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SCIENTIFIC EVALUATION OF BIOLOGICAL OPINIONS ON ENDANGERED AND THREATENED FISHES IN THE KLAMATH RIVER BASIN

INTERIM REPORT

Committee on Endangered and Threatened Fishes in the Klamath River Basin

Board on Environmental Studies and Toxicology

Division on Earth and Life Studies
National Research Council


NATIONAL ACADEMY PRESS
WASHINGTON, D.C.



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Page i SCIENTIFIC EVALUATION OF BIOLOGICAL OPINIONS ON ENDANGERED AND THREATENED FISHES IN THE KLAMATH RIVER BASIN INTERIM REPORT Committee on Endangered and Threatened Fishes in the Klamath River Basin Board on Environmental Studies and Toxicology Division on Earth and Life Studies National Research Council NATIONAL ACADEMY PRESS WASHINGTON, D.C.

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Page ii NATIONAL ACADEMY PRESS 2101 Constitution Ave., N.W. Washington, D.C. 20418 NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance. This project was supported by Grant No. 98210–1–G092 between the National Academy of Sciences and the U.S. Department of the Interior and the U.S. Department of Commerce. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the organizations or agencies that provided support for this project. International Standard Book Number: 0–309–08324–9 Additional copies of this report are available from: National Academy Press 2101 Constitution Ave., NW Box 285 Washington, DC 20055 800–624–6242 202–334–3313 (in the Washington metropolitan area) http://www.nap.edu Copyright 2002 by the National Academy of Sciences . All rights reserved. Printed in the United States of America

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Page iii THE NATIONAL ACADEMIES National Academy of Sciences National Academy of Engineering Institute of Medicine National Research Council The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Bruce M. Alberts is president of the National Academy of Sciences. The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Wm.A.Wulf is president of the National Academy of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Kenneth I.Shine is president of the Institute of Medicine. The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy's purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Bruce M.Alberts and Dr. Wm.A.Wulf are chairman and vice chairman, respectively, of the National Research Council.

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Page iv

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Page v COMMITTEE ON ENDANGERED AND THREATENED FISHES IN THE KLAMATH RIVER BASIN Members WILLIAM M. LEWIS, J R . (Chair), University of Colorado, Boulder RICHARD M. ADAMS, Oregon State University, Corvallis ELLIS B. COWLING, North Carolina State University, Raleigh EUGENE S. HELFMAN, University of Georgia, Athens CHARLES D.D. HOWARD, Consulting Engineer, Victoria, British Columbia, Canada ROBERT J. HUGGETT, Michigan State University, East Lansing NANCY E. LANGSTON, University of Wisconsin, Madison JEFFREY F. MOUNT, University of California, Davis PETER B. MOYLE, University of California, Davis TAMMY J. NEWCOMB, Virginia Polytechnic Institute and State University, Blacksburg MICHAEL L. PACE, Institute for Ecosystem Studies, Millbrook, New York J.B. RUHL, Florida State University, Tallahassee Staff SUZANNE VAN DRUNICK, Project Director RUTH E. CROSSGROVE, Editor JENNIFER SAUNDERS, Research Assistant MIRSADAK ARALIC-LONCAREVIC, Research Assistant HEATHER A. MCDONALD, Project Assistant KELLY CLARK, Editorial Assistant Sponsors NATIONAL MARINE FISHERIES SERVICE U.S. BUREAU OF RECLAMATION U.S. FISH AND WILDLIFE SERVICE

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Page vi

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Page vii BOARD ON ENVIRONMENTAL STUDIES AND TOXICOLOGY 1 Members GORDON ORIANS (Chair), University of Washington, Seattle JOHN DOULL (Vice Chair), University of Kansas Medical Center, Kansas City DAVID ALLEN, University of Texas, Austin INGRID C. BURKE, Colorado State University, Fort Collins THOMAS BURKE, Johns Hopkins University, Baltimore, Maryland WILLIAM L. CHAMEIDES, Georgia Institute of Technology, Atlanta CHRISTOPHER B. FIELD, Carnegie Institute of Washington, Stanford, California J. PAUL GlLMAN, Celera Genomics, Rockville, Maryland DANIEL S. GREENBAUM, Health Effects Institute, Cambridge, Massachusetts BRUCE D. HAMMOCK, University of California, Davis ROGENE HENDERSON, Lovelace Respiratory Research Institute, Albuquerque, New Mexico CAROL HENRY, American Chemistry Council, Arlington, Virginia ROBERT HUGGETT, Michigan State University, East Lansing JAMES H. JOHNSON, Howard University, Washington, District of Columbia JAMES F. KITCHELL, University of Wisconsin, Madison DANIEL KREWSKI, University of Ottawa, Ottawa, Ontario JAMES A. MACMAHON, Utah State University, Logan WlLLEM F. PASSCHIER, Health Council of the Netherlands, The Hague, Netherlands ANN POWERS, Pace University School of Law, White Plains, New York LOUISE M. RYAN, Harvard University, Boston, Massachusetts KIRK SMITH, University of California, Berkeley LISA SPEER, Natural Resources Defense Council, New York, New York Senior Staff JAMES J. REISA, Director DAVID J. POLICANSKY, Associate Director and Senior Program Director for Applied Ecology RAYMOND A. WASSEL, Senior Program Director for Environmental Sciences and Engineering KULBIR BAKSHI, Program Director for Committee on Toxicology ROBERTA M. WEDGE, Program Director for Risk Analysis K. JOHN HOLMES, Senior Staff Officer SUZANNE VAN DRUNICK, Senior Staff Officer RUTH E. CROSSGROVE, Managing Editor 1This study was planned, overseen, and supported by the Board on Environmental Studies and Toxicology.

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Page viii

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Page ix OTHER REPORTS OF THE BOARD ON ENVIRONMENTAL STUDIES AND TOXICOLOGY The Airliner Cabin Environment and Health of Passengers and Crew (2002) Arsenic in Drinking Water: 2001 Update (2001) Evaluating Vehicle Emissions Inspection and Maintenance Programs (2001) Compensating for Wetland Losses Under the Clean Water Act (2001) A Risk-Management Strategy for PCB-Contaminated Sediments (2001) Toxicological Effects of Methylmercury (2000) Strengthening Science at the U.S. Environmental Protection Agency: Research-Management and Peer-Review Practices (2000) Scientific Frontiers in Developmental Toxicology and Risk Assessment (2000) Modeling Mobile-Source Emissions (2000) Toxicological Risks of Selected Flame-Retardant Chemicals (2000) Copper in Drinking Water (2000) Ecological Indicators for the Nation (2000) Waste Incineration and Public Health (1999) Hormonally Active Agents in the Environment (1999) Research Priorities for Airborne Particulate Matter: I. Immediate Priorities and a Long-Range Research Portfolio (1998); II. Evaluating Research Progress and Updating the Portfolio (1999); III. Early Research Progress (2001) Ozone-Forming Potential of Reformulated Gasoline (1999) Risk-Based Waste Classification in California (1999) Arsenic in Drinking Water (1999) Brucellosis in the Greater Yellowstone Area (1998) The National Research Council's Committee on Toxicology: The First 50 Years (1997) Carcinogens and Anticarcinogens in the Human Diet (1996) Upstream: Salmon and Society in the Pacific Northwest (1996) Science and the Endangered Species Act (1995) Wetlands: Characteristics and Boundaries (1995) Biologic Markers (5 reports, 1989–1995) Review of EPA's Environmental Monitoring and Assessment Program (3 reports, 1994–1995) Science and Judgment in Risk Assessment (1994) Ranking Hazardous Waste Sites for Remedial Action (1994) Pesticides in the Diets of Infants and Children (1993) Setting Priorities for Land Conservation (1993) Protecting Visibility in National Parks and Wilderness Areas (1993) Dolphins and the Tuna Industry (1992) Science and the National Parks (1992) Assessment of the U.S. Outer Continental Shelf Environmental Studies Program, Volumes I-IV (1991–1993) Human Exposure Assessment for Airborne Pollutants (1991) Rethinking the Ozone Problem in Urban and Regional Air Pollution (1991) Decline of the Sea Turtles (1990) Copies of these reports may be ordered from the National Academy Press (800) 624–6242 or (202) 334–3313 www.nap.edu

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Page xi ACKNOWLEDGMENTS This project was supported by the U.S. Bureau of Reclamation, U.S. Fish and Wildlife Service, and National Marine Fisheries Service. We are thankful for the assistance provided by the Bureau of Indian Affairs in planning the first meeting. We are grateful for the informative briefings provided by the following individuals: Michael Belchik, Water Management and Rights Protection Division James Carpenter, Carpenter Design Inc. Paul Cleary, Oregon Department of Water Resources John Crawford, Tule Lake Irrigation District Larry Dunsmoor, The Klamath Tribes Natural Resources Thomas Hardy, Utah Water Research Laboratory Jacob Kann, Aquatic Ecosystems Sciences, LLC Ron Larson, Klamath Falls Fish and Wildlife Office Steven Lewis, Klamath Falls Fish and Wildlife Office Todd Olson, PacifiCorp Felice Pace, Klamath Forest Alliance Donald Reck, National Marine Fisheries Service Michael Ryan, U.S. Bureau of Reclamation Kenneth Rykbost, Oregon State University Klamath Experiment Station Rip Shively, U.S. Geological Survey, Klamath Field Station

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Page xii Glen Spain, Pacific Coast Federation of Fishermen's Associations Sue Ellen Wooldridge, U.S. Department of Interior The committee's work also benefited from the written and oral testimony submitted by the public, and we appreciate their participation.

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Page xiii ACKNOWLEDGMENT OF REVIEW PARTICIPANTS This report has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise, in accordance with procedures approved by the NRC's Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible and to ensure that the report meets institutional standards for objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We wish to thank the following individuals for their review of this report: Michael T.Brett, University of Washington Alex J.Horne, University of California, Berkeley John J.Magnuson, University of Wisconsin, Madison Douglas F.Markle, Oregon State University John M.Melack, University of California, Santa Barbara Lisa Speer, National Resources Defense Council Edwin A.Theriot, U.S. Army Corps of Engineers David A.Vogel, Natural Resource Scientists, Inc. Eugene B.Welch, University of Washington Donald Siegel, Syracuse University Margaret Strand, Oppenheimer, Wolff & Donnelly, LLP Although the reviewers listed above have provided many constructive comments and suggestions, they were not asked to endorse the conclusions or

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Page xiv recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by John C.Bailar, III, University of Chicago, and Paul G.Risser, Oregon State University. Appointed by the National Research Council, they were responsible for making certain that an independent examination of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this report rests entirely with the authoring committee and the institution.

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Page xv PREFACE The federal Endangered Species Act of 1973 has been invoked extensively for the protection of aquatic species in the western United States. Aquatic fauna of the West show extensive endemism because of genetic isolation associated with aridity and with the drainage of many rivers directly to the Pacific. Human intervention in the water cycle of the West is especially pervasive because of the general scarcity of water and the extensive redistribution of water in support of economic growth. Also, the West is growing and developing very rapidly. Thus, an unusual combination of biogeographic, hydrologic, and socioeconomic circumstances conspire to raise the likelihood that the legal protection of aquatic species will come into conflict with development and use of water in the West. Fishes in the Klamath River Basin are the focus of perhaps the most prominent current conflict between traditional uses of water in the West and requirements established by law for the protection of threatened and endangered species. This case is especially interesting in that the federal government is playing two potentially conflicting roles. Through the U.S. Bureau of Reclamation, the Department of the Interior is attempting to serve the needs of irrigators for water that is derived from the federal Klamath Basin Project. Not only is the delivery of water a contractual obligation of the government, it also is traditional in the sense that water delivery has occurred through the project for almost a century. At the same time, the U.S. Fish and Wildlife Service of the Department of the Interior and the National Marine Fisheries Service of the Department of Commerce are attempting to protect three threatened or endangered fishes of the Klamath Basin drainage (the Lost River

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Page xvi sucker, the shortnose sucker, and the Klamath Basin coho salmon). Interested parties, some of whom have livelihoods or cultural traditions at stake, include farmers, commercial fishing interests, Native Americans, environmental interests, hunters, and hydropower production interests. Conflicts became openly angry during 2001 when irrigators were deprived during a severe drought of traditionally available water through the government's issuance of jeopardy opinions on the endangered and threatened fishes. Economic losses were substantial and the changes in water management were a source of great frustration to irrigators. The Endangered Species Act (ESA) sets a framework for determination of future water use and management in the Klamath River Basin. The ESA is tightly focused on the requirements for survival of the threatened and endangered fishes, the survival of which is not negotiable under the ESA. Therefore, if the fishes require more water, ESA directs that they shall have it, which would imply that water managers and users must augment their water supplies, reduce their demands, or reach other accommodations consistent with the requirements of the species. While the ESA gives priority to the needs of threatened and endangered species, it also requires that any allocation of resources to these species be justified on a scientific or technical basis. The burden for scientific and technical justification falls mainly on the federal agencies, and especially the U.S. Fish and Wildlife Service and National Marine Fisheries Service, which are the source of biological opinions on the species. Assessment of the requirements of any species in a manner that is scientifically or technically rigorous is difficult and often cannot be accomplished quickly. The agencies have assembled considerable data and have interpreted the data as showing need for higher flows in the Klamath main stem and higher lake levels in the upper part of the basin. External review increases confidence in scientific and technical judgments, and is especially important when such judgments underlie important policy decisions. Accordingly, the Department of the Interior and Department of Commerce have arranged through its agencies for the National Research Council to form the Committee on Endangered and Threatened Fishes in the Klamath River Basin, whose charge is to conduct an external review of the scientific basis for the biological opinions that resulted in changes of water management for year 2001. The committee is to conduct its work in two phases. The first phase, which is reported here, gives an interim assessment of the evidence behind the biological opinions. A second phase, which will

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Page xvii occur over approximately the next year, will take a broader approach to evaluation of evidence for long-term requirements of the threatened and endangered fishes. In formulating its interim assessment, the committee has been greatly assisted by individuals who have provided it with information orally and in written form. The committee is especially indebted to the invited speakers and members of the public who attended the first meeting of the committee and also to NRC staff members Heather McDonald, Jennifer Saunders, David Policansky, and Suzanne van Drunick and to Leslie Northcott of the University of Colorado. All NRC committee reports are subject to external peer review as well as internal quality control processes. The committee and the NRC are grateful to the reviewers who contributed their time and expertise to the review process. The NRC committee is pleased to provide scientific and technical assessments that it hopes will be helpful to federal agencies as they attempt the difficult process of guiding water management toward practices that are consistent with the welfare of threatened and endangered species while also accommodating to the fullest practical extent other uses of water in the Klamath River Basin. William M.Lewis, Jr., Chair Committee on Endangered and Threatened Fishes in the Klamath River Basin

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Page xix CONTENTS Summary 1 1     Introduction 6 2     Evaluation of the Biological Opinion on Shortnose and Lost River Suckers 11 3     Evaluation of the Biological Opinion on Klamath Basin Coho Salmon 21 4     Conclusions 26 References 28 Appendix     : Statement of Task 32 Figure 1     Map of the Upper Klamath River Basin showing surface waters and landmarks mentioned in this report (modified from USFWS sources), 7

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Page xx CONTENTS Figure 2     Overview of monthly levels for Upper Klamath Lake proposed by USBR through its biological assessment of 2001, USFWS through its biological opinion of 2001, and observed conditions for the years 1960–1998. Hydrologic categories used by USBR in its proposals (dry years, critical dry years) are explained in the text. Mean depths, excluding wetlands, corresponding to water levels are as follows (feet): 4,137=3.5; 4,139=4.8; 4,140 =5.7; 4,141=6.6; 4,142=7.6 (Welch and Burke 2001, Figure 2–5), 14 Figure 3     Historical record of level at the end of September for UpperKlamath Lake (from USBR sources), 16 Figure 4     Relationship of chlorophyll a and median August lake level in Upper Klamath Lake between 1991 and 1998. Chlorophyll data are averages as reported by Welch and Burke (2001). Recruitment and mortality information is as reported by USFWS (2001), 18 Figure 5     Estimated age frequency distributions using opercles from Lost River suckers and shortnose suckers collected from 1997 fish kill in Upper Klamath Lake, Oregon. Estimates did not include all suckers collected, but were calculated using only suckers from which a length measurement (fork length) was obtained. Data are truncated from 1987 to 1994, additional information exists on other year classes of suckers. Source: USGS, unpublished data, 2001, 19 Figure 6     Three flow regimes for the Klamath River below Iron Gate Dam: USBR (USBR 2001b, minima for dry and critical years) proposed historical mean minima for dry and critical dry years, and RPA minimum flows from NMFS (2001). Hydrologic categories used by USBR in its proposals (dry years, critical dry years) are explained in the text, 24

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Page xxi INTERIM REPORT: SCIENTIFIC EVALUATION of BIOLOGICAL OPINIONS on ENDANGERED AND THREATENED FISHES in the KLAMATH RIVER BASIN

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