-3 for details). Specifically, we will use our spatially explicit (hierarchical and flow-routing) models of stream temperature and flow to

A B C

Figure 4. Panel A – remotely sensed vegetation classification of stream/river riparian corridor. Panel

B – Hydraulics as classified stream habitats. Panel C – Thermal image illustrating range and spatial

distribution of stream temperatures.

A B C

Figure 4. Panel A – remotely sensed vegetation classification of stream/river riparian corridor. Panel

B – Hydraulics as classified stream habitats. Panel C – Thermal image illustrating range and spatial

distribution of stream temperatures.

Figure 6

Muhlfeld and Hauer GNLCC Proposal 2012 15

forecast changes in the suitability of bull trout and westslope cutthroat trout habitats over the course of their entire life cycle (e.g., Jones et al. In-review). Secondly, we will couple these results (resistance surfaces) with our new genetic and demographic vulnerability mapping tool (Landguth et al. 2011) that uses a genetic and demographic vulnerability index in combination with simulations (above) to identify subpopulations at risk given a riverscape scenario of current or future river conditions. The genetic vulnerability index combines metrics of diversity within and between subpopulations, as well as temporal change in genetic diversity within a subpopulation. Similarly, our demographic vulnerability index combines of metrics of abundance, number of migrants, and change in abundance within each subpopulation. These data will be combined to assess the relative vulnerability of populations and habitats in the face of climate change and existing cumulative stressors.

2011 GNLCC Products: Muhlfeld, C.C., J. J. Giersch, F.R. Hauer, G.T. Pederson, G.L. Luikart, D.P. Peterson, C.C. Downs, and D.B.

Fagre. 2011. Climate change links fate of glaciers and an endemic alpine invertebrate. Climatic Change. 106:337-345.

Landguth, E.L., C.C. Muhlfeld and Gordon. Luikart. 2011. CDFISH: an individual-based, spatiallyexplicit, landscape genetics simulator for aquatic species in complex riverscapes. Conservation Genetics Resources. DOI: 10.1007/s12686-011-9492-6

Jones, L.A., C.C. Muhlfeld, L.A. Marshall, B.L. McGlynn, and J.L. Kershner. In-review. Using a spatially explicit stream temperature model to assess potential effects of climate warming on bull trout habitats. Canadian Journal of Fisheries and Aquatic Sciences.

Schweiger, E. William, Isabel W. Ashton, C.C. Muhlfeld, Leslie A. Jones, and Loren L. Bahls. 2011. The distribution and abundance of a nuisance native alga, Didymosphenia geminata, in streams of Glacier National Park: climate drivers and management implications. Park Science. 28(2):88-91

Amish, S.J., P.A. Hohenlohe, S. Painter, R.F. Leary, C.C. Muhlfeld, F. Allendorf, and G. Luikart. In-press. Westslope cutthroat and rainbow trout species-diagnostic SNP assays developed from next-generation RAD sequencing. Molecular Ecology Resources.

H.G. Billman, J.J. Giersch, K.M. Kappenman, C.C. Muhlfeld, M. Webb. In-review. Thermal tolerance of meltwater stonefly nymphs from an alpine stream in Waterton-Glacier International Peace Park, Montana, USA. Freshwater Science.

For more information, please visit our GNLCC website:

http://greatnorthernlcc.org/features/climate-change-aquatic-ecosystems.

Deliverables and Timeline:

High resolution climate data sets produced by our regional climate models (FY2012) High resolution (<1m) habitat classification and analysis of selected and representative

stream reaches (from alpine to valley floor, FY2012-14) Fine scale species distribution modeling with supportive data with scenarios for agency

conservation strategies and conservation efforts (FY2012) Physiological responses of aquatic organisms to changes in flow and temperature

(FY2011-2014) Vulnerability assessments for bull trout and cutthroat trout in the Transboundary

Flathead (FY2012) Completion of an Adaptation Strategy for the Transboundary Flathead (FY2013)

Data sharing in the GNLCC [Data will be made available to resource managers dealing with aquatic systems, including the Crown Managers Partnership, USGS, FWS, USFS,

Muhlfeld and Hauer GNLCC Proposal 2012 16

BLM, provincial, state management agencies, and private organizations (e.g., Trout Unlimited, Nature Conservancy) (FY2011-2014)]

Workshops to present the results and decision support tools to managers and provide hands‐on training (FY2012-14)

Multiple peer reviewed publication(s) of the study (FY2011-14)

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