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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
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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
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The National Research Council was organized by the National Academy of
Sciences in 1916 to associate the broad community of science and technology with
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Academy of Sciences and the National Academy of Engineering in providing
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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