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Factors that Influence Evolutionarily Significant Unit Boundaries and Status Assessment in a Highly Polymorphic Species, Oncorhynchus mykiss, in the Columbia Basin by Kathryn Kostow Oregon Department of Fish and Wildlife Information Report #2003-04 October 15, 2003 This document was prepared under an Interagency Personnel Agreement (IPA) between Oregon Department of Fish and Wildlife, Fish Division, Portland OR. and NOAA Fisheries, NW Fisheries Science Center, Seattle WA. Funding for this project was provided by NOAA Fisheries and Oregon Department of Fish and Wildlife Contents Page Executive Summary -------------------------------------------------------------------------- 4 Evolutionary Relationship between Trout and Steelhead -------------------------------- 4 Status of ESUs that Contain both Trout and Steelhead ----------------------------------- 5 Introduction -------------------------------------------------------------------------------------- 7 Scope and Intent of this Document ------------------------------------------------------------ 7 Constraints on Data Availability --------------------------------------------------------------- 8 Overview of Conditions that Influence Trout Distribution and Abundance in the Columbia Basin ------------------------------------------------------- 10 Evidence about the Evolutionary Relationship between Trout and Steelhead Populations --------------------------------------------------------------13 Introduction --------------------------------------------------------------------------------------- 13 Genetic Evidence --------------------------------------------------------------------------------- 13 Sympatric steelhead and trout -----------------------------------------------------------------15 Trout above artificial barriers within historic steelhead range ------------------------- 16 Trout above natural barriers ----------------------------------------------------------------- 17 Trout in the upper Willamette ---------------------------------------------------------------- 18 Otolith Data --------------------------------------------------------------------------------------- 18 Life History Data Pertinent to Interbreeding ---------------------------------------------- 19 Observations of Trout Spawning with Steelhead ------------------------------------------ 22 Evidence of Trout and Steelhead Producing the Alternate Life History ------------- 22 Major Barriers and Historic Distribution of Steelhead ---------------------------------- 28 Willamette ESU ---------------------------------------------------------------------------------34 Lower Columbia ESU ------------------------------------------------------------------------- 41 Mid-Columbia ESU --------------------------------------------------------------------------- 43 Snake ESU -------------------------------------------------------------------------------------- 45 Upper Columbia ESU -------------------------------------------------------------------------- 49 Implications of Hatchery Trout Stocking --------------------------------------------------- 51 Implications of clarki/mykiss Hybrid Zones ------------------------------------------------ 52 Conclusions ----------------------------------------------------------------------------------------52 Information about the Status of ESUs with both Trout and Steelhead ------------------------------------------------------------------------------- 54 Introduction --------------------------------------------------------------------------------------- 54 Current and Historic Distributions ---------------------------------------------------------- 54 Aspects of Trout and Steelhead Life Histories that Influence Productivity ----------55 Aspects of Trout Population Structure that Influence Status -------------------------- 57 2 Page Diversity in ESUs with both Trout and Steelhead ---------------------------------------- 59 Abundance of Trout and Steelhead by ESU ------------------------------------------------60 Willamette ESU -------------------------------------------------------------------------------- 61 Lower Columbia ESU ------------------------------------------------------------------------- 63 Mid-Columbia ESU --------------------------------------------------------------------------- 66 DESCHUTES BASIN ------------------------------------------------------------------------------- 66 JOHN DAY BASIN -------------------------------------------------------------------------- 72 UMATILLA BASIN -------------------------------------------------------------------------- 74 YAKIMA BASIN ------------------------------------------------------------------------------------ 76 OTHER BASINS ----------------------------------------------------------------------------------- 80 ESU-WIDE SUMMARY -------------------------------------------------------------------- 80 Snake ESU -------------------------------------------------------------------------------------- 81 STEELHEAD ABUNDANCE ----------------------------------------------------------------- 81 SALMON BASIN ---------------------------------------------------------------------------- 82 CLEARWATER BASIN ---------------------------------------------------------------------- 91 JOSEPH CREEK, GRANDE RONDE BASIN ---------------------------------------------------- 93 OTHER BASINS CURRENTLY OCCUPIED BY STEELHEAD --------------------------------- 95 BASINS ABOVE HELLS CANYON DAM -------------------------------------------------------- 95 ESU-WIDE SUMMARY------------------------------------------------------------------- 101 Upper Columbia ESU ----------------------------------------------------------------------- 101 STEELHEAD ABUNDANCE --------------------------------------------------------------- 102 BASINS CURRENTLY OCCUPIED BY STEELHEAD -------------------------------------- 103 BASINS ABOVE CHIEF JOSEPH/GRAND COULEE DAM --------------------------------105 Selected Risk Factors that Impact Native Trout ----------------------------------------- 105 Influence of exotic trout species on native trout ---------------------------------------- 105 Risks due to conspecific hatchery trout --------------------------------------------------- 107 Risks due to harvest -------------------------------------------------------------------------- 108 Risks due to habitat modifications --------------------------------------------------------- 109 Conclusions -------------------------------------------------------------------------------------- 110 References ------------------------------------------------------------------------------------- 112 Personal Communication --------------------------------------------------------------- 121 3 Executive Summary NOAA Fisheries Service (NMFS) listed steelhead, the anadromous life history of Oncorhynchus mykiss, as threatened or endangered under the Endangered Species Act (ESA) throughout most of the Columbia Basin in the late 1990s. In their original listing decisions, some O. mykiss trout populations, the non-anadromous life history of the species, were included in the Evolutionarily Significant Units (ESUs) along with steelhead, but were not listed. As a result of a recent court decision which found that the federal listing agencies cannot list only part of an ESU, NMFS is now reevaluating their original ESA listing decisions for O. mykiss. This paper reviews information about the relationship between trout and steelhead populations in the Columbia Basin and the relevance of this relationship to ESU determinations and the assessment of extinction risk of entire ESUs if they include both life histories. Evolutionary Relationship between Trout and Steelhead The definition of Evolutionarily Significant Unit (ESU) that has been adopted by NMFS provides the specific criteria of reproductive isolation and evolutionary significance for describing ESU boundaries (Waples 1991, 56 FR 58612). Whether or not trout and steelhead populations, which are the two adult life histories of O. mykiss, are in the same ESUs must be evaluated based on these criteria. The biological evidence about the evolutionary relationship between sympatric steelhead and trout in the Columbia Basin indicates that the life histories are not reproductively isolated to the extent that they would constitute separate ESUs. There is evidence for some interbreeding between the life histories within basins, although in most cases it is likely that sympatric trout and steelhead form demographically independent populations within ESUs, similar to those formed by summer and winter steelhead when they both occur in a basin. The evidence for lack of reproductive isolation between the life histories includes similarity at molecular genetic markers that demonstrate population and ESU structure elsewhere in O. mykiss, observations of trout and steelhead spawning on the same redds, and observations and studies that demonstrate both life histories successfully produce offspring that express the alternative life history. The information about the evolutionary relationship between steelhead below artificial barriers and the O. mykiss trout that remain within historic steelhead range above the barriers is weaker but still indicates that the native trout are generally related to the steelhead below the barriers. Populations in the two areas may now be in complete reproductive isolation from each other, although unidirectional gene flow, downstream over the barriers, may still occur. But it is probable that the original relationship between the trout and steelhead
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