Final Report By Jim S. Gregory Caselle L. Wood Lost River Fish Ecology, INC. Trout Unlimited 5306 Zollinger Rd. 151 North Ridge Suite 151 Mackay, ID 83251 Idaho Falls, Idaho 83402 for Bureau of Reclamation 1150 North Curtis Road, Suite 100 Boise, ID 83706-1234 February 2013 Table of Contents Introduction .................................................................................................................................................. 4 Basic Overview of Fish Habitat Conditions ................................................................................................... 6 Pond Series................................................................................................................................................ 8 Water Quality ............................................................................................................................................ 9 Age Naming Conventions ............................................................................................................................ 10 Chinook ....................................................................................................................................................... 11 Genetics .................................................................................................................................................. 11 Adult Migration and Timing .................................................................................................................... 11 Redd Numbers ........................................................................................................................................ 12 Redd Locations ........................................................................................................................................ 14 Available Spawning Habitat .................................................................................................................... 17 Hatching .................................................................................................................................................. 18 Summer Habitat ...................................................................................................................................... 18 Distribution, Density, and Population ..................................................................................................... 20 Supplementation .................................................................................................................................... 24 Summer Movement of Juveniles ............................................................................................................ 25 Out-migration vs. Retention of Juveniles................................................................................................ 26 Size and Condition .................................................................................................................................. 30 Winter Habitat ........................................................................................................................................ 30 Out-migration of Smolts ......................................................................................................................... 31 Survival to Emigration and to Lower Granite Dam ................................................................................. 31 Time in the Ocean ................................................................................................................................... 32 Return Rate and Productivity .................................................................................................................. 33 Harvest .................................................................................................................................................... 34 Possible Limiting Factors ......................................................................................................................... 34 Data Gaps ................................................................................................................................................ 37 Steelhead .................................................................................................................................................... 38 Adult Migration and Timing .................................................................................................................... 38 Redd Locations ........................................................................................................................................ 38 Hatching .................................................................................................................................................. 39 February 2013 Yankee Fork Drainage Fisheries Summary And Analysis 2 Distribution, Density, and Population ..................................................................................................... 39 Supplementation .................................................................................................................................... 43 Winter Habitat ........................................................................................................................................ 44 Out-migration ......................................................................................................................................... 45 Return Rate and Productivity .................................................................................................................. 45 Possible limiting factors .......................................................................................................................... 45 Data Gaps ................................................................................................................................................ 46 Bull Trout ..................................................................................................................................................... 47 Cutthroat Trout ........................................................................................................................................... 48 Whitefish ..................................................................................................................................................... 49 Other Native Fish ........................................................................................................................................ 50 Non-Native Fish ........................................................................................................................................... 50 References .................................................................................................................................................. 51 February 2013 Yankee Fork Drainage Fisheries Summary And Analysis 3 Introduction Recently, there has been renewed interest from multiple agencies in recovering anadromous fish populations through habitat improvement in the Yankee Fork watershed. The first step in this process was the completion of the Yankee Fork Tributary Assessment which evaluated tributary-scale features and processes in order to identify geomorphic reaches with potential for habitat improvement (BOR 2012). This document, the Yankee Fork Drainage Fisheries Summary and Analysis, is intended as a supplement to the Yankee Fork Tributary Assessment with the objective of describing the life histories of fish species in the Yankee Fork drainage using both recent and historical data. Additionally, where possible, we have attempted to identify life stages of anadromous fishes that may be underperforming in the Yankee Fork in comparison to fish from adjacent basins. Such determinations will help us identify life stages that may benefit from habitat improvement. The Yankee Fork of the Salmon River (Yankee Fork) is a large tributary to the upper main-stem Salmon River, located in central Idaho. The Yankee Fork watershed drains an area of approximately 122,000 acres (USFS 2006; BOR 2012). Several native fish species are present in the drainage including spring/summer Chinook salmon (Oncorhynchus tshawytscha), summer steelhead (O. mykiss), and mountain whitefish (Prosopium williamsoni), which primarily inhabit the main-stem Yankee Fork and major tributaries, westslope cutthroat trout (O. clarkii lewisi), which occupy the smaller tributaries, and bull trout (Salvelinus confluentus), and sculpin (Cottus spp.), which are found throughout the drainage (Gamett and Bartel 2008; Figure 1). No non-native salmonids were collected by USFS fisheries crews during 2006 and 2007 sampling (Gamett and Bartel 2008). Several of these native species’ populations have declined throughout or in portions of their range (BOR 2012) and multiple agencies are interested in restoring habitat in those areas. Snake River Chinook salmon, Snake River steelhead, and bull trout are listed as threatened under the Endangered Species Act (ESA) and westslope cutthroat trout are designated as a sensitive species within the Intermountain Region by the US Forest Service (USFS). Information related to the trends of resident and fluvial fish populations within the Yankee Fork is somewhat limited in comparison to anadromous fish. Anadromous fish (Chinook and steelhead) populations have declined significantly from historic levels of abundance (Reiser and Ramey 1987). These declines are