Columbia Headwaters Recovery Unit Implementation Plan for Bull Trout (Salvelinus Confluentus)

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Columbia Headwaters Recovery Unit Implementation Plan for Bull Trout (Salvelinus Confluentus) U.S. Fish & Wildlife Service Columbia Headwaters Recovery Unit Implementation Plan for Bull Trout (Salvelinus confluentus) Migratory bull trout, originating from Lake Koocanusa in the Kootenai River drainage, Montana. Photograph by Joel Sartore for National Geographic; photographed with Wade Fredenberg, USFWS, on Ram Creek, British Columbia, September 2011. Columbia Headwaters Recovery Unit Implementation Plan for Bull Trout (Salvelinus confluentus) September 2015 Prepared by U.S. Fish and Wildlife Service Montana Ecological Services Office Kalispell Suboffice Kalispell, Montana Northern Idaho Field Office and Eastern Washington Field Office Spokane, Washington Table of Contents Introduction .................................................................................................................................. D-1 Upper Clark Fork Geographic Region .......................................................................... D-2 Lower Clark Fork Geographic Region ......................................................................... D-2 Flathead Geographic Region ........................................................................................ D-2 Kootenai Geographic Region ....................................................................................... D-4 Coeur d’Alene Geographic Region .............................................................................. D-4 Life History Characteristics .......................................................................................... D-4 Current Status of Bull Trout in the Columbia Headwaters Recovery Unit .................................. D-5 Status Overview ............................................................................................................ D-5 Implementation Planning Process ................................................................................ D-7 Factors Affecting Bull Trout in the Columbia Headwaters Recovery Unit ................................. D-9 Habitat Threats............................................................................................................ D-26 Demographic Threats.................................................................................................. D-28 Nonnative Species Threats ......................................................................................... D-30 Climate Change Threat ............................................................................................... D-32 Ongoing Columbia Headwaters Recovery Unit Conservation Measures .................................. D-42 Research, Monitoring, and Evaluation ....................................................................................... D-46 Habitat Research and Monitoring Needs .................................................................... D-47 Demographic Research and Monitoring Needs .......................................................... D-47 Nonnative Fish Research and Monitoring Needs ....................................................... D-50 Recovery Measures Narrative .................................................................................................... D-53 Upper Clark Fork Geographic Region ........................................................................ D-55 Lower Clark Fork Geographic Region ....................................................................... D-75 Flathead Geographic Region ...................................................................................... D-94 Kootenai Geographic Region ................................................................................... D-106 Coeur d’Alene Geographic Region .......................................................................... D-113 Implementation Schedule ......................................................................................................... D-117 References ................................................................................................................................ D-153 Appendix I. Core Areas and Local Populations within the Columbia Headwaters Recovery Unit ................................................................................................................................. D-162 i Appendix II. Completed Recovery Tasks from 2002 Draft Recovery Plan ............................ D-168 Appendix III. Summary of the Comments on the Draft Recovery Unit Implementation Plan for the Columbia Headwaters Recovery Unit ............................................................... D-171 List of Figures Figure D-1. Map of the Columbia Headwaters Recovery Unit for Bull Trout. ....................... D-3 List of Tables Table D-1. Core Areas reviewed in Columbia Headwaters Recovery Unit implementation planning meetings................................................................................................ D-8 Table D-2. Primary threats by core area in the Columbia Headwaters Recovery Unit ....... D-10 Table D-3. Fifteen complex core areas of the Columbia Headwaters Recovery Unit (comparing stream system length, current bull trout occupancy, and suitable habitat modeled for 2040 and 2080).................................................................. D-37 Table D-4. Fifteen complex core areas of the Columbia Headwaters Recovery Unit (comparing overlap between currently occupied bull trout habitat and suitable habitat modeled for 2040 and 2080).................................................................. D-41 Table D-5. Columbia Headwaters Recovery Unit Implementation Schedule ................... D-121 ii Columbia Headwaters Recovery Unit Implementation Plan Introduction This recovery unit implementation plan (RUIP) describes the threats to bull trout and the site-specific management actions necessary for recovery of the species within the Columbia Headwaters Recovery Unit, including estimates of time required and cost. This document supports and complements the Recovery Plan for the Coterminous United States Population of Bull Trout (USFWS 2015a), which describes recovery criteria and a general range-wide recovery strategy for the species. Detailed discussion of species status and recovery actions within each of the six recovery units are provided in six RUIPs that have been developed in coordination with State, Federal, Tribal, and other conservation partners. This document incorporates our responses to public comment on the Draft Columbia Headwaters RUIP (USFWS 2015b) received during the comment period from June 4 to July 20, 2015 (Appendix III). The Columbia Headwaters Recovery Unit (CHRU) includes western Montana, northern Idaho, and the northeastern corner of Washington. Major drainages include the Clark Fork River basin and its Flathead River contribution, the Kootenai River basin, and the Coeur d’Alene Lake basin. In this implementation plan for the CHRU we have slightly reorganized the structure from the 2002 Draft Recovery Plan, based on latest available science and fish passage improvements that have rejoined previously fragmented habitats. We now identify 35 bull trout core areas (compared to 47 in 2002) for this recovery unit. Fifteen of the 35 are referred to as “complex” core areas as they represent large interconnected habitats, each containing multiple spawning streams considered to host separate and largely genetically identifiable local populations. The 15 complex core areas contain the majority of individual bull trout and the bulk of the designated critical habitat (USFWS 2010a, 2010b). However, somewhat unique to this recovery unit is the additional presence of 20 smaller core areas, each represented by a single local population. These “simple” core areas are found in remote glaciated headwater basins, often in Glacier National Park or federally-designated wilderness areas, but occasionally also in headwater valley bottoms. Many simple core areas are upstream of waterfalls or other natural barriers to fish migration. In these simple core areas bull trout have apparently persisted for thousands of years despite small populations and isolated existence. As such, simple core areas meet the criteria for core area designation and continue to be valued for their uniqueness, despite limitations of size and scope. Collectively, the 20 simple core areas contain less than 3 percent of the total bull trout core area habitat in the CHRU, but represent significant genetic and life history diversity (Meeuwig et al. 2010). Throughout this D-1 recovery unit implementation plan, we often separate our analyses to distinguish between complex and simple core areas, both in respect to threats as well as recovery actions. In order to effectively manage the RUIP structure in this large and diverse landscape, we have separated the core areas into the following five natural geographic assemblages (see Figure D-1), largely reminiscent of the 2002 recovery planning structure (USFWS 2002). Upper Clark Fork Geographic Region Starting at the Clark Fork River headwaters, the Upper Clark Fork Geographic Region comprises seven complex core areas, each of which occupies one or more major watersheds contributing to the Clark Fork basin (i.e., Upper Clark Fork River, Rock Creek, Blackfoot River, Clearwater River and Lakes, Bitterroot River, West Fork Bitterroot River, and Middle Clark Fork River core areas). Lower Clark Fork Geographic Region The seven headwater core areas flow into the Lower Clark Fork Geographic Region, which comprises two complex core areas, Lake Pend Oreille and Priest Lake. Because of the systematic
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