2006 Final Report - Genetic relationships among anadromous and resident Oncorhynchus mykiss in Cedar River, Washington: Implications for steelhead recovery planning

The goal of this research project was to understand genetic population structure of Cedar River resident and anadromous O. mykiss to assist with conservation and recovery strategies. Cedar River drains into Lake Washington, which is artificially connected to Puget Sound by a shipping channel and lockage system. Landsburg Dam at Cedar River mile 21 had blocked anadromous adults from 17.5 mainstem miles and associated tributary habitat from 1900 until September 2003 when a fish ladder became operational. Restoration of steelhead to the upper watershed was intended but steelhead abundance had been critically low during the last 14 years. In contrast, resident or non-anadromous O. mykiss were present throughout the river, and appeared abundant in below-dam areas. To evaluate genetic relationships between anadromous and resident populations, we sampled 180 resident phenotypic O. mykiss in below- and above-dam Cedar River areas, 24 phenotypic O. mykiss smolts from a lower Cedar River trap, and 57 putative Cedar River steelhead that had been captured at the shipping locks. We also sampled wild and hatchery steelhead in the adjacent and historically-connected Green River, lake-resident O. mykiss, and non-native hatchery rainbow trout stocks. We sampled adult and smolt O. clarki in Cedar and nearby rivers in order to identify O. mykiss/O. clarki genetic hybrids in samples. We collected data for 22 microsatellite DNA loci in all samples and used six nuclear DNA loci for additional species identification. We found that nearly all resident adult O. mykiss sampled in Cedar River below- and above-dam areas were native-origin and not introduced hatchery trout. Below- and above-Landsburg Dam resident O. mykiss samples were divergent from each other, but above-dam fish were genetically more similar to below-dam resident O. mykiss than to wild steelhead. This suggested that above-dam O. mykiss, which had a long isolation from steelhead, could get downstream successfully prior to the fish ladder. Below-dam resident O. mykiss as a group were divergent from steelhead, but individual genotypic analyses showed that many resident fish were most likely derived from native steelhead. Based on genetic assignment tests, some smolts had higher likelihoods of originating from resident O. mykiss than from anadromous O. mykiss. The percentage of smolts estimated to have resident fish ancestry varied depending on type of assignment test and populations included in baselines. Among all fish sampled in Cedar River, regardless of phenotype, we found about 14.5% O. mykiss/O. clarki genetic hybrids. We speculate that the resident life-history exhibited by some Cedar River O. mykiss may have become recently more common due to modified fish communities and freshwater habitats, coincidental to poor steelhead returns. Similar to other studies, our results suggested that non-anadromous O. mykiss may contribute to reducing extinction risk for steelhead. However, to improve the status of steelhead, resident phenotypes must produce smolts that have successful marine migrations.