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Frontiers in Polar Biology in the Genomic Era Committee on Frontiers in Polar Biology Polar Research Board NATIONAL RESEARCH COUNCIL OF THE NATIONAL ACADEMIES THE NATIONAL ACADEMIES PRESS Washington, D.C. www.nap.edu
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THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001 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 material is based upon work supported by the National Science Foundation under NSF Grant No. OPP-0132773, Master Agreement No. 9911018. Any opinions, findings, conclu- sions, or recommendations expressed in this publication are those of the authorts) and do not necessarily reflect the views of the National Science Foundation. International Standard Book Number 0-309-08727-9 (Book) International Standard Book Number 0-309-51229-8 (PDF) Library of Congress Catalog Card Number 2003093146 Cover design by Van Nguyen. Additional copies of this report are available from the National Academies Press, 500 Fifth Street, N.W., Lockbox 285, Washington, DC 20055; (800) 624-6242 or (202) 334-3313 (in the Washington metropolitan area); Internet, http://www.nap.edu Copyright 2003 by the National Academy of Sciences. All rights reserved. Printed in the United States of America.
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THE NATIONAL ACADEMIES Advisers to the Nation on Science, Engineering, and Medicine 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 govern- ment 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. Harvey V. Fineberg 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 govern- ment. 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 commu- nities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Bruce M. Alberts and Dr. Wm. A. Wulf are chair and vice chair, respectively, of the National Research Council. www. nationa l-academies.org
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COMMITTEE ON FRONTIERS IN POLAR BIOLOGY H. WILLIAM DETRICH III (Chair), Department of Biology, Northeastern University, Boston, Massachusetts JODY W. DEMING, School of Oceanography, University of Washington, Seattle CLAIRE FRASER, The Institute for Genomic Research, Rockville, Maryland JAMES T. HOLLIBAUGH, Department of Marine Sciences, University of Georgia, Athens WILLIAM W. MOHN, Department of Microbiology and Immunology, University of British Columbia, Vancouver JOHN C. PRISCU, Department of Land Resources and Environmental Sciences, Montana State University, Bozeman GEORGE N. SOMERO, Hopkins Marine Station, Stanford University, Pacific Grove, California MICHAEL F. THOMASHOW, Michigan State University, East Lansing DIANA H. WALL, Natural Resource Ecology Laboratory, Colorado State University, Fort Collins Staff Evonne Tang, Study Director Ann Carlisle, Administrative Associate Bryan Ericksen, PRB Intern (January 14, 2002 through May 3, 2002) v
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POLAR RESEARCH BOARD ROBIN BELL (Chair), Lamont-Doherty Earth Observatory, Palisades, New York MARY ALBERT, Cold Regions Research and Engineering Laboratory, Hanover, New Hampshire RICHARD B. ALLEY, Pennsylvania State University, University Park AKHIL DATTA-GUPTA, Texas A&M University, College Station GEORGE DENTON, University of Maine, Orono HENRY P. HUNTINGTON, Huntington Consulting, Eagle River, Alaska DAVID W. KARL, University of Hawaii, Honolulu MAHLON C. KENNICUTT, Texas A&M University, College Station (ax-officio) AMANDA LYNCH, University of Colorado, Boulder W. BERRY LYONS, Byrd Polar Research Laboratory, Columbus, Ohio ROBIE MACDONALD, Fisheries and Oceans Canada, Institute of Ocean Sciences, British Columbia MILES MCPHEE, McPhee Research Company, Naches, Washington CAROLE L. SEYFRIT, Old Dominion University, Norfolk, Virginia PATRICK WEBBER, Michigan State University, East Lansing (ax-officio) Staff Chris Elfring, Director Sheldon Drobot, Staff Officer Evonne Tang, Staff Officer (on loan from the Board on Life Sciences) Ann Carlisle, Administrative Associate Al
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Preface The polar biological sciences stand on the threshold of a revolution, because the availability of genome sciences and other new enabling tech- nologies has opened the door to study an incredible array of important questions and issues, both fundamental and practical. As this revolution occurs, we will enter a new era that holds the promise of a greatly enhanced understanding of polar ecosystems, their biodiversity, and the interactions of their constituent organisms and communities. Genome sciences is "the study of the structure, content, and evolution of genomes," including the "analysis of the expression and function of both gene and proteins." These approaches will help us to determine not only the organ- isms that are present in polar blames but also to look into their evolution to thrive in extreme cold, their interactions as biological systems, and their capacity to handle global change. Our knowledge of polar eco- systems will become not only global in scope but also more mechanistic in explanation. The Committee on Frontiers in Polar Biology was charged to examine the opportunities and challenges for conducting research on Arctic and Antarctic organisms and ecosystems using genomic technologies. This study was requested by the Office of Polar Programs and the Biology Directorate of the National Science Foundation. Encompassing both poles and essentially all biological disciplines, the task was both stimulating and difficult. I am deeply indebted to my colleagues on the committee, whose breadth of expertise, insights, and selfless efforts have driven this study idea to reality. On behalf of the committee, I also wish to extend my . . V11
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vIll PREFACE gratitude to the many biologists (see Appendix C) of all disciplines who participated in our workshop on Frontiers in Polar Biology (September 9-11, 2002~. Their ideas and thoughtful criticism contributed significantly to shaping the committee's thinking and to the generation of this report. This report opens with an Introduction (Chapter 1) to genomics, the paleogeological and paleoclimatic history of the polar regions, the unique features that shape biological and evolutionary processes in polar regions, and a summary of the applicability of genomic technologies to polar biology. Subsequently, we define the key questions in polar biology that are amenable to genomic approaches (Chapter 2~; identify critical species whose genomes, transcriptomes, proteomes, and metabolomes should be analyzed under the aegis of a Polar Genome Science Initiative (Chapter 3~; develop strategies to facilitate interactions and technology transfer within the polar biological community, between polar and nonpolar biologists, and through educational outreach to academic and lay audiences (Chap- ter 4~; and discuss other technologies, facilities, and infrastructure whose development would complement the genome initiative (Chapter 5~. The report concludes with the committee's findings and recommendations for implementation of these ideas (Chapter 6~. The report's recommendations, if implemented, will require increased funding by the National Science Foundation; and we recognize that this may not be an easy decision. Nevertheless, the committee presents an ambitious research agenda. We believe that we are ready to move for- ward: Prior genome projects have developed a strong infrastructure and considerable talent, and the costs for genome-related science are rapidly dropping. We believe that in the near future the commonly heard ques- tion "What is the justification for sequencing the genome of organism Genome species?" will shift to the imperative, "You must sequence the genome of your organisms (or metagenome of an environmental com- munity) so that you obtain a comprehensive understanding of your bio- logical system." The competitive peer review system of the National Science Foundation will ensure that the most rigorous and relevant genome projects are supported and that results of the highest quality are disseminated widely. This report would not exist but for the heroic efforts of the supporting staff of the Polar Research Board: Evonne Tang, Ann Carlisle, Bryan Erickson, and Chris Elfring. They ensured that the committee stayed focused "on goal" through their expertise, tireless support, and efficient marshaling of resources. I believe I speak for the committee when I say that their assistance guaranteed that our participation in this study was both successful and delightful. H. William Detrich III, Chair Committee on Frontiers in Polar Biology
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Acknowledgments This report is a product of the cooperation and contribution of many individuals. The committee would like to thank all the participants of the Frontiers in Polar Biology Workshop on September 9 and 10, 2002 (see Appendix C) and the following individuals for their input: Don K. Button, University of Alaska, Fairbanks Glenn F. Cola, Old Dominion University Kenneth Dunton, University of Texas at Austin Wade H. Jeffrey, University of West Florida John Lisle, U.S. Geological Survey Harlan Miller, University of Georgia Jill A. Peloquin, College of William and Mary Scott Rogers, Bowling Green State University Walker O. Smith, College of William and Mary Warwick F. Vincent, Universite Laval Patricia Yager, University of Georgia This report has been reviewed in draft form by persons chosen for their diverse perspectives and technical expertise, in accordance with pro- cedures approved by the National Research Council'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 pub- lished report as sound as possible and to ensure that the report meets institutional standards for objectivity, evidence, and responsiveness to IX
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x ACKNOWLEDGMENTS 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: Brian Barnes, University of Alaska, Fairbanks Andrew Cossins, The University of Liverpool, United Kingdom David M. Karl, University of Hawaii, Manoa Norman Huner, University of Western Ontario, Canada Robie Macdonald, Fisheries and Oceans Canada, British Columbia Adam G. Marsh, University of Delaware, Lewes Norman Pace, University of Colorado, Boulder Lyle G. Whyte, McGill University, Quebec, Canada Although the reviewers listed above have provided many construc- tive comments and suggestions, they were not asked to endorse the con- clusions or recommendations, nor did they see the final draft of the report before its release. The review of this report was overseen by Christopher R. Somerville, Director of the Department of Plant Biology, Carnegie Institute of Washington. Appointed by the National Research Council, he was 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 com- mittee and the institution.
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Contents SUMMARY 1 INTRODUCTION What Is Genomics? 15 Geologic and Climatic Trends That Influenced Evolution in the Polar Regions, 16 Physical Parameters That Shape Biological Processes, 21 Evolution in Polar Regions, 22 Examples of Research Areas That Could Be Addressed with Genomic Tools, 22 2 IMPORTANT QUESTIONS IN POLAR BIOLOGY Evolution and Biodiversity of Polar Organisms, 26 Polar Physiology and Biochemistry, 53 Polar Microbial Communities, 64 Human Impacts, 73 Summary, 80 3 THE POLAR GENOME SCIENCE INITIATIVE Selection of Organisms and Consortia for Genome Analysis, 82 Structure of a Polar Genome Project, 93 Creation of a Polar Genome Science Initiative, 102 1 15 25 82
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xI! 4 COMPLEMENTS TO GENOME SCIENCE: ENABLING TECHNOLOGIES, FACILITIES, AND INFRASTRUCTURE Enabling Technologies, 105 Facilities and Infrastructure, 109 CONTENTS 105 AN INTEGRATED POLAR BIOLOGY COMMUNITY: 119 INTERACTIONS AMONG SCIENTISTS, EDUCATION, AND OUTREACH Facilitating Interactions and Technology Transfer Across Scientific Disciplines, 119 Education and Outreach, 123 6 FINDINGS AND RECOMMENDATIONS A New Unifying Approach to Polar Biological Research, 128 Coordination Is Essential, 129 Virtual Genome Science Centers, 130 Enabling Technologies, 130 Increasing Awareness and Education, 130 Impediments to Integrated Polar Science, 131 REFERENCES APPENDIXES A Committee Member Biosketches B Workshop on Frontiers in Polar Biology Agenda C Workshop on Frontiers in Polar Biology Participants D Acronyms 128 133 157 161 163 164