ASSEMBLING THE TREE OF LIFE HARNESSING LIFE’S HISTORY TO BENEFIT SCIENCE AND SOCIETY This document is based on three National Science Foundation Tree of Life Workshops held in 1999 and 2000 at Yale University, the University of California Davis, and the University of Texas Austin. See http://research.amnh.org/biodiversity/center/features/tol.html for full reports of each workshop. Editorial Committee: Joel Cracraft, American Museum of Natural History Michael Donoghue, Yale University Jerry Dragoo, University of New Mexico David Hillis, University of Texas Terry Yates, University of New Mexico Participants: James Staley, Anne Frondorf, Meredith Blackwell, University of Washington U.S.Geological Survey Louisiana State University Naomi Ward, Gary Waggoner, Judy Blake, Louisiana State University U.S.Geological Survey The Jackson Laboratory Quentin Wheeler, Chris Henze, Rob DeSalle, Cornell University NASA Ames Research Labs American Museum of Natural History Ward Wheeler, Tamara Munzner, Jonathan Eisen, American Museum of Natural History Stanford University The Institute for Genomic Research Kevin P. White, Jeffrey Boore, Douglas Futuyma, Yale University DOE Joint Genome Institute University of Michigan Brad Shaffer, Stuart Brand, Jacques Gauthier, University of California Davis All Species Foundation Yale University Gavin Naylor, David C. Cannatella, Pablo Goloboff, Iowa State University University of Texas Austin University of Tucuman, Argentina Peter Cranston, John Huelsenbeck, Darlene Judd, University of California Davis University of Rochester Oregon State University Chuck Delwiche, Robert Jansen, Junhyong Kim, University of Maryland University of Texas Austin Yale University Tom Bruns, Kevin Kelly, University of California Berkeley All Species Foundation Meredith Lane, Academy of Natural Sciences Dirk Redecker, Leonard Krishtalka, University of California Berkeley University of Kansas Paul Lewis, University of Connecticut Roderick D. M. Page, Jim Reichman, University of Glasgow National Center for Ecological Diana Lipscomb, Analysis and Synthesis George Washington University David Maddison, University of Arizona Tim Rowe, Francois Lutzoni, University of Texas Austin The Field Museum Emilia Martins, University of Oregon Thomas Schmidt, Wayne Madisson, Michigan State University University of Arizona Bill Piel, University of Leiden Chris Simon, Brent Mishler, University of Connecticut University of California Berkeley Tim Lilburn, Michigan State University David Swofford, Maureen O’Leary, Florida State University State University of New York Stony Brook Michael Freeston, Kings College, Aberdeen Tandy Warnow, Jeffrey Palmer, University of Texas Austin Indiana University Jim Gannon, Parabon Computation Greg Wray, Kathleen Pryer, Duke University Duke University Susanne Chambers, Parabon Computation Anne Yoder, Michael Sanderson, Yale University University of California Davis Hasan Jamil, Mississippi State University Elizabeth Zimmer, Pam Soltis, Smithsonian Institution University of Florida Peter Karp, SRI International NSF Observers: Matt Kane, Mary McKitrick, James Rodman, Joann Roskoski, Terry Yates, and Grace Wyngaard. This document is an outgrowth of discussions and the reports of the three workshops, which were supported by a grant (DEB-0089975) from the National Science Foundation to the American Museum of Natural History. Any opinions, findings, conclusions, or recommendations expressed in this document are those of the participants, and do not necessarily represent the official view, opinions, or policy of the National Science Foundation. The Tree of Life depicts the evolutionary relationships of Earth’s taxonomic diversity — including all living and extinct forms — over the past 3.5 billion years of its existence. The hierarchical arrangement of this phylogeny provides a comparative and predictive framework for all fundamental and applied biology. Our understanding of the Tree of Life has advanced rapidly over the past decade fueled by enor- mous progress in the fields of genomics and information technology. Now, with new theoretical and technical innova- tions that cut across many areas of scientific research, systematic biologists are poised to develop a comprehensive understanding of life’s history that will advance all biology and provide enormous benefits to society. ne of the most profound ideas to emerge from to build our understanding of the relationships among them. modern science is the realization that all life, from At present, we know relatively little about the phylogenetic Othe smallest microorganism to the largest vertebrate, relationships of Earth’s species or even among many of the is connected through genetic relatedness on a vast evolutionary major branches of the Tree. Only 60 or 70 thousand species tree. This Tree of Life provides the framework for much of have been studied and even for these the data are far from our modern understanding of biology because it reveals the complete. The lack of a universal tree is severely hampering diversity of life as well as the historical basis for similarity progress in many areas of science and limiting the ability of and differences among organisms. Increased knowledge of society to address critical problems affecting human health phylogenetic relationships will improve human health, push and environmental management. the frontiers of comparative developmental biology, meet Nevertheless, we have reached a turning point. The conver- threats to agriculture and forestry from invasive species and gence of three important developments—conceptual and pests, and improve management of our natural resources. methodological advances in phylogenetic analysis, the rise of Perhaps most important, without substantial growth in our comparative genomics with its vast quantities of data, and rapid knowledge of the Tree of Life, it will become increasingly advances in information technology and processing—have now difficult and inefficient to manage, understand, and manipulate made possible the construction of a robust Tree of Life depicting biological information held in numerous databases worldwide, the genealogical relationships of all known species. including the burgeoning information from the genomic sciences. Although many scientific challenges still remain, they also Resolving the Tree of Life is unquestionably among the represent opportunities to advance integrative solutions across most complex scientific problems facing biology and presents numerous scientific disciplines. The size and complexity of challenges much greater than sequencing the human genome. this endeavor will require vision, sufficient human resources, The entire Tree of Life is almost unimaginably vast. Although and coordination and collaboration at an international level. 1.75 million species of organisms have been discovered and Yet, assembling an accurate universal tree depicting the described, it is estimated that tens of millions remain to be relationships of all life on Earth, from microbes to mammals, discovered. Placing these species on the Tree calls for increased holds enormous potential and value for society. It is imperative amounts of information about each, as well as new analytical tools that we begin now. The Tree of Life: Benefits to Society through Phylogenetic Research “Simple identification via phylogenetic Using phylogenetic analysis to discover classification of new life forms for biotechnology analyses with the sequences of previously organisms has, described organisms. This has led to major to date, yielded new discoveries. hylogenetic analysis is playing a major role in discovering more patent filings and identifying new life forms that could yield many new For several decades microbiologists than any other use Pbenefits for human health and biotechnology. Many have been searching for new bacteria in microorganisms, including bacteria and fungi, cannot be culti- extreme environments such as hotsprings of phylogeny in vated and studied directly in the laboratory, thus the principle or marine hydrothermal vents. The thermal industry.” road to discovery is to isolate their DNA from samples collected springs of Yellowstone National Park Bader et al. (2001) from marine or freshwater environments or from soils. The DNA have yielded a host of new and important samples are then sequenced and compared in phylogenetic bacterial species, many of which were identified using phyloge- netic analysis of DNA sequences. The most famous Desufurococcus mobilis bacterium from Yellowstone pJP 74 is Thermus aquaticus.An Sulfolobus aciducaldarius enzyme derived from pJP 7 this species —DNA Taq Pyrodictium occultum polymerase— powers a pJP 8 process called the poly- Pyrobaculum islandicum merase chain reaction Pyrobaculum aerophilum (PCR), which is used in Thermoproteus tenax pJP 6 thousands of laboratories Thermofilum pendens to make large amounts pJP 81 of DNA for sequencing. pJP 33 This discovery led to the Methanopyrus kandleri creation of a major new Thermococcus celer biotechnological industry Archaeoglobus fulgidus and has revolutionized pJP 9 medical diagnostics, foren- A phylogeny of some archaeobacteria. Newly discoverd life forms are in red. sics, and other biological sciences. Many microorganisms in extreme environments may yield innovative products for biotechnology. Thermophilic bacteria found in Yellowstone hot springs Fungi — an unknown world revealed by phylogenetic analysis Common fungi often have ungi are among the most ecologically important organisms. mycorrhizal associations