Management Plan for Conservation of Yellowstone Cutthroat Trout in Idaho Idaho Department of Fish and Game Boise, Idaho April 2007 TABLE OF CONTENTS Page EXECUTIVE SUMMARY .................................................................................................. 1 GOALS ............................................................................................................................. 3 OBJECTIVES ................................................................................................................... 3 SYSTEMATICS AND PREVIOUS STATUS ASSESSMENTS........................................... 4 GEOGRAPHIC MANAGEMENT UNITS ........................................................................ 5 Beaver/Camas/Medicine Lodge creeks ......................................................................... 8 Blackfoot River .............................................................................................................. 9 Henrys Fork Snake River............................................................................................... 17 Henrys Lake .................................................................................................................. 19 Palisades/Salt River ...................................................................................................... 20 Portneuf River ............................................................................................................... 22 Raft River ...................................................................................................................... 25 Rock/Bannock creeks .................................................................................................... 27 Snake River Proper ....................................................................................................... 29 South Fork Snake River................................................................................................. 31 Teton River.................................................................................................................... 34 Willow Creek ................................................................................................................. 37 POPULATION STATUS.................................................................................................... 39 YCT Abundance in Idaho............................................................................................... 40 YCT Trends in Idaho ..................................................................................................... 46 Teton River Trends........................................................................................................ 47 South Fork Snake River Trends..................................................................................... 51 Pre-Post Study Trends .................................................................................................. 54 YCT Genetics in Idaho................................................................................................... 58 YCT Hybridization ...................................................................................................... 58 YCT Diversity and Population Structure ..................................................................... 62 HABITAT........................................................................................................................... 67 HISTORY OF ENDANGERED SPECIES ACT ACTIONS ................................................. 67 THREATS......................................................................................................................... 68 Hybridization/Introgression ............................................................................................ 68 Impoundments............................................................................................................... 68 Water Diversions ........................................................................................................... 69 Culverts ......................................................................................................................... 70 Mineral Extraction.......................................................................................................... 70 Exploitation.................................................................................................................... 70 Competition and Predation ............................................................................................ 72 Whirling Disease............................................................................................................ 72 Grazing.......................................................................................................................... 73 Fish Stocking................................................................................................................. 73 Private Ponds................................................................................................................ 77 LONG-TERM ASSESSMENT ........................................................................................... 77 MANAGEMENT ACTIONS................................................................................................ 77 Fishing Regulations....................................................................................................... .... 77 i TABLE OF CONTENTS (Continued) Page Fish Stocking................................................................................................................. 78 Restoring Connectivity................................................................................................... 79 Management Priorities and Actions ............................................................................... 81 Beaver/Camas/Medicine Lodge creeks...................................................................... 82 Blackfoot River........................................................................................................... 83 Goose/Big Cottonwood/Dry creeks ............................................................................ 84 Henrys Fork Snake River ........................................................................................... 85 Henrys Lake............................................................................................................... 86 Palisades/Salt River ................................................................................................... 87 Portneuf River ............................................................................................................ 88 Raft River................................................................................................................... 88 Rock/Bannock creeks ................................................................................................ 89 Snake River Proper.................................................................................................... 90 South Fork Snake River ............................................................................................. 91 Teton River ................................................................................................................ 92 Willow Creek .............................................................................................................. 93 PROGRAM MEASURES .................................................................................................. 94 OUTREACH EFFORTS .................................................................................................... 94 CONCLUSION.................................................................................................................. 95 ACKNOWLEDGEMENTS ................................................................................................. 97 LITERATURE CITED........................................................................................................ 98 LIST OF FIGURES Figure 1. Location of YCT Geographic Management Units (GMUs) in Idaho ............ 6 Figure 2. Beaver/Camas/Medicine Lodge creeks GMU. Streams that are currently thought to contain or lack YCT are labeled. Dots indicate survey sites from the Native Salmonid Assessment project and depict what species were present at the site in proportion to their abundance. Any brown trout that were captured were not included in these plots........................... 8 Figure 3. Blackfoot River GMU. Streams that are currently thought to contain or lack YCT are labeled. Dots indicate survey sites from the Native Salmonid .... Assessment project and depict what species were present at the site in .. proportion to their abundance. Any brown trout that were captured were not included in these plots.......................................................................... 10 ii TABLE OF CONTENTS (Continued) Page Figure 4. Goose/Big Cottonwood/Dry creeks GMU. Streams that are currently thought to contain or lack YCT are labeled. Dots indicate survey sites from the Native Salmonid Assessment project and depict what species were present at the site in proportion to their abundance. Any brown trout that were captured were not included in these plots.......................................................................... 16 Figure 5. Henrys Fork Snake River and Henrys Lake GMUs. Streams that are currently thought to contain or lack YCT are labeled. Dots indicate survey sites from the Native Salmonid