Report submitted by Trout Unlimited to U.S. Bureau of Land Management per Cooperative Agreement PAA

Transcription

1 A Landscape-based Protocol to Identify Management Opportunities for Aquatic Habitats and Native Fishes on Public Lands, Phase II: Upper Colorado River Basin Daniel C. Dauwalter, Helen M. Neville, and Jack E. Williams Trout Unlimited, Arlington, Virginia Report submitted by Trout Unlimited to U.S. Bureau of Land Management per Cooperative Agreement PAA May 2011 Executive Summary Effective conservation of resources managed by the Bureau of Land Management (BLM) will require rapid, proactive and strategic approaches that incorporate landscape-scale evaluation of management, habitat restoration, and enhancement opportunities. At present, landscapescale assessments used by the BLM, such as rapid ecoregional assessments 1 or resource management plans, may insufficiently characterize aquatic habitats and biota, partly due to a lack of BLM fisheries and hydrology expertise available to the field and district offices developing them. Because aquatic systems and their watersheds are naturally hierarchical, landscape-scale planning must incorporate natural watershed boundaries to be effective. We evaluated Trout Unlimited s Conservation Success Index (CSI), a strategic, landscape-scale planning tool for cold-water conservation that is focused on watersheds, for its potential as a framework for informing BLM rapid ecoregional assessments and developing landscape-scale aquatic conservation strategies. The CSI synthesizes disparate bodies of information on fish populations, habitat conditions, and future threats in a comprehensive and consistent framework that can be used across jurisdictional boundaries. It consists of 20 indicators that describe four general categories: range-wide conditions, population integrity, habitat integrity, and future security. Through use of diverse information sources, the CSI can help inform management strategies, such as protection versus restoration management, across the landscape. Though the CSI was developed for salmonids and coldwater habitats, we show how it can be modified to include warmwater species and used as a framework for informing BLM rapid ecoregional assessments and developing landscape-scale aquatic conservation strategies based on cold and warmwater habitats. In Phase I of this effort we focused on the Green River Basin 1 1

2 in Wyoming, Utah, and Colorado. Phase II includes a revision of Phase I and covers the entire Upper Colorado River Basin. Thus, Phase II notably expands the number of indicators used to characterize coldwater and warmwater fish strongholds which together represent native fish strongholds but it also expands the geographic coverage of analyses. With a focus in Phase II that includes all of the Upper Colorado River Basin, we incorporated information on sensitive warmwater fishes (the flannelmouth sucker Catostomus latipinnis, the bluehead sucker Catostomus discobolus, and the roundtail chub Gila robusta), as well as the Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus that often occur on lands managed primarily by the BLM across Wyoming, Utah, and Colorado. We also show how the CSI can be expanded to help identify areas that could potentially be managed as Native Fish Conservation Areas. Integrating information on cold and warmwater fishes with habitat conditions and future threats, such as climate change, energy development, and invasive species, allows management strategies to be identified across the landscape for potential incorporation into rapid ecoregional assessments and resource management plans. Thus, the CSI has the potential to help inform BLM management in ways that can facilitate persistence of native fishes and naturally functioning aquatic and riparian habitats across the West. Introduction The Need for a Landscape-scale Aquatic Conservation Strategy on Public Lands The Bureau of Land Management (BLM) is charged with managing approximately 264 million acres of public lands, primarily located in the West. This comprises one-eighth of the landmass of the United States and includes some of the nation s most significant biological and physical resources. Many of these lands are targeted for energy development, will be affected by climate change, and have experienced an influx of non-native terrestrial and aquatic species. For example, coalbed methane production has increased dramatically in the Power River Basin in Wyoming, and produced water can vary widely in water quality that can be detrimental to aquatic organisms (Davis et al. 2009; Farag et al. 2010). A multitude of non-native species now occur on public lands and threaten the viability of native species, and their invasion has been facilitated by anthropogenic alterations of the landscape (Olden et al. 2006) and climate change (Rahel and Olden 2008). Conserving resources on public lands will become more complex as managers will need to anticipate the effects of future threats such as climate change that are expected to change how ecosystems function and provide services to resource users (Christensen et al. 2004; Williams et al. 2009). Effective conservation of BLM resources will require rapid, proactive and strategic approaches that enable landscape-scale strategies to guide management, restoration, and enhancement of aquatic resources. Such approaches require the ability to synthesize and compare population and habitat data among species and across various spatial scales to improve our understanding of resource conditions. While rapid ecoregional assessments (REAs) are likely to provide timely guidance for land management strategies, many fail to account sufficiently for aquatic species 2

3 and their habitats. Thus, despite clear direction in BLM policies and manuals, rapid ecoregional assessments, as well as Resource Management Plans (RMPs), may not adequately address fisheries and aquatic needs, partly due to a lack of BLM fisheries and hydrology expertise available to field and district offices composing those plans. Not only is it important for land managers to have an understanding of aquatic resource conditions across broad landscapes, but it is also important to know which watersheds have the highest aquatic values in order to tailor management for those specific watersheds. Aquatic conservation strategies need to be focused on watersheds if they are to conserve aquatic species and habitats effectively. River systems and their watersheds are naturally hierarchical, and aquatic habitats and their inhabitant species are influenced by complex watershed processes that function at both watershed and local spatial scales (Frissell et al. 1986). Thus, land management strategies must not only consider how management decisions impact local habitat conditions but also how they affect watershed conditions that then influence habitats through indirect pathways. Strategies must also consider how upstream management affects habitats downstream. Failure to incorporate watershed processes and conditions is a commonly cited reason why stream restoration projects are often unsuccessful (Williams et al. 1997). Watersheds managed to emphasize the conservation of aquatic resources is one strategy that that can be used to conserve aquatic species and habitats. Native Fish Conservation Areas (NFCAs) represent a watershed-scale approach to aquatic resource management that is designed around natural watershed boundaries to account for the natural connectivity and processes of river networks (Williams et al. 2011). Conservation of entire fish communities and their supporting watersheds should provide a cost-effective approach to conservation when compared to species-by-species approaches more typical of threatened and endangered species conservation efforts. NFCA management should emphasize habitat diversity and connectivity resulting from natural ecosystem processes, care for all life stages of focal species, focus on large watersheds that facilitate long-term community persistence, and enable sustainable long-term management. The size of watersheds managed as NFCAs should be dependent on the specific aquatic ecosystem and native fish community rather than jurisdictional boundaries and ownerships. While NFCAs could be managed solely for species conservation and have a strict protective status, their practical application is likely to allow for some management of other compatible uses, such as livestock grazing or recreational fishing, at a level that does not inhibit conservation goals. Trout Unlimited s Conservation Success Index Trout Unlimited recently developed the Conservation Success Index (CSI) to provide a strategic, landscape-scale planning tool for cold-water conservation that is focused on watersheds (see Williams et al. 2007a). The CSI is a geographic information system (GIS)-based, subwatershedscale (6 th level hydrologic unit code) assessment that synthesizes and communicates the rangewide condition and management needs of coldwater fishes. State, federal and tribal agencies 3

4 have produced numerous range-wide assessments and recovery plans across the range of aquatic species that include information on the status and trends of populations and habitat conditions. Likewise, various geospatial datasets are also publicly available that reflect watershed and aquatic habitat conditions. The CSI synthesizes these disparate sources of information in a comprehensive framework across the range of focal species and across jurisdictional boundaries. It analyzes 20 indicators of population and habitat status that can be grouped into four general categories: range-wide conditions, population integrity, habitat integrity, and future security (Figure 1). The aggregate structure of the CSI facilitates spatially explicit comparisons across the landscape at several different levels: overall conditions (total CSI scores), general population or habitat conditions (e.g., population integrity or habitat integrity group scores), or specific conditions or threats (e.g., watershed condition indicator or energy development indicator scores). Additional analyses related to threats such as energy development and climate change allow for development of a conservation strategy that provides a landscape-scale blueprint for management efforts on public lands. Figure 1. Conservation Success Index framework and scoring structure. Each subwatershed is scored from 1 to 5 using 20 indicators within four main groups (indicator scoring details in Appendix A). Indicator scores are added per group to obtain an overall group score. Group scores are then added to obtain a composite CSI score for each subwatershed. 4

5 Upper Colorado River Basin The Colorado River heads at La Poudre Pass in Rocky Mountain National Park, Colorado and flows for approximately 1,450 miles to the Gulf of California. The watershed encompasses 246,000 square miles in parts of seven U.S. states Wyoming, Colorado, Utah, New Mexico, Arizona, California, and Nevada and part of Mexico. The largest tributary to the Colorado River is the Green River, which was the focus of Phase I of this agreement. The Green River originates in west-central Wyoming in the Wind River Range and flows for nearly 1,200-km to its confluence with the Colorado River in Utah. Other major tributaries in the Upper Colorado River Basin, the focus of this Phase II assessment, include the Duchesne (Lower Green basin), Price (Lower Green basin), San Rafael, Escalante, Dirty Devil, Yampa, White, Dolores, Gunnison, San Juan, rivers (Figure 2). 5 Land ownership in the Upper Colorado River Basin is 80% public and 20% private. Public lands are primarily managed by the BLM (37% of all land), the U.S. Forest Service (19%), and Bureau of Indian Affairs (16%), but individual states, the U.S. Bureau of Reclamation, U.S. Fish and Wildlife Service, and the National Park Service also manage land in the basin. Several factors have been implicated in the decline of native fishes in the Upper Colorado River Basin. Dams, introduced fishes, water diversions, livestock grazing, and development of sport fisheries were typically cited as causes for these declines (Bezzerides Figure 2. Major river basins in the Upper Colorado River Basin. and Bestgen 2002; Young 2008). For example, the Green River was treated with rotenone prior to filling Flaming Gorge Reservoir. The treatment was intended to decrease the abundance of non-game fishes in order to establish a trout fishery when the reservoir was filled (Holden 1991; Wiley 2008). Many native fish populations were decimated from the rotenone treatment, and the changes in riverine habitat due to the dam were cited as the reason why populations never recovered. Oil and gas exploration and development have accelerated in recent years and threaten extant populations; bluehead sucker, for example, occur less often when there are more oil and gas wells (Dauwalter et al. 2011b). Hybridization with non-native species and habitat degradation are also reasons for continued declines (Bezzerides and Bestgen 2002; Gelwicks et al. 2009; McDonald et al. 2008).

6 Evaluating the CSI as a Broadscale Aquatic Assessment Tool for Public Lands Though the CSI was developed for salmonid fishes and coldwater habitats, we show herein how it can be modified to include warmwater streams and species and used as a framework for informing BLM rapid ecoregional assessments and developing landscape-scale aquatic conservation strategies based on cold and warmwater habitats. Within a larger goal of expanding the application of the CSI beyond coldwater resources to meet BLM needs for landscape-scale aquatic habitat assessments, here we use the CSI to evaluate the native stream fish community and its habitat in a focal area, the Upper Colorado River Basin in Wyoming, Utah, and Colorado. We broaden application of the CSI from a focus on native salmonids to include three declining warmwater fishes that occur on lower-elevation lands managed primarily by the BLM (the flannelmouth sucker Catostomus latipinnis, the bluehead sucker Catostomus discobolus, and the roundtail chub Gila robusta), as well as the Colorado River cutthroat trout Oncorhynchus clarkii pleuriticus. The combined status of these four species indicates the health of headwater and mid-elevation streams in the Upper Colorado River Basin. Additional native fishes, such as speckled dace Rhinichthys osculus and mountain sucker Catostomus platyrhynchus, occur sympatrically with the three warmwater fishes but their respective distributions are poorly known. Therefore, conservation actions for streams containing the three warmwater fishes plus the Colorado River cutthroat trout are likely to protect a wider community of native species than these four focal species. By identifying remaining community strongholds as well as restoration opportunities for degraded habitats at a landscape scale, the CSI can aid in determining management strategies for protection, monitoring, restoration and reintroduction of focal species. The CSI also enables inclusion of other key drivers that threaten natural resource systems across the West, such as climate change, energy development, and invasive species. In this assessment we identify, at the subwatershed scale (6 th hydrologic unit code), areas that represent native fish strongholds where various management actions should have the strongest collective benefit for native fishes in the Upper Colorado River Basin. We also show how the CSI can inform identification of watershed-scale areas with high biological value where management can benefit both cold- and warmwater species, termed Native Fish Conservation Areas (NFCAs). As we describe below, strongholds and NFCAs differ in the strongholds simply identify subwatersheds that have high native fish values but do not necessarily incorporate all upstream watershed extents and both cold and warmwater species. In contrast, NFCAs were identified through a more formal process that incorporated known and potential species distributions, watershed connectivity, and habitat integrity and future security that was incorporated into a tiered framework that was vetted with agency and non-governmental organization (NGO) partners. By focusing on strongholds or NFCAs and maintenance and restoration of natural processes, the BLM can meet its obligation under the Federal Land Policy and Management Act to ensure species persistence over the long-term. This integrated approach to aquatic resource conservation focused on the 6

7 Upper Colorado River Basin is part of a larger initiative to help provide guidance on how aquatic needs and conditions can be integrated into REAs and RMPs developed by the BLM. Adapting the CSI to Incorporate Cold and Warmwater Fishes and Habitats Figure 3. Total CSI scores for the Colorado River cutthroat trout across its currently occupied range. Total scores have traditionally been developed only within the current range of the target species; habitat integrity and future security scores are also computed for the historical range (historical range shown in dark grey). 7 Our goal was to adapt the CSI to be used as a proactive, landscape-scale tool to identify aquatic conservation strategies in the Upper Colorado River Basin. This process involved developing indicators that describe focal cold and warmwater fishes that can be combined to identify areas of overlap in the distribution of four target species, and then evaluating current habitat condition and future risks to assist in identifying management needs in strategic areas. Typically, the CSI is developed only within the historical range of the target coldwater species. In the Colorado River Basin this is the historical range of Colorado River cutthroat trout (Figure 3). Total CSI scores, range-wide condition scores, and population integrity scores are typically only computed for the current range of the target species, while habitat integrity and future security are also computed for the historical range. In the Upper Colorado River Basin this resulted in a lack of CSI coverage throughout the interior basin that comprises most of the warmwater fish habitat, including unoccupied watersheds upstream of occupied habitat. Adapting the CSI beyond coldwater resources and its previous single-species focus required that the traditional Range-wide Condition and Population Integrity indicators be modified or replaced with indicators that describe both cold and warmwater fishes and where they occur in close proximity (see below). In Phase I this resulted in one group of five indicators

8 that represented both cold and warmwater fishes. In Phase II we continued to modify the CSI by expanding the number of indicators by having one group of five indicators for coldwater fish (Colorado River cutthroat trout) and one group of indicators for warmwater fishes (flannelmouth sucker, bluehead sucker, and roundtail chub). This allowed traditional CSI indicators to be used for Colorado River cutthroat trout, but a new suite of indicators for the warmwater fishes. As in Phase I, adapting the CSI also required that the spatial extent of the analysis encompassed all subwatersheds across the entire Upper Colorado River Basin. Cold and Warmwater Fish Distributions and Native Fish Strongholds Figure 4. Populations of Colorado River cutthroat trout and sites where flannelmouth suckers, bluehead suckers, and roundtail chubs were collected in the Upper Colorado River Basin. 8 Our first step in adapting the CSI was to map the distributions of focal native species. Colorado River cutthroat trout populations were identified using the database compiled by the Colorado River Cutthroat Trout Recovery Team (Hirsch et al. 2006). Only data on conservation populations were used; conservation populations are those deemed important to conservation because they are at least 90% genetically pure (tested or suspected) or were otherwise determined to be important to cutthroat trout conservation due to unique life histories or other attributes (Hirsch et al. 2006). The primary source for the distribution of the warm water native fishes was a survey of warmwater streams conducted by Wyoming Game and Fish Department (Gelwicks et al. 2009; Kern et al. 2007), data from the Utah Natural Heritage Program, and Colorado Division of Wildlife s fisheries database (Figure 4). Native Fish Strongholds We then modified the CSI to highlight areas that maximized both the distribution of each species within a subwatershed and the overlap among the four native species. In Phase I this was simply done by deletion of Population Integrity Indicators and changing the indicators for the Range-wide

9 Condition group, renamed Native Fish Strongholds, to incorporate both cold- and warmwater species. However, for Phase II there are two new groups of indicators: Coldwater Fish Stronghold and Warmwater Fish Stronghold (Figure 5). Combined, these two groups can be used to identify Native Fish Strongholds comprised of both cold and warmwater fishes. The Coldwater Fish Stronghold indicators accounted for the distribution and population health of Colorado River cutthroat trout. Indicator 1 was scored from 1 to 5 based the percent of historical habitat currently occupied by conservation populations in each subwatershed (6 th code hydrologic unit) (see Appendix A for scoring details). Indicator 2 was scored based on the percentage of subwatersheds occupied by cutthroat trout in each subbasin (4 th code hydrologic unit). Indicator 3 was scored based on the density (fish / mile) of each cutthroat trout conservation population. Indicator 4 was scored based the connectivity of cutthroat trout habitat. Indicator 5 was scored based on the life history diversity of cutthroat trout populations. Figure 5. The CSI was modified by changing the Range-wide Condition and Population Integrity group of indicators to account for distribution and population health of multiple target fish species. These new groups termed Coldwater Fish Stronghold and Warmwater Fish Stronghold can be combined to represent Native Fish Strongholds at the subwatershed scale. For the Warmwater Fish Strongholds group, Indicator 1 was scored based on the presence of bluehead sucker at the subwatershed (6 th code HUC), watershed (5 th code HUC), and subbasin (4 th code HUC) spatial scales (again, see Appendix A for scoring details). Indicator 2 was scored based on the presence of flannelmouth sucker at the subwatershed, watershed, and subbasin spatial scales. Indicator 3 was scored based on the presence of roundtail chub at the 9

10 subwatershed, watershed, and subbasin spatial scales. Indicator 4 was scored based on the number of warmwater species (bluehead sucker, flannelmouth sucker, and roundtail chub) present in the subwatershed. Indicator 5 was scored based on the number of warmwater species (bluehead sucker, flannelmouth sucker, and roundtail chub) present in the watershed. Data limitations prohibited more extensive development of population health indicators for the warmwater species, such as those indicating hybridization and abundance or comparisons to historical distributions. Figure 6. CSI Colorado River Cutthroat Trout and Warmwater Fishes Stronghold group scores for all subwatersheds in the Upper Colorado River Basin. Coldwater stronghold scores, based solely on Colorado River cutthroat trout, were highest in the Uinta mountains and lower LaBarge Creek (Figure 6). Clusters of higher Coldwater Stronghold scores also occurred in the Wyoming Range, Upper Little Snake River along the Wyoming-Colorado border, Upper White River in Colorado, Upper White River in Utah, and other smaller clusters scattered throughout the basin. Warmwater Stronghold scores were highest and clustered in the lower Blacks Fork, mainstem Green River, lower White River in Colorado, Upper Muddy Creek, San Rafael River, Colorado River mainstem, and lower Gunnison and San Miguel rivers (Figure 6). Stronghold scores, representing both cold and warmwater species, were highest in Upper Muddy Creek, Upper Henrys Fork, Elkhead Creek, Milk Creek, Avintaquin Creek in the Strawberry River, Garfield Creek, North Fork Gunnison River, and Boulder Creek in the Escalante River basin. Other clusters of higher scores were also distributed across the basin (Figure 7). 10

11 Figure 7. CSI Native Fish Stronghold group scores for all subwatersheds in the Upper Colorado River Basin. Habitat Integrity In addition to adapting the CSI to identify native fish strongholds, we analyzed Habitat Integrity and Future Security across the Upper Colorado River Basin to identify needed course-scale management actions across the landscape. Habitat integrity was summarized at the subwatershed scale (6 th level Hydrologic Unit Code; approximately 10,000 acres) using previously-established CSI habitat integrity indicators (Appendix A). The CSI incorporates five indicators of habitat integrity: Land Stewardship, Watershed Connectivity, Watershed Conditions, Water Quality, and Flow Regime. The Land Stewardship indictor represents the fraction of each subwatershed with lands that have an official protected status with high habitat integrity. Protected lands are federal or state lands with regulatory or congressionallyestablished protections (e.g., wilderness areas, Research Natural Areas, Areas of Critical Environmental Concern). The Watershed Connectivity indicator compares the amount of currently connected habitat to the amount of historically connected habitat at the subwatershed and subbasin (4 th level HUC) scales. The Watershed Conditions indicator incorporates the amount of land that has been converted for agriculture or pasture land in each subwatershed. The Water Quality indicator incorporates information on 303(d) listed streams, the amount of agricultural land, number of active mines, number of oil and gas wells, and amount of roads along stream corridors. The Flow Regime indicator represents the number of dams in each subwatershed and subbasin, as well as the mile of canals that divert water from streams. Detailed information for the habitat integrity indicators is provided in Appendix A, Williams et al. (2007a), and on the CSI website: Habitat integrity in the Upper Colorado River Basin ranged from low to high but most subwatersheds scored as moderately high to high (Figure 8). Integrity is high in higher elevation areas where more land is formally protected as wilderness or has not otherwise been converted for human use. Habitat Integrity is moderate away from major streams where water is scarce and land has yet to be converted, but is low in areas where oil and gas development is prominent (Figure 8). Land converted to hay fields and pastures resulted in low habitat integrity in valleys of major rivers. For example, habitat integrity was low in watersheds between the cities of Green River and Evanston, Wyoming where the Smiths Fork of the Black Fork is 303(d) impaired. Watershed connectivity is low in some subwatersheds where water diversion structures inhibit fish passage (Figure 9). The lower Duchesne River, Uncompahgre 11

12 River near Montrose, Colorado, and upper San Rafael River have extensive canal networks and man-made impoundments that influence the natural flow regime in those areas. Figure 8. CSI Habitat integrity and Future Security scores for subwatersheds in the Upper Colorado River Basin. Habitat Integrity and Future Security were determined using indicators from Trout Unlimited s Conservation Success Index. Future Security The future security of subwatersheds in the Upper Colorado River Basin was summarized to determine the future risks to extant populations, aquatic habitats, and conservation efforts focused in each watershed. Future security was summarized at the subwatershed scale using the five CSI indicators for future security: Land Conversion, Resource Extraction, Energy Development, Climate Change, and Introduced Species. The Land Conversion indicator evaluates the risk of unconverted land being converted based on private land ownership, slope (<15%), and proximity to roads and urban areas. The Resource Extraction indicator includes information on the amount of hard rock mineral claims and productive forest types that could be managed for timber production. The Energy Development indicator accounts for the fraction of subwatersheds with energy reserves or oil and gas leases and sites identified for future hydropower development. The Climate Change indicator portrays the risk of a 3 C 12

13 climate warming scenario, and includes temperature warming, wildfire, winter flooding, and drought risks (Williams et al. 2009). The Introduced Species indicator incorporates information on the presence of introduced species deemed injurious to the target species in each subwatershed. Detailed information for the future security indicators is provided in Appendix A, Williams et al. (2007a), and on the CSI website: Figure 9. Water diversion structure on Big Sandy River. Photo by K. Gelwicks, WGFD. 13 The presence of non-native species was determined using the Colorado River Cutthroat Trout Recovery Team database (Hirsch et al. 2006), the recent Green River Basin survey targeting the three species conducted by Wyoming Game and Fish Department (Gelwicks et al. 2009), Utah Division of Wildlife Resources recent fish surveys (UDWR 2006), and the Colorado Division of Wildlife fish database. Species considered injurious to Colorado River cutthroat trout and the three species were: brook trout Salvelinus fontinalis, rainbow trout Oncorhynchus mykiss, brown trout Salmo trutta, Yellowstone cutthroat trout O. c. bouvieri, white sucker Catostomus commersonii, longnose sucker Catostomus catostomus, burbot Lota lota, smallmouth bass Micropterus dolomieu, and northern pike Esox lucius. These species can displace native cutthroat trout and warmwater fishes through competition and predation (Metcalf et al. 2008; Peterson et al. 2004) as well as threaten them with extinction through hybridization (McDonald et al. 2008; Muhlfeld et al. 2009). Where data on the presence of non-native fishes were unavailable, information on the density of roads was used, assuming that the probability of species introductions increases when there are more roads within watersheds providing access points for human-mediated introductions. Future security of watersheds in the Upper Colorado River Basin was moderately low to moderately high (Figure 8). Most low future security scores resulted from a few primary factors. First, climate change is expected to impact aquatic habitats and fishes through one of three mechanisms (Figure 10). A 3 C increase in air temperatures under a climate warming scenario is projected to cause coldwater habitats to become unsuitable for trout. Climate warming is expected to increase the risk of uncharacteristic wildfires and drought in many parts of the basin. At least one of these factors related to climate change posed a high risk to the future security of most watersheds in the basin. Second, nearly all low-elevation areas in the basin have energy reserves that could be developed in the future, and much of the basin has been leased for oil and gas development (Figure 11). Invasive species are also present in many parts of the basin and pose hybridization, predation, and competition risks to native species.

14 Figure 10. Climate change risk in the Upper Colorado River Basin. 14

15 Figure 11. Federal oil and gas leases and agreements, coal reserves, and potential hydropower sites are used in the CSI as an indicator of the future security of fish populations and aquatic habitats related to energy development. Using CSI Scores to Identify Broadscale Conservation Strategies Across Entire Landscapes The Native Fish Stronghold, Habitat Integrity and Future Security Scores can be used to highlight areas within the Upper Colorado River Basin where specific management, protection or conservation actions may be most beneficial to native fishes. Subwatersheds with high native fish stronghold scores (>20) and high habitat integrity scores (>20) represent good areas for protective management (Figure 12). Where strongholds scores are high (>20) but habitat integrity is low ( 20), habitat restoration is a logical focus for that watershed to ensure native fishes persist into the future. In contrast, subwatersheds with high habitat integrity (>20) but low native fish stronghold scores ( 20) may require population restoration management; where habitat integrity is high (>20) but populations have been extirpated, reintroduction may be an overarching management strategy. Watersheds with low stronghold and habitat integrity scores (each 20) are likely to need both habitat and population restoration, and possibly reintroductions after habitat restoration depending on the species and habitats present. 15

16 Figure 12. Broadscale strategies based on different components of CSI scores for primary current and historic habitats used by target species. For example, population restoration (including reintroduction) opportunities exist where Stronghold scores are low but Habitat Integrity scores are high. In areas with high Stronghold scores but low Habitat Integrity scores, Habitat Integrity scores can be decomposed to determine limiting habitat factors, such as when watershed connectivity may be poor and reconnection efforts are needed. 16

17 Using the CSI to Identify Native Fish Conservation Areas Native Fish Conservation Areas represent a management approach to ensure the long-term persistence of native fish communities at the watershed scale (Williams et al. 2011). Recognizing the importance of our initial Phase I work identifying native fish strongholds and management opportunities for BLM, in 2009 the National Fish and Wildlife Foundation (NFWF) adopted the NFCA framework to inform a new Keystone Initiative aimed at native fish conservation in the Upper Colorado River Basin, focusing again on Colorado River cutthroat trout, flannelmouth sucker, bluehead sucker, and roundtail chub. Potential NFCAs were identified to guide a funding framework for the NFWF Keystone Initiative over the next 10+ years, where funding will be directed towards promoting long-term persistence of entire native fish communities in watersheds identified as potential NFCAs. For the identification of NFCAs for NFWF we used a slightly different approach than our initial efforts in Phase I of this BLM work, so we present these modified analyses here. The Conservation Success Index played a key role in identifying potential NFCAs for NFWF s Keystone Initiative. As described by Dauwalter et al. (2011a), known and potential distributions of Colorado River cutthroat, flannelmouth sucker, bluehead sucker, and roundtail chub were used within an integrated spatial analysis that incorporated watershed connectivity as well as information on habitat integrity and future security - as described by the CSI - to rank all watersheds for conservation. Watersheds of different tiers were then identified within the top 25% of ranked watersheds as potential NFCAs. Potential NFCAs were then vetted with state and federal agencies and non-governmental organizations based on the efficacy of watershed conservation in each potential NFCA and watershed rankings were modified accordingly. 2 The revised rankings of potential NFCAs were used to finalize potential NFCAs that are to serve as focus watersheds for NFWF s Keystone Initiative. The integrated spatial analysis used to identify potential NFCAs built upon the CSI in several ways. First, the analysis included potential species distributions (for bluehead sucker, flannelmouth sucker, and roundtail chub) that were predicted based modeled likelihood of occurrences based on habitat characteristics (see Dauwalter et al. 2011b). This approach was a way to sort out sporadic occurrences of species in unsuitable habitat and the absence of species in suitable habitat for species where information is sparse. This approach illustrates the benefit of using what is termed species distribution models in landscape-scale analyses (Elith and Leathwick 2009). This contrasts, for example, the Warmwater Fish Strongholds indicators that were only based on known occurrences of flannelmouth sucker, bluehead sucker, and roundtail chub within subwatersheds. 2 Potential NFCAs identified in Colorado have not been vetted with agencies and are only considered to be preliminary. 17

18 The spatial analysis also incorporated connectivity among watersheds. The value of individual watersheds was adjusted based on the value of adjacent upstream and downstream watersheds. These linkages are important to consider when identifying watersheds for conservation because activities in the upstream watershed can influence conservation outcomes (Moilanen et al. 2008). While the modified CSI as described above does a good job of describing conditions within individual subwatersheds (12-digit HUCs) that are useful for broadscale landscape assessments, such as rapid ecoregional assessments or RMPs, subwatershed values do not incorporate conditions in adjacent subwatersheds, such as cumulative impacts from all upstream areas, that can be important to consider for some applications. For example, although a subwatershed may have high native fish values, detrimental impacts from areas upstream may limit the effectiveness of conservation actions in that watershed. The Habitat Integrity and Future Security indicators were used as costs in the spatial analysis to identify NFCAs. Given equal biological value, conservation is more likely to be realized when habitats are currently intact and the future of habitats and populations is secure. Therefore, the CSI provided important background information to rank watersheds that were otherwise equal in biological value (Figure 13). The known and predicted species distributions, watershed connectivity, and CSI-based cost were used in an integrated spatial analysis that ranked watersheds based on their conservation value for the target species while accounting for connectivity and costs of conservation (Figure 13). A tiered framework was then overlain on the high-ranking watersheds to indentify proximal cold and warmwater populations: Tier I watersheds have cutthroat trout and at least one warmwater species (flannelmouth sucker, bluehead sucker, and roundtail chub) in the same subwatershed (12-digit HUC), Tier II watersheds have cutthroat trout and at least one warmwater species in the same watershed (10-digit HUC), Tier III watersheds have only cutthroat trout or one or more warmwater species in the same watershed (10-digit HUC) (Figure 13). These high-ranking watersheds with designated tiers were then vetted with agency partners to determine which watershed could best serve as potential NFCAs (Figure 14). Watersheds within a top 25% ranking were then re-ranked by partners based on local information on the efficacy of achieving long-term conservation gains. 18

19 Figure 13. Watershed were ranked using a spatial prioritization that incorporated watershed connectivity, known and predicted species occurrences, and the CSI. These were then used to identify potential Native Fish Conservation Areas (NFCAs) (Figure 14). 19

20 Figure 14. Potential Native Fish Conservation Areas (NFCAs) in the Upper Colorado River Basin. NFCAs in Colorado have not been formally vetted with agencies and are considered preliminary. 20

21 Last, the CSI was used to summarize current and future threats within NFCAs in addition to broad-scale conservation strategies. Overall, potential NFCAs had habitat conditions that were moderate to moderately-high with moderate risk to future threats (Table 1). Upper Little Snake River, Upper White River, Escalante River Headwaters, Muddy Creek (N.F. Gunnison), and West Fork San Juan have habitat integrity and stronghold scores across subwatersheds that suggest they would benefit more from protective management than restoration management. In contrast, the remaining potential NFCAs have moderate habitat conditions and are more likely to need at least some habitat restoration to function naturally. As one example, Muddy Creek in the North Fork of the Gunnison River has populations of Colorado River cutthroat trout in close proximity to each other that could potentially be restored to allow natural metapopulation dynamics to reestablish and promote long-term persistence of these populations; restoration actions in this watershed that extend downstream could also benefit warmwater fishes. Many watersheds will likely need proactive planning to offset the future threats of climate change and non-native species, even in wilderness areas since these threats don t recognize formal land protections (Figure 11). NFCAs with lower future security should also be the focus of monitoring efforts to determine if threats begin to manifest themselves and impact populations and habitats. Thus, the CSI was not only incorporated into a broader analysis to identify NFCAs, but it was used to identify place-based conditions within specific subwatersheds and identify strategies within them, demonstrating the multifaceted utility of the CSI for both broad-scale assessments and prioritization of specific watersheds and identification of management needs within them. Table 1. Overview of potential Native Fish Conservation Areas (NFCAs) for native fish conservation in the Upper Colorado River Basin. Habitat integrity and future security scores range from 5 to 25; mean scores across all subwatersheds are reported with ranges in parentheses. *NFCAs in Colorado have not been formally vetted with agencies and are considered preliminary. Basin Watershed Acres Warmwater Cutthroat NFCA Stronghold Habitat Upper Green Yampa Species Henrys Fork 337,746 Bluehead sucker, flannelmouth sucker Big Muddy Creek (Blacks Fork) Big Sandy Creek Little Sandy Creek Upper Muddy Creek (Little Snake River) 128,047 flannelmouth sucker, roundtail chub 216,862 Bluehead sucker, flannelmouth sucker 107,571 Bluehead sucker, flannelmouth sucker 135,194 Bluehead sucker, flannelmouth sucker, roundtail chub 21 Populations Tier (23 36) (23 32) Extirpated (19 24) Extirpated (19 24) (32 42) Integrity 17.4 (10 25) 15.8 (13 19) 17.6 (14 24) 16.3 (10 21) 17.0 (17 17) Future Security 16.2 (13 20) 13.2 (12 16) 15.3 (12 21) 16.0 (15 17) 14.8 (13 19) Upper L. Snake 131,739 Bluehead sucker ( ( (16 River* 30) 25) 21) Elkhead 142,615 Bluehead sucker, ( (13 15 (11

22 White Lower Green Upper Colorado Creek* flannelmouth 39) 25) 17) sucker, roundtail chub Deep Creek* 32,397 Bluehead sucker ( ( (16 Milk Creek* 55,384 Bluehead sucker, flannelmouth sucker, roundtail chub Upper White River* Piceance 417,453 Flannelmouth Creek* Lower White River* Strawberry River 22 25) (27 36) 409,793 Bluehead sucker (17 29) (15 sucker 26) Mainstem None (23 only 30) Bluehead sucker, flannelmouth sucker, roundtail chub 483,166 Bluehead sucker, flannelmouth sucker San Rafael 991,869 Bluehead sucker, flannelmouth sucker Escalante Headwaters Parachute Creek* Divide Creek* 128,656 Garfield Creek* Gunnison Muddy Creek (N.F. Gunnison) * San Juan West Fk. San Juan* Discussion 400,704 Bluehead sucker, flannelmouth sucker 126,855 Bluehead sucker, flannelmouth sucker, roundtail chub Bluehead sucker, flannelmouth sucker, roundtail chub 28,608 Bluehead sucker, roundtail chub 164,257 Bluehead sucker, flannelmouth sucker (23 37) (24 34) (27 34) (27 36) (23 36) (38 38) (17 37) 43,990 Roundtail chub (20 29) Efficacy of the CSI as a Broad-scale Aquatic Assessment Tool for Public Lands 18) 17.3 (14 20) 21.3 (12 25) 16.8 (13 19) 17.5 (16 20) 18.4 (11 25) 17.3 (5 25) 20.3 (14 25) 17.0 (11 20) 15.9 (10 23) 18 (18 18) 21.3 (18 25) 24.3 (23 25) 17) 13.5 (12 15) 17.6 (14 20) 16.0 (14 18) 14.9 (13 17) 16.8 (14 20) 16.3 (11 22) 17.9 (15 21) 14.2 (13 16) 16.4 (11 23) 13 (13 13) 17.3 (13 24) 21.7 (19 23) We adapted the CSI in several ways to facilitate its use as a landscape-scale aquatic assessment tool that can be used by the BLM for landscape-level planning and resource management plan development. This was done by modifying the original CSI Indicator Groups Range-wide Condition and Population Integrity to represent Coldwater Fish Strongholds and Warmwater Fish Strongholds, which together can be used to identify native fish strongholds. The CSI was also modified from having the geographic coverage based solely the historical range of one focal (trout) species to extending coverage to the entire Upper Colorado River Basin. Thus, the

23 modified CSI can be used to describe native fish strongholds, habitat conditions, and future security of populations and habitats across the entire landscape of the Upper Colorado River Basin, as well as identify place-based strategies at a coarse scale. Like any coarse-scale assessment, finer-scale data and local information is also needed to identify specific management actions within certain watersheds. Therefore, data provided by the CSI should not be viewed as a replacement for the local knowledge and expertise that is provided by field biologists. Ideally, the CSI is designed to be a landscape-scale compliment to local knowledge. Nel et al. (2008) stated that networks of conservation areas should represent all target species, promote persistence of targeted species, incorporate opportunities and constraints in each area, and align with other conservation and planning initiatives. Formally incorporating watershed-scale protective and restoration management strategies into landscape-level planning by federal agencies accommodates the scale at which metapopulation dynamics operate (Compton et al. 2008; Dunham and Rieman 1999; Hanski and Gilpin 1991; Hilderbrand and Kershner 2000). In addition, securing populations of the various species across multiple watersheds in the region, such as a network of Native Fish Conservation Areas, will help to ensure that those species persist across the landscape in the face of stochastic disturbances in individual watersheds that can cause local extirpations, such as floods or wildfires (Dunham et al. 2003a; Williams et al. 2007b). Preserving species in the face of local disturbances is a main argument for ensuring conservation areas are distributed spatially across the region of interest. Figure 15. Native Fish Stronghold scores and Wyoming Game and Fish Department Habitat Priorities identified as part of their Strategic Habitat Plan. 23 Our native fish stronghold indicators identify areas where multiple native species listed as sensitive occur on the landscape. These areas and the potential NFCAs we identified also align with other agency identified priorities. For example, Wyoming Game and Fish Department has identified habitat priority areas based on aquatic and combined aquatic and terrestrial habitats. While those areas were identified for multiple reasons, oftentimes they were identified as priorities based on the presence of

24 Colorado River cutthroat trout, flannelmouth sucker, bluehead sucker, and roundtail chub populations. For this reason, our native fish stronghold indicators score high in many of the areas identified as habitat priority areas in Wyoming (Figure 15). These areas of overlap can synergize interagency coordination efforts directed at native fish conservation efforts targeting multiple species. Although native fish strongholds and potential NFCAs were identified using the CSI, opportunities exist for native fish conservation outside of the network of identified watersheds. For example, Upper Bitter Creek in Wyoming contains the only non-hybridized population of flannelmouth sucker in Wyoming and, therefore, represents an important element of conservation for that species despite the fact that it has no coldwater habitat nor bluehead sucker or roundtail chub populations. The modification and application of TU s Conservation Success Index (CSI) in the Upper Colorado River Basin illustrates its potential application as a rapid ecoregional assessment tool for land managers. It provides a snapshot of aquatic ecosystem health by defining watershed and fish community condition across multiple scales and identifies natural and anthropogenic stressors that threaten aquatic species and their habitats. By identifying those areas that contain complexes of native fishes, and identifying key threats to those species and habitats, it provides needed context for informed decision-making; that is, the CSI can be used as a decision support tool. Decision support tools are intended as a planning tool to aid decisions regarding land-use planning and the allocation of actions and monies towards conservation of the targeted species (Sarkar et al. 2006), and to identify actions and management practices which are fundamentally compatible or incompatible with the species conservation objectives. Hence, the CSI can provide a framework for aiding managers in making land management decisions that incorporate Colorado River cutthroat trout and the three warm-water native species conservation needs. By stratifying the landscape under this framework, and applying management guidance consistent with those strategies identified for each area, it will ensure BLM meets its obligation under the Federal Land Policy and Management Act to ensure species persistence over the long term. Characterization of the landscape into categories of species conservation importance provides a framework within which management direction can be developed and applied for different land management programs. Management direction will be different within each watershed strategy identified by the CSI (protection or restoration (including reconnection)). For example, grazing practices which meet land health standards at local and regional scales should be fundamentally compatible with species conservation objectives and could occur in all areas. If grazing activities are not meeting land health objectives and impede attainment of species conservation objectives, this information allows the decision maker to weigh the trade-offs within this conflict. The level of management activity could also vary between watersheds and across time. For example, watersheds that are targeted for protection that have a healthy baseline may be able to sustain a higher level of management activity over a longer period of 24

25 time. Alternatively, watersheds that are targeted for restoration may require reducing impacts in order to re-establish ecological and physical function. In this pilot test of the CSI as a rapid ecoregional assessment (REA) tool, potential NFCAs were also identified as watershed-scale areas that are important for native fish conservation. Under a conservation strategy, these watersheds are those that are essential to the long-term persistence of the species, and those with high Habitat Integrity have the highest degree of fidelity to natural processes. In other words, they have not been impacted to a significant degree and retain all natural ecological and physical functions. Land management actions designed and implemented consistent with retaining ecological and physical functions would be the most compatible for protecting those areas. Those actions which could not be mitigated or designed to have minimal impact, would not be consistent with the conservation objectives. This approach is consistent with current policy for Areas of Critical Environmental Concern (ACEC), certain Natural Landscape Conservation Areas (e.g., wild and scenic rivers), wilderness, or wilderness study areas, where only land management activities designed consistent with the primary objectives of the area are permitted. In other words, under a multiple use doctrine the highest value of a native fish stronghold or NFCA is for species conservation. Confronting Future Threats A crucial component of the CSI is that it incorporates future threats to aquatic species and habitats. The CSI identified where three key drivers of landscape change over time are likely to occur and have a direct impact on species survival, potentially requiring adaptations in management strategies. These are Energy Development, Climate Change, and the continued advance of Invasive Species (both terrestrial and aquatic). Low scores for these indicators should not be construed as a rationale for abandoning areas as conservation targets; rather, each of these drivers elevates the significance of future management decisions within specific areas. Responsible development of energy resources requires a landscape level view of conditions so that those areas of high-energy potential (and their associated transmission corridors) can be compared with those areas of high conservation value. Where there is overlap, conflict may exist. This level of assessment is essential for informed decision-making, and allows the decision maker to identify mitigation, allocate resources, or make determinations to avoid certain areas. Within these areas of high-energy potential, the use of water to generate renewable energy is often highly consumptive, or is managed in a manner that creates significant impacts to aquatic species. Support of infrastructure, particularly road networks and distribution yards will require oversight to ensure they don t negatively impact instream habitat structure and habitat connectivity. Climate change will compound and exacerbate issues with water consumption and warming of coldwater habitats. Changes in runoff patterns, loss of snowpack storage, and shifts in rainfall patterns will all conspire to further impact water-dependent resources. Responsible 25

26 management of riparian areas, reconnecting channels to their floodplains, and implementation of other management actions to ensure the storage and natural release of water will be necessary to partially mitigate impacts and protect stream temperatures from climate change. Focusing management towards watershed-scale areas for native fish conservation in anticipation of these changes will be of greater value than protecting watersheds that may quickly change from current hydrologic regimes to those that do not support targeted species (e.g., more channels becoming intermittent or ephemeral, water temperature increases beyond species tolerance levels, etc.). The continued advance of invasive species, both terrestrial and aquatic, will threaten areas of high ecologic integrity. Aquatic invasive species may rapidly expand into habitats not currently infested, and may require special management considerations to control their spread. Management focused on invasive species potentially reduces management flexibility. For example, uninfected waters may need to be quarantined from uses that may potentially serve as a vector for transmitting and spreading the invasive species. Water-based recreation uses (boating, swimming, wading, fishing, etc.) may need to be managed closely; grazing use may need to shift; and equipment used in construction and fire suppression may need the application of best management practices before moving from one watershed into another. Habitats that are less resilient to stressors due to past management practices may accelerate the spread of these invasive species. Regardless of the scenario that plays out, knowing the aquatic resource conditions across the landscape, as well as within specific watersheds, provides a proactive science-based approach for species conservation and recovery efforts. Knowledge of the conditions and trends of watershed health can help determine the overall resilience of watersheds and their ability to absorb and positively respond to various stressors. This knowledge creates decision space and flexibility for managers when making decisions on resource allocation and use. Acknowledgments The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the opinions or policies of the U.S. Government. Mention of trade names or commercial products does not constitute their endorsement by the U.S. Government. We thank the Wyoming Game and Fish Department, Utah Natural Heritage Program, Utah Division of Wildlife Resources, and Colorado Division of Wildlife for fish distribution data and their reviews of preliminary results contained herein; especially Tyler Abbott (BLM), Justin Jimenez (BLM), and John Sanderson (TNC). Funding was kindly provided by the Bureau of Land Management, National Fish and Wildlife Foundation, and Trout Unlimited s Coldwater Conservation Fund. 26

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33 246 in R. F. Carline and C. LoSapio, editors. Wild Trout IX: Sustaining wild trout in a changing world. Wild Trout Symposium, Bozeman, Montana. Williams, J. E., R. N. Williams, R. F. Thurow, L. Elwell, D. P. Philipp, F. A. Harris, J. L. Kershner, P. J. Martinez, D. Miller, G. H. Reeves, C. A. Frissell, and J. R. Sedell Native Fish Conservation Areas: a vision for large-scale conservation of native fish communities. Fisheries 36:in press. Williams, J. E., C. A. Wood, and M. P. Dombeck Watershed restoration: principles and practices. American Fisheries Society, Bethesda, Maryland. Wyoming Oil and Gas Conservation Commission. Wyoming Active Oil and Gas Wells. 9. Young, M. K Colorado River cutthroat trout: a technical conservation assessment. General Technical Report RMRS-GTR-207-WWW, USDA Forest Service, Rocky Mountain Research Station, Fort Collins, Colorado. 33

34 Appendix A. Modified Subwatershed Scoring and Rule Set for Trout Unlimited s Conservation Success Index. The modified CSI consists of three main groups of indicators: 1. Native coldwater fish strongholds 2. Native warmwater fish strongholds 3. Habitat integrity 4. Future security Below is an overview of each CSI group and the indicators within each group. Each section contains an overview of the group indicators Native Coldwater Fish Strongholds: Indicators used to identify native fish strongholds: Overview: 1. Percent historic habitat occupied in subwatershed (6 th level HUC) 2. Percent of subwatersheds (6 th level HUC) occupied by cutthroat trout within subbasin (4 th level HUC) 3. Native trout population density 4. Native trout population extent 5. Life history diversity in native trout populations Indicator: 1. Percent historic Colorado River cutthroat trout habitat occupied in subwatershed Indicator Scoring: Occupied stream habitat CSI Score 0%; Non-historic habitat % % % % 5 Explanation: Percent of historic Colorado River cutthroat currently occupied in subwatershed (6 th code hydrologic unit) Rationale: Subwatershed is a better candidate as a native fish stronghold when more historic Colorado River cutthroat habitat is currently occupied 34

35 Data Sources: The presence of cutthroat trout populations was based on the Colorado River cutthroat trout Recovery Team database (Hirsch et al. 2006) Indicator: 2. Percent historically occupied subwatersheds currently occupied within subbasin. Indicator Scoring: Percent subwatersheds CSI Score occupied by subbasin 0%; Non-historic habitat % % % % 5 Explanation: The percentage of historically occupied subwatersheds that are currently occupied by cutthroat trout within each subbasin. The percentage is the same for all subwatersheds within a subbasin. Rationale: Species that occupy a larger proportion of subwatersheds are likely to be more broadly distributed and have an increased likelihood of persistence. Data Sources: The presence of cutthroat trout populations was based on the Colorado River cutthroat trout Recovery Team database (Hirsch et al. 2006). Indicator: 3. Native trout population density. Indicator Scoring: Fish per mile CSI Score >400 5 Explanation: Population density expressed as number of adult fish per mile. Rationale: Subwatershed is a better candidate as a native fish stronghold when native trout are more abundant. 35

36 Data Sources: Density of cutthroat trout populations was based on the Colorado River cutthroat trout Recovery Team database (Hirsch et al. 2006). Indicator: 4. Native trout population extent. Indicator Scoring: Degree of connectedness CSI Score No population 1 4 (Population Isolated) 2 3 (Weakly Connected) 3 2 (Moderately Connected) 4 1 (Strongly Connected) 5 Explanation: The linear miles of habitat occupied by native trout population. Rationale: Populations occupying larger extents of habitat have increased likelihood of persistence. Data Sources: Extent of cutthroat trout populations was based on the Colorado River cutthroat trout Recovery Team database (Hirsch et al. 2006). Indicator: 5. Life history diversity in native trout populations. Indicator Scoring: Conservation population CSI Score No population 1 One life history form present: 2 Resident only Two life histories present: Fluvial 3 and Resident with historic lakes but no current adfluvial forms 4 Two or three life histories present: Fluvial and resident with no lake 5 populations; Any combination with Adfluvial present 36

37 Explanation: Life history diversity expressed as resident, fluvial, and adfluvial life history forms. Rationale: Populations with fluvial and adfluvial life histories have increased likelihood of persistence. Data Sources: Life history diversity of cutthroat trout populations was based on the Colorado River cutthroat trout Recovery Team database (Hirsch et al. 2006). Native Warmwater Fish Strongholds: Indicators used to identify native fish strongholds: Overview: 1. Presence of bluehead sucker at multiple scales 2. Presence of flannelmouth sucker at multiple scales 3. Presence of roundtail chub at multiple scales 4. Number of three species present in subwatershed (6 th level HUC) 5. Number of three species present in watershed (5 th level HUC) Indicator: 1. Presence of bluehead sucker at multiple scales Indicator Scoring: Presence CSI Score Not present in HUC 4 1 Present in HUC 4 2 Present in HUC 5 4 Present in HUC 6 5 Explanation: Presence of bluehead sucker at multiple scales Rationale: Subwatershed is a better candidate as a warmwater stronghold bluehead sucker are present, but subwatershed is also valuable as a stronghold when bluehead sucker are present in watershed or subbasin. Data Sources: Wyoming Game and Fish Department database, Utah Natural Heritage Program database, and Colorado Division of Wildlife database. Indicator: 2. Presence of flannelmouth sucker at multiple scales 37

38 Indicator Scoring: Presence CSI Score Not present in HUC 4 1 Present in HUC 4 2 Present in HUC 5 4 Present in HUC 6 5 Explanation: Presence of flannelmouth sucker at multiple scales Rationale: Subwatershed (HUC 6) is a better candidate as a warmwater stronghold flannelmouth sucker are present, but subwatershed is also valuable as a stronghold when flannelmouth sucker are present in watershed (HUC 5) or subbasin (HUC 4). Data Sources: Wyoming Game and Fish Department database, Utah Natural Heritage Program database, and Colorado Division of Wildlife database. Indicator: 3. Presence of roundtail chub at multiple scales Indicator Scoring: Presence CSI Score Not present in HUC 4 1 Present in HUC 4 2 Present in HUC 5 4 Present in HUC 6 5 Explanation: Presence of roundtail chub at multiple scales Rationale: Subwatershed (HUC 6) is a better candidate as a warmwater stronghold roundtail chub are present, but subwatershed is also valuable as a stronghold when roundtail chub are present in watershed (HUC 5) or subbasin (HUC 4). Data Sources: Wyoming Game and Fish Department database, Utah Natural Heritage Program database, and Colorado Division of Wildlife database. Indicator: 4. Number of three species present in subwatershed (6 th level HUC) Indicator Scoring: 38

39 Number of three species CSI Score Explanation: The number of three species (bluehead sucker, flannelmouth sucker, and roundtail chub) in the subwatershed (HUC 6). Rationale: Subwatershed (HUC 6) has higher value was a warmwater stronghold when more species are present. Data Sources: Wyoming Game and Fish Department database, Utah Natural Heritage Program database, and Colorado Division of Wildlife database. Indicator: 4. Number of three species present in watershed (5 th level HUC) Indicator Scoring: Number of three species CSI Score Explanation: The number of three species (bluehead sucker, flannelmouth sucker, and roundtail chub) in the watershed (HUC 5). Rationale: Subwatershed has higher value was a warmwater stronghold when more species are present in the watershed (HUC 5). Data Sources: Wyoming Game and Fish Department database, Utah Natural Heritage Program database, and Colorado Division of Wildlife database. Habitat Integrity: Indicators for the integrity of aquatic habitats. Overview: 1. Land stewardship 2. Watershed connectivity 39

40 3. Watershed conditions 4. Water quality 5. Flow regime Indicator: 1. Land stewardship. Indicator Scoring: Protected stream Subwatershed CSI Score habitat protection none any 1 1 9% <25% 1 1 9% 25% % <25% % 25% % <50% % 50% 5 30% any 5 Explanation: The percent of stream habitat AND percent subwatershed that is protected lands. Protected lands are federal or state lands with regulatory or congressionally-established protections, such as: federal or state parks and monuments, national wildlife refuges, wild and scenic river designations, designated wilderness areas, inventoried roadless areas on federal lands, Research Natural Areas, Areas of Critical Environmental Concern, others areas of special protective designations, or private ownership designated for conservation purposes (e.g., easements). Rationale: Stream habitat and subwatersheds with higher proportions of protected lands typically support higher quality habitat than do other lands. Data Sources: Protected areas data were compiled from the ESRI, Tele Atlas North American / Geographic Data Technology dataset on protected areas (ESRI 2004) and the U.S. Department of Agriculture, Forest Service s National Inventoried Roadless Areas dataset (USDA Forest Service 2008). Stream habitat was determined using all streams in the National Hydrography Dataset Plus (USEPA and USGS 2005). Indicator: 2. Watershed connectivity. Indicator Scoring: Number of CSI Score 40

41 stream/canal intersections Explanation: The number of stream-canal intersections. Rationale: Increased hydrologic connectivity provides more habitat area and better supports multiple life histories, which increases the likelihood of persistence (Colyer et al. 2005). Diversions, when they do not directly inhibit fish passage, can represent false movement corridors, cause fish entrainment, and act as population sinks (Roberts and Rahel 2008; Schrank and Rahel 2004). Data Sources: Connectivity was determined using all streams was determined using all streams in the National Hydrography Dataset Plus (USEPA and USGS 2005). Indicator: 3. Watershed condition. Indicator Scoring: Land conversion CSI Score 30% % % 3 5 9% 4 0-4% 5 CSI score is downgraded 1 point if road density is 1.7 and <4.7 mi/square mile. If road density is 4.7 mi/square mile it is downgraded 2 points. Explanation: The percentage of converted lands in the subwatershed, and the density of roads. Rationale: Habitat conditions are the primary determinant of persistence for most populations (Harig et al. 2000). Converted lands are known to degrade aquatic habitats (Shepard et al. 2002; White and Rahel 2008). Road density is computed for the subwatershed; roads are 41

42 known to cause sediment-related impacts to stream habitat (Eaglin and Hubert 1993; Lee et al. 1997; Waters 1995). Lee et al. (1997) recognized 6 road density classifications as they related to aquatic habitat integrity and noted densities of 1.7 and 4.7 mi/mi 2 as important thresholds. Data Sources: Converted lands were determined using the National Land Cover Database (USGS 2001), with all Developed, Pasture/Hay, and Cultivated Crops land cover types considered to be converted lands. Road density was determined using Integrated Road Transportation of Idaho data (IGDC 2008). Indicator: 4. Water quality. Indicator Scoring: Miles 303(d) Streams Agricultural Land Number Active Mines Number active oil/gas wells Road mi/ Stream mi CSI Score > % % % % % Score for worst case. Explanation: The presence of 303(d) impaired streams, percentage agricultural land, number of active mines, number of active oil and gas wells, and miles of road within 150 ft of streams in the subwatershed. Rationale: Decreases in water quality, including reduced dissolved oxygen, increased turbidity, increased temperature, and the presence of pollutants, reduces habitat suitability for salmonids and other native fishes. Agricultural land can impact aquatic habitats by contributing nutrients and fine sediments, and deplete dissolved oxygen. Mining activity can deteriorate water quality through leachates and sediments. Oil and gas development is associated with road building, water withdrawals, and saline water discharge (Cakmakce et al. 2008; Murray-Gulde et al. 2003; Rice et al. 2000). Roads along streams can also contribute large amounts of fine sediments that smother benthic invertebrates, embed spawning substrates, and increase turbidity (Davies-Colley and Smith 2001; Lloyd 1987). Data Sources: 303(d) impaired streams was determined using U.S. Environmental Protection Agency data (USEPA 2002). The National Land Cover Database (USGS 2001) was used to 42

43 identify agricultural lands; Hay/Pasture and Cultivated Crops were defined as agricultural land. Active mines were identified by using the Mineral Resources Data System (USGS 2008a). Active oil and gas wells from Wyoming Oil and Gas Conservation Commission (Wyoming Oil and Gas Conservation Commission 9 A.D.). Road density within a 150 ft buffer was computed using ESRI roads (ESRI 2005a) and the National Hydrography Dataset Plus (USEPA and USGS 2005). Indicator: 5. Flow regime. Indicator Scoring: Number of Miles of Storage (acreft)/stream CSI Score dams Canals mile , ,000 2, Score for worst case. Explanation: Number of dams, miles of canals, and acre-feet of reservoir storage per perennial stream mile. Rationale: Natural flow regimes are critical to proper aquatic ecosystem function (Poff et al. 1997). Dams, reservoirs, and canals alter flow regimes (Benke 1990). Reduced or altered flows reduce the capability of watersheds to support native biodiversity and salmonid populations. Data Sources: The National Inventory of Dams (USACE 2008) was the data source for dams and their storage capacity. Data on canals were obtained from the National Hydrography Dataset Plus (USEPA and USGS 2005). Perennial streams were obtained from the National Hydrography Dataset Plus (USEPA and USGS 2005). Future Security Indicators for the future security of populations and aquatic habitats. Overview: 1. Land conversion 2. Resource extraction 3. Energy development 4. Climate change 5. Introduced species 43

44 Indicator: 1. Land conversion. Indicator Scoring: Land Vulnerable to Conversion CSI Score % % % % % 5 Explanation: The potential for future land conversion is modeled as a function of slope, land ownership, roads, and urban areas. Land is considered vulnerable to conversion if the slope is less than 15%, it is in private ownership and not already converted, it is within 0.5 miles of a road, and within 5 miles of an urban center. Rationale: Conversion of land from its natural condition will reduce aquatic habitat quality and availability (Burcher et al. 2007; Stephens et al. 2008). Data Sources: Slope was computed from elevation data from the National Hydrography Dataset Plus (USEPA and USGS 2005). Land cover was determined from the National Land Cover Database (USGS 2001), and all land cover classes except developed areas, hay/pasture, and cultivated crops cover types were considered for potential conversion. Urban areas were determined using 2000 TIGER Census data (ESRI 2005b), roads from ESRI Roads (ESRI 2005a), and land ownership using USGS data on Land Ownership in Western North America (USGS 2004). Indicator: 2. Resource extraction. Indicator Scoring: Forest management Hard Metal Mine Claims CSI Score % % % 26-50% % 11-25% % 1 10% 4 0% 0% 5 Score for worst case. 44

45 Explanation: Percentage of subwatershed available for industrial timber production and the percent of subwatershed with hard metal mining claims (assuming an average of 20 acres per claim) outside of protected areas. Protected lands were removed from availability and include: federal or state parks and monuments, national wildlife refuges, wild and scenic river designations, designated wilderness areas, inventoried roadless areas on federal lands, Research Natural Areas, Areas of Critical Environmental Concern, others areas of special protective designations, or private ownership designated for conservation purposes. Rationale: Productive forest types have a higher likelihood of being managed for timber production than unproductive types, and, hence, future logging poses a future risk to aquatic habitats and fishes (Eaglin and Hubert 1993). Areas with hard metal claims pose a future risk to mining impacts than areas without claims. Claims indicate areas with potential for hard mineral mining, and mining can impact aquatic habitats and fishes (Rahn et al. 1996). Data Sources: Timber management potential identifies productive forest types using the existing vegetation type in the Landfire dataset (USFS 2008). The number of mining claims was determined using Bureau of Land Management data (Hyndman and Campbell 1996), and each claim was assumed to potentially impact 20 acres. Protected areas data were compiled from the ESRI, Tele Atlas North American / Geographic Data Technology dataset on protected areas (ESRI 2004) and the U.S. Department of Agriculture, Forest Service s National Inventoried Roadless Areas dataset (USDA Forest Service 2008). Indicator: 3. Energy Development. Indicator Scoring: Leases or CSI Score reserves New Dams 4 th New Dams 6 th % % % % 1 4 0% 0 5 Score for worst case Explanation: The acreage of oil, gas, and coal reserves and the number of dam sites located for potential development outside of protected areas within each subbasin and subwatershed. Rationale: Increased resource development will increase road densities, modify natural hydrology, and increase the likelihood of pollution to aquatic systems. Changes in natural flow 45

46 regimes associated with dams are likely to reduce habitat suitability for native salmonids and increase the likelihood of invasion by non-native species(fausch 2008). If lands are protected then the watersheds will be less likely to be developed. Data Sources: Oil and gas leases and agreements from BLM Geocommunicator (USBLM 2008). Potential dam sites are based on Idaho National Laboratory (INL) hydropower potential data (INL 2004). Protected areas data were compiled from the ESRI, Tele Atlas North American / Geographic Data Technology dataset on protected areas (ESRI 2004) and the U.S. Department of Agriculture, Forest Service s National Inventoried Roadless Areas dataset (USDA Forest Service 2008). Indicator: 4. Climate change. Indicator Scoring: TU Climate Change Analysis Climate Risk Factors CSI Score High, High, Any., Any 1 High, Any, Any, Any 2 Mod., Mod., Mod, (Mod or Low) 3 Mod, Mod, Low, Low 4 Low, Low, Low, (Mod or Low) 5 Explanation: Climate change is based on TU Climate Change analysis, which focuses on 4 identified risk factors related to climate change: a. Increased Summer Temperature: loss of lower-elevation (higher-stream order) habitat impacts temperature sensitive species b. Uncharacteristic Winter Flooding: rain-on-snow events lead to more and larger floods c. Uncharacteristic Wildfire: earlier spring snowmelt coupled with warmer temperatures results in drier fuels and longer burning, more intense wildfire d. Drought: moisture loss under climate warming will overwhelm any gains in precipitation and lead to higher drought risk 46

47 Each of the four factors is ranked as low, moderate, or high. Increased summer temperature due to climate change was modeled as a 3 C increase. Uncharacteristic winter flooding can result from basins transitioning from snow dominated to rain-on-snow dominated with increased winter flooding. Uncharacteristic wildfires result from changes in climate and fire fuels. Drought risk is based on the Palmer Drought Severity Index, but was adjusted for elevation and precipitation. Rationale: Climate change is likely to threaten most salmonid populations because of warmer water temperatures, changes in peak flows, and increased frequency and intensity of disturbances such as floods and wildfires (Williams et al. 2009; Williams et al. 2007b). A 3 C increase in summer temperature has the potential to impact coldwater species occupying habitat at the edge of their thermal tolerance. Increased winter flooding can cause local populations to be extirpated. Wildfire can change aquatic habitats, flow regimes, temperatures, and wood inputs that are important to salmonids (Dunham et al. 2003b). Drought is expected to reduce water availability (Hoerling and Eischeid 2007; Westerling et al. 2006) and the availability of aquatic habitat. These risks are further discussed by Williams et al.(2009) Data Sources: Temperature and precipitation data were obtained from the PRISM Group(PRISM Group 2008). Elevation data was obtained from the National Elevation Dataset (USGS 2008b), and LANDFIRE data for the Anderson Fire Behavior Fuel Model 13 (USFS 2008) was used as input for wildfire risk. The Palmer Drought Severity Index was used for drought risk (Palmer 47

48 1965), but was adjusted for elevation (elevations above 2690 have lower risk (Westerling et al. 2006)) and the deviation from mean annual precipitation (areas with more precipitation on average have lower risk). Indicator: 5. Introduced species. Indicator Scoring: If introduced species have been documented in a subwatershed Present in 4th Present in 6th Road Density CSI Score Yes Yes Any 1 Yes No >4.7 2 Yes No Yes No <1.7 4 No No Any 5 Score worst case. If introduced species have not been documented in a subwatershed Present in Road Density CSI Score 4th Yes >4.7 1 Yes Yes Yes <2.7 4 No any 5 Score worst case. If introduced species have not been documented in a subwatershed or subbasin Road Density CSI Score > <1.7 5 Score worst case. 48

49 Explanation: The presence of introduced, injurious species in a subbasin and subwatershed and road density. Road density is the length of road per subwatershed area, and represents the potential for future introduction of non-native species into the subwatershed. Rationale: Introduced species can reduce native fish populations through predation, competition, hybridization, and the introduction of non-native parasites and pathogens (Fausch et al. 2006). In the absence of data on presence of non-native species in a subwatershed or subbasin, road density can be used as a surrogate for risk of non-native fish introductions by perpetrators (Rahel 2004). Data Sources: Data on non-native, injurious species were obtained from a variety of sources. Wyoming Game and Fish Department considers white sucker, longnose sucker, and burbot to be the non-native species of highest concern to the flannelmouth sucker, bluehead sucker, and roundtail chub (K. Gelwicks, Wyoming Game and Fish Department, personal communication). The non-native white sucker hybridizes readily with the flannelmouth sucker and bluehead sucker (Gill et al. 2007; McDonald et al. 2008), and burbot are suspected to prey on native warmwater fishes (Sweet 2007). Non-native trout can also cause population declines or extirpation of Colorado River cutthroat trout through competition, predation, and hybridization. Information on the presence of non-native species was obtained from recent Wyoming Game and Fish Department stream surveys targeted at the three warmwater species, recent surveys by Utah Division of Wildlife Resources, and Colorado Division of Wildlife fish database, and the geodatabase associated with the Colorado River cutthroat trout range-wide assessment (Hirsch et al. 2006). Although Quist et al.(2006) found that non-native creek chubs had high diet overlap with roundtail chub in Muddy Creek, Wyoming, creek chub were considered to have minimal impacts on native fish populations. The longnose sucker has also been found to hybridize with native suckers (Gelwicks et al. 2009). 49

50 Appendix B. Detailed second-tier analysis of identified NFCAs using CSI data. *NFCAs in Colorado have not been formally vetted with agencies and are considered preliminary; therefore, they are not included here. Upper Muddy Creek The Upper Muddy Creek watershed is in the Yampa River Basin southwest of Rawlins, Wyoming. Muddy Creek is a tributary to the Little Snake River, and Upper Muddy Creek is one of two streams sampled by Wyoming Game and Fish Department where all three warmwater fishes flannelmouth sucker, bluehead sucker, and roundtail chub - were collected at the same sampling location (Figure 1B). There is also a conservation population of genetically pure Colorado River cutthroat trout in Littlefield Creek in the Upper Muddy Creek watershed. This population now overlaps in distribution with native warmwater fishes. The Upper Muddy Creek watershed was proposed as an Area of Critical Environmental Concern in the revised Resource Management Plan for the Rawlins Field Office, Bureau of Land Management due to the presence of native cold and warmwater fishes and presence of critical winter habitat for big game. Figure 1B. The Upper Muddy Creek watershed. 50

51 Brook trout and white suckers are non-native species that also occur in the Upper Muddy Creek watershed. Hybridization is occurring in Upper Muddy Creek (Compton 2007; Gelwicks et al. 2009). There is concern that hybridization between white sucker and flannelmouth sucker have allowed introgression between flannelmouth sucker and bluehead sucker two species previously isolated by reproductive barriers (McDonald et al. 2008). The presence of these injurious non-native species may lower the success of other conservation activities focused in the watershed, but their presence also indicates that directed non-native fish removal is a much needed conservation action. Although not considered as large a threat as the other non-native species, the creek chub Semotilus atromaculatus is another non-native species that occurs in Muddy Creek and has been shown to potentially compete with roundtail chubs for food resources (Quist et al. 2006). The Upper Muddy Creek watershed has moderate habitat integrity with no protected lands, poor water quality, and poor connectivity. Land ownership is a checkerboard mix of private land (35%), U.S. Bureau of Land Management (55%), and State of Wyoming (10%) land but none of the watershed has an official protected status. Water quality is impaired, with almost one-half of the Upper Muddy Creek watershed is 303(d) listed for habitat degradation; a portion of Littlefield Creek also received a PFC rating of non-functional. Muddy Creek has several barriers that prevent fish from moving freely within the watershed (Figure 2B) (Compton et al. 2008). Figure 2B. Rock gabion in Upper Muddy Creek. Photo by R. Beatty. 51

52 The future security of the Muddy Creek watershed is high with a few exceptions. There is very high risk of further energy development throughout the watershed, including recent plans to develop wind power in the McKinney Creek area. Non-native species injurious to cutthroat trout and native warmwater fishes, as discussed above, occur in the watershed and have the potential to out-compete native fishes and cause extinction through hybridization. There is low risk for lands being converted for agriculture. There is also low risk for future flow modification and climate change in the watershed. Conservation opportunities in the watershed include restricting energy development and implementing land protection measures, as well as removal of non-native fishes. Potential conservation activities in Upper Muddy Creek include habitat restoration, non-native fish removal, barrier removal and management, proactive protective measures. Habitat restoration includes grazing management and restoration of riparian vegetation and stream morphology to natural conditions, including McKinney Creek, and Muddy Creek above Littlefield Creek. Wyoming Game and Fish Department recently worked with a local landowner to develop an off-stream watering site for cattle (R. Compton, Wyoming Game and Fish Department, personal communication). A small section of Littlefield Creek also received a nonfunctional PFC rating. Non-native fish removal would benefit cold and warmwater natives. Brook trout occupy McKinney Creek. Although brook trout are isolated from Colorado River cutthroat trout are isolated by a barrier, their presence in the watershed does increase the risk of future colonization of Littlefield Creek. Removal of white sucker, hybrid suckers, and creek chubs would also benefit native warmwater fishes. Mechanical removal (e.g., electrofishing) can be effective in reducing non-native fish populations, but it is not 100% effective and would need to be conducted periodically over time. A fish weir at the confluence of McKinney Creek could be used to capture non-native fishes moving upstream to spawn. Chemical treatment is also an option but would need to be planned in accordance with private landowners, and native fishes would need to be held off site while piscicides are applied. The Weber headcut structure would need to be maintained as a fish barrier to prevent non-native fishes from colonizing from downstream, and other structures within Muddy Creek could be removed or retrofitted to facilitate fish passage and allow native fishes access to the entire watershed to complete their life cycles. Wind power development is forecasted near McKinney Creek, and oil and gas development is ongoing in portions of the watershed and active measures should be taken to ensure development does not impact aquatic habitat. The Rawlins Field Office of the Bureau of Land Management proposed upper Muddy Creek as an Area of Critical Environmental Concern to afford the watershed more protection from future threats to the native fish community (P. Lionberger, Bureau of Land Management, pers. comm.). Although the ACEC designation was not adopted, Upper Muddy Creek will be managed by the Bureau of Land Management as a Wildlife Habitat Management Alternative. Big Muddy Creek Big Muddy Creek originates in the Uinta Mountains in Utah on the Wasatch National Forest and flows north into Wyoming east of Evanston where it joins with the Black Fork of the Green 52

53 River. Colorado River cutthroat trout inhabit the headwaters, whereas flannelmouth suckers and roundtail chubs occupy the lower watershed near I-80 (Figure 3B). Figure 3B. Big Muddy Creek watershed. Rainbow trout have been introduced into the watershed, and non-native white suckers are also present. Rainbow trout hybridize with native cutthroat trout (Young 2008) and were stocked into Vacher Reservoir in the 1990 s. Cutthroat trout were also stocked into West Muddy Creek in 1950 and Populations are somewhat introgressed with non-native cutthroat trout and rainbow trout, except in some isolated headwater reaches. White suckers are found throughout the lower watershed and white sucker x flannelmouth hybrids were collected during recent fish surveys (Gill et al. 2007). The Big Muddy Creek watershed has moderate-high habitat integrity. The creek itself is largely in private ownership (Figure 6B), and there is a checkerboard ownership pattern between private landowners (71%) and the Bureau of Land Management in the lower watershed (21%). The State of Wyoming owns several sections throughout the watershed (5%), and the Forest Service owns a small portion of the headwaters (2%). No part of the watershed has a formal protected status. Connectivity is generally good, but a culvert at I-80 and a diversion structure 53

54 with an approximate 3 ft. drop, both in the lower watershed, appear to limit the upstream extent of flannelmouth suckers and roundtail chubs. There are also several private stock ponds on streams tributary to Big Muddy Creek that do not appear to affect native cutthroat trout or warmwater fishes. Watershed conditions are good as very little of the watershed has been converted for human use; only land along lower Big Muddy Creek as been converted to hay/pasture. Roads along streams in the lower watershed offer the only potential water quality problem, and stock ponds and canals that divert water affect streamflows along the mid-course of Big Muddy Creek. Big Muddy Creek has low-moderate security from future risks. Approximately 50% of the watershed is amenable to being converted for human use, and the proximity to Evanston increases the risk of land conversion. Approximately one half of the watershed has been leased for oil and gas development. Climate change is expected to have moderate to high impact on the watershed. East Muddy Creek has a high risk for uncharacteristic wildfire, whereas the rest of the Muddy Creek watershed has a moderate risk to wildfire. The entire watershed has a low risk to winter flooding under a changing climate, but the lower watershed has a moderate risk to warming temperatures that could be unsuitable for cutthroat trout. The presence of nonnative cold and warmwater fishes threatens the future security of both native cutthroat trout and warmwater fishes. Big Muddy Creek has several conservation opportunities. Providing fish passage in the lower watershed at the I-80 culvert and a diversion structure would likely allow roundtail chubs and flannelmouth suckers to extend their distribution further into the watershed. Protective measures that restrict oil and gas development would benefit native fish populations into the future. Ensuring ample streamside vegetation in the upper watershed would mitigate the potential impacts of climate warming on cutthroat trout populations. Henrys Fork The Henrys Fork of the Green River is a large watershed that flows directly into Flaming Gorge Reservoir along the Wyoming-Utah border. Most perennial tributaries originate on the north slope of the Uinta Mountains. Colorado River cutthroat trout occupy headwater streams at higher elevations. Bluehead suckers and flannelmouth suckers have recently been collected on the mainstem Henrys Fork and Burnt Fork (Figure 4B). 54

55 Figure 4B. The Henrys Fork watershed. Non-native cutthroat trout and non-native suckers occupy portions of the Henrys Fork watershed. Yellowstone cutthroat trout were stocked into the upper Henrys Fork and have introgressed with native Colorado River cutthroat trout. Brook trout are also in several tributary streams and are known to outcompete cutthroat trout (Peterson et al. 2004). White suckers have also been found to be hybridizing with native suckers in the lower portion of the Henrys Fork (Gill et al. 2007). Habitat integrity is moderately high to high throughout the watershed except in Birch Creek where it is moderately low. Much of the Henrys Fork heads in the Uinta Mountains (40%), although several tributaries arise in more arid lands (Figure 7B). The Bureau of Land Management owns the lower elevation shrublands (32%), and private lands encompass much of the perennial streams and mainstem Henrys Fork. The States of Wyoming and Utah own sections throughout the watershed (6%), while private landowners own tracts along the larger streams (22%). The headwaters of the Henrys Fork are largely protected as wilderness, whereas the lower watershed has no formal protection. Much of the watershed is interconnected, except for the upper Henrys Fork where there are several barriers and on Birch Creek where several canals intersect streams. Watershed conditions are good, except in Birch 55

56 Creek and Wildhorse Draw where some land has been converted to hay/pasture. Water quality is moderate in Birch Creek because of road along streams, but otherwise should be good throughout the Henrys Fork watershed. Streamflows in Burnt Fork, Louse Creek, and Birch Creek are moderately impacted by water diversions. The future security of the Henrys Fork watershed is moderate overall but slightly higher at higher elevations. There is low risk to future land conversion or resource extraction, but the northern portion of the watershed is at high risk to energy development and climate change; a warming climate poses a moderate risk of wildfires and drought. Conservation measures include protecting the watershed from energy development and climate change risk, as well as non-native fish management. Protection from oil and gas development would benefit native fishes from potential water quality impacts associated with well drilling and watershed disturbances associated with infrastructure. Restoring and maintaining healthy riparian vegetation and maintaining sufficient streamflows would reduce the impacts of climate warming and drought. The existing dam in the lower watershed could be managed as a fish barrier to prohibit recolonization of non-native fishes if the Henrys Fork is to be the focus of non-native fish removal efforts; however, the large size of the watershed require substantial resources to remove non-native fishes. Big Sandy River The Big Sandy River watershed is located north of Rock Springs, Wyoming and east of US 191. Big Sandy River heads in Wyoming s Wind River Range on the Bridger National Forest. Big Sandy River is historical habitat for Colorado River cutthroat trout that have since been extirpated (Figure 5B). Flannelmouth suckers and bluehead suckers occur in Big Sandy Creek, and roundtail chub historically occurred in Big Sandy Creek but were not documented in recent surveys (Gill et al. 2007). Several non-native fish species occur in the Big Sandy watershed. Brook trout, brown trout, and rainbow trout occur in the upper watershed, whereas white suckers, longnose suckers, and burbot are found in the lower watershed. White suckers and longnose suckers threaten the flannelmouth sucker and bluehead sucker with hybridization (Gill et al. 2007; Sweet 2007), although some spatial segregation is evident during the spawning season (Sweet and Hubert 2010). Burbot have been suspected to be predatory on native juvenile suckers and limit their recruitment to the adult population (Sweet 2007). 56

57 Figure 5B. The Big Sandy River and Little Sandy Creek watersheds. The habitat integrity of Big Sandy River watershed is moderately high to high, except for the Potson Reservoir subwatershed. The Forest Service owns the upper watershed (23% total) (Figure 5B). The Bureau of Land Management owns a majority (65%) of the watershed at lower elevations, except where the State of Wyoming owns several land parcels (6%) scattered throughout the watershed and along Big Sandy River where ownership is predominantly private (4%). The Bureau of Reclamation (2%) owns land around Big Sandy Reservoir, which is located just above the confluence with Little Sandy Creek. The only protected habitat is upstream in the Bridger Wilderness. Connectivity of the watershed is largely intact. Watershed conditions are good since little land has been converted for human use, but roads along streams are a factor potentially impacting water quality. Canals diverting water along the midcourse of Big Sandy River impact streamflows. The Big Sandy watershed is largely secure from future threats. The primary threat is from oil and gas development in the lower watershed; almost the entire lower one half of the watershed is leased. Non-native trout, suckers, and burbot pose additional threats to the future security of native suckers. There is a low threat of future land conversion. Projected 57

58 climate change poses only a moderate threat of uncharacteristic wildfires and no threat due to winter flooding or temperature warming. Only future drought poses a serious risk in the lower watershed under a changing climate. There are several conservation opportunities in the Big Sandy River. One is to remove nonnative suckers through mechanical or chemical removal. Mechanical removal is not 100% efficient, and would need to be done periodically over time. Chemical removal is more effective but would entail creating some type of fish-holding facility for native fishes during treatment. Another opportunity is to create a fish barrier above Big Sandy Reservoir to limit upstream movement of burbot and white suckers that reside in the reservoir. There is a large concrete water diversion structure near the midcourse of Big Sandy Creek that is a potential barrier to movement. While cutthroat trout are extirpated from the watershed, the presence of non-native trout is a potential problem for cutthroat trout restoration. Removal of nonnative trout is not likely to be feasible since the high elevation, remote headwater lakes in the Bridger Wilderness would need to be treated prior to cutthroat trout restoration. Meeks Lake, another high elevation lake, contains a population on non-native longnose sucker that likely seed downstream populations (Sweet 2007). In addition, private landowners stock trout into Big Sandy River, which would make native trout restoration, and even chemical treatment, difficult. Little Sandy Creek Little Sandy Creek is adjacent to Big Sandy River to the south, north of Rock Springs, Wyoming and west of US 191. Colorado River cutthroat trout were native to Little Sandy Creek but have since been extirpated (Figure 5B). Flannelmouth suckers and bluehead suckers are found in Little Sandy Creek above the Eden Diversion. Non-native trout and suckers are found in Little Sandy Creek. Brook trout and brown trout have been documented in the upper Little Sandy watershed, whereas rainbow trout have been collected in the lower watershed. White suckers have also been collected in lower Little Sandy Creek and threaten native suckers with hybridization (Gill et al. 2007). Habitat integrity is high in the headwaters of Little Sandy Creek but low-moderate downstream. Like Big Sandy River, the Forest Service owns the upper watershed (Bridger National Forest; 11%), and the Bureau of Land Management own most of the lower watershed (69%). Most of Little Sandy Creek is privately owned (12%), especially along its lower reaches, but the State of Wyoming also owns land sporadically along the creek and across the watershed (6%). The Bureau of Reclamation owns part of Little Sandy Creek watershed near Big Sandy Reservoir (3%). Part of the upper watershed is protected as Bridger Wilderness on the Bridger National Forest. Connectivity of the lower watershed is interrupted by water diversion structures and a small reservoir. Watershed conditions are good upstream but moderate below where land has been converted for hay/pasture. There are no threats to water quality in the watershed, but 58

59 water diversions alter streamflow patterns in downstream reaches and portions of Mitchell Slough received a non-functional PFC rating. The future security of Little Sandy Creek is moderately high in the upper watershed but moderately low in the lower watershed. There is low risk of land being converted for human use, but there is a high risk of oil and gas development because most of the lower watershed has been leased. There is a moderate risk throughout the watershed for uncharacteristic wildfires and high risk of drought under a climate change, and the lower watershed has a moderate risk for temperature warming should attempts be made to restore native cutthroat trout. Conservation opportunities in Little Sandy Creek center on non-native fish removal. Non-native white suckers and white sucker-native sucker hybrids comprise approximately 80% of all catostomids in Little Sandy Creek, despite high abundance of flannelmouth suckers. Although mechanical removal of non-native suckers is possible, it is not 100% efficient. Chemical treatment of Little Sandy Creek would require off-channel holding facilities for native fishes during treatment. Restoration of Mitchell Slough might also benefit native fishes downstream of its confluence with Little Sandy Creek. Ensuring sufficient streamflows would buffer native sucker populations from future droughts that are projected under a warming climate. Strawberry River The Strawberry River and its tributaries between Strawberry Reservoir and Starvation Reservoir contains populations of Colorado River cutthroat trout, flannelmouth sucker, and bluehead sucker (Figure 6B). Ownership 13% Tribal, 32% Forest Service, 19% State of Utah, 36% Private, and very little BLM land. The Strawberry River has non-native species that could impede native fish conservation. Brown trout are naturalized in the Strawberry River mainstem, and Colorado River cutthroat trout have introgressed with non-native rainbow trout, with Strawberry Reservoir being a premier rainbow and cutthroat trout and kokanee salmon fishery. Habitat integrity is moderate, with scores ranging from 14 to 20. Streamflows in the mainstem are regulated by flow releases from Strawberry Reservoir. Likewise, Current Creek reservoir alters streamflows and isolates cutthroat trout populations above the reservoir with those downstream. Lake Canyon and Red Creek have lands converted for agriculture and poor water quality, whereas the headwaters of Avintaquin Creek are in good condition. 59

60 Figure 6B. The Strawberry River watershed, and its tributaries, between Strawberry Reservoir and Starvation Reservoir. The future security of populations and habitat in the Strawberry River is moderately high. Most subwatersheds score low for presence of non-native species. Climate change is a high risk to some watersheds, particularly for uncharacteristic wildfires and drought under a warming climate. Tabby Swale in the Red Creek drainage also has high risk for future energy development. Native fish conservation efforts in the Strawberry River area include strategic non-native fish management, especially with regard to maintaining the genetic purity of conservation populations of cutthroat trout. There are also opportunities for improving water quality. Although oil and gas development has occurred in the watershed, there are opportunities for mitigation, as well as protecting areas that have been leased for development. Maintaining or restoring healthy stream systems will help to offset future climate change impacts from droughts and fires. 60

61 San Rafael River The San Rafael River is a tributary to the Green River that arises in the Wasatch Plateau region of Utah. It is approximately 90 miles in length, with its major tributaries being Ferron, Cottonwood, and Huntington creeks, flowing through the San Rafael Swell and San Rafael Gorge. Headwater streams have populations of Colorado River cutthroat trout, and flannelmouth sucker, bluehead sucker, and roundtail chub occur sporadically in the San Rafael mainstem to its confluence with the Green River. Several fishes listed as Endangered under the Endangered Species Act also use the lower San Rafael near its confluence with the Green River. Land ownership is 34% Forest Service, most of which is in the upper watershed, and 43% BLM, 10% State of Utah, and 13% private (Figures 7B, 8B). Figure 7B. The Upper San Rafael basin that includes Huntington Creek, Cottonwood Creek, and Ferron Creek. Like other rivers and streams in the Colorado River Basin, non-native fishes are found throughout the watershed. Red shiners, fathead minnows, black bullheads, and channel catfish have all been collected, as have non-native trouts in tributary streams. Popular sport fisheries exist, for example, in Huntington Creek that prohibit native fish conservation in some areas. 61

62 Habitat integrity ranges from poor to good in the upper San Rafael basin. Watershed conditions, connectivity, water quality, and flow regime have all been impacted where the headwater tributaries converge to form the San Rafael River. However, Miller Fork Canyon (Huntington Creek), Big Bear Creek (Ferron Creek), and the middle San Rafael mainstem have relatively intact habitat conditions aside from somewhat altered flow regimes. Figure 8B. The Lower San Rafael basin. Future security of habitats and native fish populations is relatively high in headwater tributaries. However, lower Huntington Creek has high risk for energy development, and much of the lower portions of Huntington Creek, Ferron Creek, and Cottonwood Creek have high risk for drought and stream temperature warming under climate warming scenarios. Non-native species pose a risk to future populations throughout the San Rafael watershed. Many opportunities exist for native fish conservation in the San Rafael watershed. Strategic barrier management is needed to reconnect fragmented native fish populations but also prohibit upstream invasion by non-native warmwater fishes. Non-native warmwater fishes have occupied the lower San Rafael for some time (McAda et al. 1980), and suppression of non- 62

63 native fishes could benefit natives in this area. Ensuring adequate streamflows and healthy riparian areas would help offset drought and stream temperature risks due to increasing global temperatures. Protecting existing habitats and populations for energy development is also a key strategy. Upper Escalante River The Escalante River forms at the confluence of North and Birch creeks near the town of Escalante. Headwater streams originate on the Aquarius Plateau, and the Escalante River flows through sandstone gorges, including Grand Staircase-Escalante National Monument, before entering Lake Powell. Land ownership in the watershed is BLM (33%), Forest Service (62%), with state and private lands comprising less than 5% each. The Upper Escalante watershed contains multiple populations of Colorado River cutthroat trout, and flannelmouth sucker, bluehead sucker, and roundtail chub have been collected around the town of Escalante, as well as some bluehead suckers further upstream in tributaries. Several lake populations of Colorado River cutthroat trout also occur in the watershed (Figure 9B). Habitat integrity is generally good throughout the watershed, aside from some local but specific threats. Water development infrastructure influences streamflows in a few places in the watershed. For example, Upper North Creek has several dams, as do the Boulder Creek headwaters. The mainstem Escalante River is also 303(d) listed due to temperature impairment and dewatering. Roads along riparian areas also influence habitat integrity in some parts of the watershed. Land conversion and resource extraction pose little risk to the future security of aquatic habitats and fish populations in the Escalante River headwaters. Rather, climate change, nonnative fishes, and energy development in that order pose the biggest future risks. Drought related to climate change poses the biggest risk, but there is also moderate risk due to uncharacteristic wildfire, water temperature warming, and winter flooding due to rain-on-snow events. Coal reserves pose a potential future energy risk in Birch Creek and North Creek watersheds. Non-native salmonids and warmwater fishes also pose competition, predation, and hybridization risks to native fishes. There are several opportunities for native fish conservation in the Escalante River headwaters. Cutthroat trout populations could be expanded and reconnected in Boulder and North creeks to increase their likelihood of persistence. Warmwater fishes in the mainstem would benefit from streamflow restoration that limited low flow periods and dewatering. Both of these would increase the resilience of native fishes in the face of future disturbances driven by land uses or climate change. 63

64 Figure 9B. Escalante River headwaters. 64