United States Department of Agriculture Biological Characteristics Forest Service Pacific Northwest and Population Status of Research Station General Technical Anadromous Salmon in Report PNW-GTR-468 January 2000 Southeast Alaska Karl C. Halupka, Mason D. Bryant, Mary F. Willson, and Fred H. Everest Authors KARLC. HALUPKAwas a postdoctoral research associate at the time this work was done; and MASON D. BRYANTand FRED H. EVEREST(retired) are research fish- eries biologists and MARYF. WILLSON was a research ecologist, Forestry Sciences Laboratory, 2770 Sherwood Lane, Juneau, AK 99801. Halupka currently is a fisheries biologist, National Marine Fisheries Service, Santa Rosa, CA, and Willson is the science director, Great Lakes Program, The Nature Conservancy, Chicago, IL. Cover art by: Detlef Buettner Abstract Halupka, Karl C.; Bryant, Mason D.; Willson, Mary F.; Everest, Fred H. 2000. Biological characteristics and population status of anadromous salmon in south- east Alaska. Gen. Tech. Rep. PNW-GTR-468. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station. 255 p. Populations of Pacific salmon (Oncorhynchus spp.) in southeast Alaska and adjacent areas of British Columbia and the Yukon Territory show great variation in biological characteristics. An introduction presents goals and methods common to the series of reviews of regional salmon diversity presented in the five subsequent chapters. Our primary goals were to (1) describe patterns of intraspecific variation and identify specific populations that were outliers from prevailing patterns, and (2) evaluate escapement trends and identify potential risk factors confronting salmon populations. We compiled stock-specific information primarily from management research con- ducted by the Alaska Department of Fish and Game. We used mainly exploratory and descriptive statistical procedures to examine patterns of intraspecific variation, and linear regression to evaluate escapement trends. We describe the most perva- sive limitations of available data and recommend cautious evaluation of our results. These reviews nonetheless provide insight into the ecological and evolutionary ramifications of intraspecific variation for managing diversity and sustaining productivity of salmon resources. Keywords: Pacific salmon, Oncorhynchus, southeast Alaska, intraspecific diversity, population status, variation. Contents 1 General Introduction 1 Purpose, Scope, and Objectives 3 Study Area 6 The Database 7 Methods 11 Acknowledgments 11 Literature Cited 15 Coho Salmon (Oncorhynchus kisutch) 15 Abstract 15 Introduction 20 Methods 25 Results 45 Discussion 52 Risk Factors 54 Conclusions 58 Acknowledgments 58 Literature Cited 67 Chinook Salmon (Oncorhynchus tshawytscha) 67 Abstract 68 Introduction 77 Methods 78 Results 91 Discussion 98 Risk Factors 100 Conclusions 104 Acknowledgments 104 References 113 Sockeye Salmon (Oncorhynchus nerka) 113 Abstract 113 Introduction 119 Methods 121 Results 139 Discussion 147 Risk Factors 149 Conclusions 153 Acknowledgments 153 References 165 Pink Salmon (Oncorhynchus gorbuscha) 165 Abstract 165 Introduction 175 Methods 178 Results 195 Discussion 200 Risk Factors 202 Conclusions 204 Acknowledgments 205 References 215 Chum Salmon (Oncorhynchus keta) 215 Abstract 215 Introduction 220 Methods 222 Results 236 Discussion 244 Risk Factors 247 Conclusions 249 Acknowledgments 249 References 255 English Equivalents General Introduction Purpose, Scope, Fisheries program managers of the Tongass National Forest (U.S. Department of and Objectives Agriculture, Forest Service) identified the need to summarize biological characteristics and determine population status of anadromous salmonids in southeast Alaska because of declines in stocks of anadromous salmonids in California, Oregon, Idaho, and Washington (Nehlsen and others 1991). The purpose of this paper is to identify distinct or sensitive stocks that may require special consideration during planning of land-management activities within the Tongass National Forest, and to determine population trends as stable, increasing, or declining. We reviewed stocks of coho (Oncorhynchus kisutch), chinook (O. tshawytscha), sockeye (O. nerka), pink (O. gorbuscha), and chum (O. keta) salmon in southeast Alaska. Steelhead are reported separately (Lohr and Bryant 1999). For each species, we established a context for evaluating potentially distinctive populations by beginning with a summary of the life history typical of populations in the region. Management and enhancement programs also were reviewed to assess the potential for these programs to either contribute to unusual levels of variation or pose a risk to wild stocks. Stock-specific data, collected primarily by the Alaska Department of Fish and Game (ADF&G) in their management research programs, were the basis of our analyses of biological characteristics and population trends. Results of these analy- ses are discussed in the context of managing salmon diversity and in regard to conceptual issues in ecology and evolutionary biology. The final component of each species report is an evaluation of natural and human-caused risk factors that may contribute to declines in salmon abundance. Stock-specific risk factors are evaluated for stocks with distinctive characteristics or declining populations. Background We defined a stock, following Ricker (1972) and Nehlsen and others (1991), as a population of fish that spawns in a particular tributary of a drainage, during a particu- lar time of year. This definition implies that gene flow among stocks is limited. Although low rates of gene flow often are assumed to be sufficient to homogenize allele frequencies among populations, gene flow does not preclude evolutionary divergence (Slatkin 1987). Biologically distinctive stocks are those that diverge from other stocks in the region in their expression of one or more phenotypic characteris- tics. Body length, migratory timing, and various demographic characteristics were the bases of our analysis of biological distinctiveness. We evaluated demographic characteristics of populations as indicators of distinctive features of most individuals in these populations. The traits we evaluated were limited to those considered to be 1 relevant to commercial fisheries management, because these are the only traits for which data are available for enough stocks in southeast Alaska to make a compara- tive analysis possible. These traits are only a small sample of characteristics important to salmonid diversity, and they are not necessarily the traits most likely to display local adaptation. Stocks that display distinctive phenotypic characteristics may be important to the evo- lutionary potential of their species, assuming that some component of the variance in those phenotypic traits is heritable. Moderate levels of additive genetic variance have been found in most life-history traits of salmonids analyzed (Hard 1995). Phenotypic plasticity in response to environmental variables is common in salmonids (reviewed in Ricker 1972), but the basis of plasticity may be heritable (Thorpe 1994, Thorpe and others 1983). Phenotypic variation also may facilitate and accelerate evolutionary processes (West-Eberhard 1989); therefore, populations exhibiting particular patterns of phenotypic plasticity may possess unique elements of genetic diversity. Analyzing phenotypic traits to identify components of intraspecific diversity provides a useful complement to genetic analysis (Utter and others 1993). Patterns detected by phenotypic analysis reflect different evolutionary processes that operate at different spatial and temporal scales compared to patterns detected by genetic analysis (Utter and others 1993). For example, electrophoresis can fail to distinguish populations having highly divergent life histories (e.g., Sacramento River winter-run chinook; Bartley and others 1992), and more sophisticated (and costly) techniques such as analysis of mitochondrial DNA polymorphism may correlate better with phenotypic divergence (Nielsen and others 1994). Lack of significant variation in allozyme frequencies measured electrophoretically should not be interpreted as signifying a lack of adaptive variation in phenotypic traits (Smoker and others 1993). We incorpo- rated genetic information (primarily from allozyme analysis) into our evaluation to define broad-scale ancestral lineages (Utter and others 1993) and to identify particu- lar stocks with unusual allele frequency combinations. For all species, though, a limited subset of stocks in the region have been sampled for genetic analysis, and the degree of overlap between stocks included in genetic surveys and stocks for which biological data are available differs considerably among species. Areas inhab- ited by stocks identified as distinctive, based on phenotypic characters, may be the most appropriate focus of future biochemical and genetic studies. We have attempted to describe the diversity of anadromous salmon at several levels. Specific populations with distinctive characteristics represent the finest level of resolu- tion for intraspecific diversity. At larger geographic scales, stocks can be grouped by shared characteristics such as patterns of allozyme frequencies and use of particular spawning habitats, migratory pathways, or timing windows. These factors used to group stocks can influence or reflect patterns of gene flow and natural selection and therefore are relevant to the evolutionary dynamics of these groups. The baseline