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

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.

Participants:

Meredith Blackwell, Louisiana State University

Judy Blake, 

The Jackson Laboratory

Rob DeSalle, 

American Museum of Natural History

Jonathan Eisen, The Institute for Genomic Research

Douglas Futuyma, 

University of Michigan

Jacques Gauthier, 

Yale University

Pablo Goloboff, University of Tucuman, Argentina

Darlene Judd, 

Oregon State University

Junhyong Kim, 

Yale University

Meredith Lane, 

Academy of Natural Sciences

Paul Lewis, 

University of Connecticut

Diana Lipscomb, 

George Washington University

Francois Lutzoni, 

The Field Museum

Wayne Madisson, University of Arizona

Brent Mishler, 

University of California Berkeley

Maureen O’Leary, 

State University of New York Stony Brook

Jeffrey Palmer, 

Indiana University

Kathleen Pryer, 

Duke University

Michael Sanderson, University of California Davis

Pam Soltis, 

University of Florida

James Staley, 

University of Washington

Naomi Ward, 

Louisiana State University

Quentin Wheeler, Cornell University

Ward Wheeler, 

American Museum of Natural History

Kevin P. White, Yale University

Brad Shaffer, University of California Davis

Gavin Naylor, Iowa State University

Peter Cranston, 

University of California Davis

Chuck Delwiche, 

University of Maryland

Tom Bruns, 

University of California Berkeley

Dirk Redecker, 

University of California Berkeley

Roderick D. M. Page, University of Glasgow

David Maddison, 

University of Arizona

Emilia Martins, University of Oregon

Bill Piel, 

University of Leiden

Tim Lilburn, Michigan State University

Michael Freeston, Kings College, Aberdeen

Jim Gannon, 

Parabon Computation

Susanne Chambers, 

Parabon Computation

Hasan Jamil, 

Mississippi State University

Peter Karp, 

SRI International

Anne Frondorf, U.S.Geological Survey

Gary Waggoner, 

U.S.Geological Survey

Chris Henze, 

NASA Ames Research Labs

Tamara Munzner, Stanford University

Jeffrey Boore, 

DOE Joint Genome Institute

Stuart Brand, 

All Species Foundation

David C. Cannatella, 

University of Texas Austin

John Huelsenbeck, 

University of Rochester

Robert Jansen, 

University of Texas Austin

Kevin Kelly, 

All Species Foundation

Leonard Krishtalka, 

University of Kansas

Jim Reichman, 

National Center for Ecological 

Analysis and Synthesis

Tim Rowe, University of Texas Austin

Thomas Schmidt, 

Michigan State University

Chris Simon, University of Connecticut

David Swofford, 

Florida State University

Tandy Warnow, 

University of Texas Austin

Greg Wray, 

Duke University

Anne Yoder, 

Yale University

Elizabeth Zimmer, 

Smithsonian Institution
O

ne of the most profound ideas to emerge from 

modern science is the realization that all life, from 

the smallest microorganism to the largest vertebrate, 

is connected through genetic relatedness on a vast evolutionary

tree. This Tree of Life provides the framework for much of

our modern understanding of biology because it reveals the

diversity of life as well as the historical basis for similarity 

and differences among organisms. Increased knowledge of

phylogenetic relationships will improve human health, push 

the frontiers of comparative developmental biology, meet

threats to agriculture and forestry from invasive species and

pests, and improve management of our natural resources.

Perhaps most important, without substantial growth in our

knowledge of the Tree of Life, it will become increasingly 

difficult and inefficient to manage, understand, and manipulate

biological information held in numerous databases worldwide,

including the burgeoning information from the genomic sciences.

Resolving the Tree of Life is unquestionably among the

most complex scientific problems facing biology and presents

challenges much greater than sequencing the human genome. 

The entire Tree of Life is almost unimaginably vast. Although

1.75 million species of organisms have been discovered and

described, it is estimated that tens of millions remain to be 

discovered. Placing these species on the Tree calls for increased

amounts of information about each, as well as new analytical tools

to build our understanding of the relationships among them.

At present, we know relatively little about the phylogenetic

relationships of Earth’s species or even among many of the

major branches of the Tree. Only 60 or 70 thousand species

have been studied and even for these the data are far from 

complete. The lack of a universal tree is severely hampering

progress in many areas of science and limiting the ability of

society to address critical problems affecting human health 

and environmental management. 

Nevertheless, we have reached a turning point. The convergence of three important developments—conceptual and

methodological advances in phylogenetic analysis, the rise of

comparative genomics with its vast quantities of data, and rapid

advances in information technology and processing—have now

made possible the construction of a robust Tree of Life depicting

the genealogical relationships of all known species.

Although many scientific challenges still remain, they also

represent opportunities to advance integrative solutions across

numerous scientific disciplines. The size and complexity of

this endeavor will require vision, sufficient human resources,

and coordination and collaboration at an international level.

Yet, assembling an accurate universal tree depicting the

relationships of all life on Earth, from microbes to mammals,

holds enormous potential and value for society. It is imperative

that we begin now.

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 enormous progress in the fields of genomics and information technology. Now, with new theoretical and technical innovations 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.
The Tree of Life: Benefits to Society through

Phylogenetic Research

P

hylogenetic analysis is playing a major role in discovering

and identifying new life forms that could yield many new

benefits for human health and biotechnology. Many

microorganisms, including bacteria and fungi, cannot be cultivated and studied directly in the laboratory, thus the principle

road to discovery is to isolate their DNA from samples collected

from marine or freshwater environments or from soils. The DNA

samples are then sequenced and compared in phylogenetic

analyses with the sequences of previously

described organisms. This has led to major

new discoveries.

For several decades microbiologists

have been searching for new bacteria in

extreme environments such as hotsprings

or marine hydrothermal vents. The thermal

springs of Yellowstone National Park 

have yielded a host of new and important 

bacterial species, many of which were identified using phylogenetic analysis of DNA sequences. 

The most famous 

bacterium from Yellowstone

is Thermus aquaticus. An

enzyme derived from 

this species —DNA Taq 

polymerase — powers a

process called the polymerase chain reaction

(PCR), which is used in

thousands of laboratories

to make large amounts 

of DNA for sequencing.

This discovery led to the

creation of a major new

biotechnological industry

and has revolutionized

medical diagnostics, forensics, and other biological

sciences. Many microorganisms in extreme environments may

yield innovative products for biotechnology.

F

ungi are among the most ecologically important organisms.

By feeding on dead or decaying organic material, fungi help

recycle nutrients through ecosystems. Additionally, fungi are

important economically as foods and as biotechnological sources

for medicines, insecticides, herbicides, and many other products.

About 200,000 species of fungi are known, but there may 

be millions more to be discovered because most are extremely

small and found in poorly studied habitats such as soils.

Increasingly, phylogenetic analysis is being used to discover 

new microfungi through isolation and sequencing of DNA.

Biological studies on these new species hold great promise 

for developing novel natural products. 

2

Common fungi often have

mycorrhizal associations in

early stages of development,

and thus are important 

parts of Earth’s ecosystems.

Fungi — an unknown world revealed by

phylogenetic analysis

Using phylogenetic analysis to discover

new life forms for biotechnology

pJP 74

pJP 7

pJP 8

pJP 6

pJP 81

pJP 33

pJP 9

Thermophilic bacteria found in Yellowstone hot springs

A phylogeny of some archaeobacteria. 

Newly discoverd life forms are in red.

Desufurococcus mobilis

Sulfolobus aciducaldarius

Pyrodictium occultum

Pyrobaculum islandicum

Pyrobaculum aerophilum

Thermoproteus tenax

Thermofilum pendens

Methanopyrus kandleri

Thermococcus celer

Archaeoglobus fulgidus

“Simple identification 

via phylogenetic 

classification of 

organisms has,

to date, yielded 

more patent filings 

than any other use 

of phylogeny in 

industry.”

Bader et al. (2001)
K

nowledge of the phylogenetic relationships of the 

world’s crop plants and domestic animals is crucial 

for understanding their origins and for their continued

improvement. Over the past few years new discoveries have been

made on the relationships of the major cereal grains, especially

wheat, rice, and corn, as well as other crops such as tomatoes.

Nevertheless, the origins of many other important sources of

food and fiber upon which large segments of the human population

depend remain uncertain. Identifying the close relatives of these

organisms is crucial from the standpoint of potential genetic

improvements. The task is urgent because these wild relatives may

become extinct due to habitat loss before they can be studied.

Cultivated maize (or

corn, Zea mays mays) is 

of enormous economic

value, and its continued

improvement is of paramount

importance for sustaining the

human population. Theories on

the relationships of corn to

other grasses have varied widely,

owing to the highly unusual

structure of the familiar fruiting stalk or cob. Attention has

focused on several grasses from

Mexico and Guatemala known

as “teosintes,” although the

exact relationships among these

plants has remained unclear

until recently. Armed with new

molecular and computer techniques, scientists have identified

two teosinte lineages as the

closest relatives of cultivated

maize. This phylogenetic

knowledge has helped trace the

origin of cultivated maize to

9,000 years ago in the highlands of Mexico and to identify

the precise genetic changes

responsible for the highly modified corn cob and other unique

features of the modern cultivars.

Modern developmental biology plays a pivotal role in

understanding human health and the aging process.

Fundamental to this field of science is building

knowledge about how different sets of genes interact to produce

the distinct morphologies of the developing and adult organism.

This “genetic tool kit,” as these genes are called, has a deep 

evolutionary history, thus very similar developmental genes 

are found in organisms as diverse as sponges and humans. Over

time, these genes have increased in functional and developmental

complexity. This has led to increased structural diversity, including

that seen in humans and other complex animals.

The Tree of Life is essential for interpreting the origin and

subsequent modification of developmental genes called HOX

genes during the history of animals (above). These genes help

specify the development of the animal body plan and thus are

the subject of intense scientific study within fundamental and

applied biology. Early animals such as sponges (Silicea and

Calcarea) appear to lack a HOX gene complex. A small set 

of genes is present in the more advanced jellyfish and sea

anemones (Cnideria), but the HOX gene cluster becomes 

even more elaborated in bilaterally symmetrical organisms.

Developmental biologists could not fully understand these

genetic and developmental changes without the information

afforded by the Tree of Life, which provides a comparative

framework for deciphering the genomic milieu underlying 

developmental processes. As knowledge of relationships

improves, new insights into how genes and their functional

interactions have changed over time will be possible. This, 

in turn, will lead to greater knowledge about normal and 

abnormal development, which will contribute to improvements 

in human health.

3

The origins of cultivated maize

and crop improvement

Improving global agriculture through use

of the Tree of Life

Tracing developmental change using the

Tree of Life

Maize genetic diversity in the 

highlands of Mexico. Information 

provided by the Tree will support 

efforts to sustain our agriculture 

through genetic improvements.

Phylogenetic relationships among

domesticated

maize (corn;right)

and its wild relatives (teosintes; above) showing

the very different fruiting stalks.

Knowledge of relationships helped

understand the morphological and

genetic changes that produced the

cultivated corn cob.

Zea perennis

Zea diploperennis

Zea mays mexicana

Zea mays parviglumis

Zea mays mays 

domesticated corn

teosintes
A

ustralia has more poisonous snakes than any other 

continent, and many people die from snakebites each 

year. Developing effective antivenins is thus a high 

priority, but little is known about the venins of most species.

Phylogenetic analysis is helping with this task because venin 

properties correlate strongly with evolutionary relationships.

Although the red-bellied black snake looks very different from 

the king brown, it is actually closely related and can be treated 

with the same antivenin. Conversely, the western brown looks 

very similar to the king brown, but it is only distantly related 

and thus responds best to different antivenin. The phylogeny is 

also predictive: the recent demonstration that the poorly-known

bardick is closely related to the death adder (orange lineage) 

predicts that the former is also highly dangerous and might

respond to widely-available death adder antivenin.

I

nvasive species are a worldwide problem. The United

States spends about $137 billion annually to control

or mitigate the effects of exotic species, thus identifying potential invasives in ecosystems is of crucial 

economic and ecological importance. Phylogenetic

analysis is an important tool in this effort.

An exotic alga was recently found at several 

locations along the California coast and scientists

used phylogenetic analysis of DNA sequences 

to identify the alga as Caulerpa taxifolia. Although

the alga is thought to be native to Australia

where it is a natural part of the ecosystem, the

California alga proved to be closely related to a 

highly invasive strain that has caused extensive 

ecological damage in the Mediterranean. 

This discovery pointed to the need for an

immediate eradication program before damage to

the coastal ecosystem of California could take place. 

Using phylogenetic knowledge to discover

snakebite antivenins

Using phylogenetic analysis to protect

ecosystems from invasive species

Black whip snake

Talpan

Fierce snake

Common brown

Western brown

Dugte 

Collatt’s snake

Spotted black

Butler’s snake

King brown

Red-bellied black

Death adder

Barclick

Small-eyed snake

Australian copperhead

Tiger snake

Rough-scaled snake

Broad-headed snake

Recommended Antivenene

Taipan

Brownsnake

Blacksnake

Death adder

Tiger snake

Western brown King brown Red-bellied black

4

Coulerpa taxifolia
T

he use of phylogenetic analysis has

become a powerful tool within the

health sciences for understanding the

history of disease transmission. 

One of the earliest applications of phylogenetic methods to disease transmission

and medical forensics investigated whether a

Florida dentist infected with the HIV virus

had transmitted the disease to his patients

following invasive dental procedures. Once it

was suspected the dentist might be the source

of infection for several HIV-positive patients,

other patients were tested. The sequences of

viral envelope genes of those testing positive,

along with the genes of local controls (HIVpositive nonpatients of the dentist), were

determined and a phylogenetic analysis was

performed on all the sequences (left). The

gene sequence of the dentist clustered with

those from his patients, thus supporting the

original hypothesis. At the same time, the

tree also showed that other patients (F and D

on the tree) as well as the local controls had

not contracted HIV from the dentist.

Understanding how organisms, as well as their genes and gene products, are related to one another has become a

powerful tool for identifying disease organisms, tracing the history of infections, and predicting disease outbreaks.

5

The Tree of Life and Human Health

Identifying Emerging Diseases: West Nile Virus

Disease Transmission and Medical Forensics

When an encephalitis-like viral infection emerged in 

people living in the New York region in 1999, it was

first suspected to be the St. Louis encephalitis virus.

Transmitted by mosquitos, the virus was simultaneously found

to be associated with a high mortality in wild and domesticated

birds. It has currently spread as far west as California and has

resulted in numerous human deaths.

In two separate studies, health workers used phylogenetic

analysis to identify viral isolates from mosquitos and birds as 

a new outbreak of the West Nile virus rather than St. Louis

encephalitis. The viral tree (right) demonstrated that the New

York isolate was most closely related to one found in dead birds in

Israel, East Africa, and eastern Europe. This knowledge provided

health officials with key information about the basic biology 

of the virus that was needed for diagnosis and predicting its

spread. Such knowledge was critical in preventing human and 

animal infection. 

Isolation of the West Nile virus

from flamingos and other captive

and wild birds in the New York

area was one of the first indications of a new emergent disease. 

Several species of mosquitos, including the

recently invasive tiger mosquito, transmit

West Nile virus from bird and mammal

hosts to human populations. Understanding

the phylogenetic relationships of disease

vectors such as mosquitos is important in

tracing the origin and spread of diseases.

Romania 1996

Israel 1952

South Africa

Egypt 1951

Senegal 1979

Italy 1998

Romania 1996

Kenya 1998

New York 1999

Israel 1998

Central African

Republic 1967

Ivory Coast 1981

Kunjin 1966-91

India 1955-80

Patient G

Patient C

Patient E

Patient B

Patient A

Dentist

Local Control 3

Local Control 2

Patient F

Local Control 9

Local Control 35

Patient D
6

I

n the spring of 1993, a previously undescribed disease

emerged in the American Southwest, killing 10 people during

a 10-week period from

April to June. For the first

few weeks, the mortality rate

was 70%. There was no cure,

no successful medications or

treatment, and the disease agent

(virus, bacterium, or toxin)

was completely unknown. It

was soon discovered, however,

that the disease-causing agent

was an unknown hantavirus,

later named Sin Nombre

virus, and that its reservoir

was the common deer mouse.

Analyses of published

phylogenies for hantaviruses

reveal that the new virus was

related to Old World strains

but differed in many ways,

suggesting it was not likely

to have been introduced

recently from the Old World.

When phylogenetic trees 

of the viral genes were compared with those of rodents related to deer mice, a high degree

of concordance in the pattern of branching was discovered,

suggesting a long co-evolutionary history in the Americas

(right). This finding, moreover, led to the prediction that most,

if not all, major mice lineages would be found to have a closely

associated hantavirus. 

Since the discovery of Sin Nombre virus, some 25 

additional hantaviruses have been described from the 

New World alone, totally

consistent with the prediction of the tree. Fourteen

of these newly recognized

hantaviruses have been

detected in countries

throughout Central and

South America, and many

of these viruses are pathogenic for humans. The

phylogeny predicts that yet

unknown hantaviruses are

likely present in other

rodent hosts in North and

South America and elsewhere in the world, especially in poorly studied

regions of Africa and Asia. 

The documentation of

a co-evolutionary relationship between hantaviruses 

and their rodent hosts has

triggered similar investigations of other emerging

pathogens, including those that cause African and South

American hemorrhagic fevers. These studies, in turn, are leading

to the discovery of many new species of both viruses and 

their hosts, which increases our ability to diagnose and treat

these diseases.

Rattus norvegicus (Brown Rat)

Microtus pennsylvanicus (Meadow Vole)

Peromyscus maniculatus (Deer Mouse)

Peromyscus maniculatus (Deer Mouse)

Peromyscus leucopus (Whte-footed Mouse)

Peromyscus leucopus (Whte-footed Mouse)

Peromyscus leucopus (Whte-footed Mouse)

Reithrodontomys megalotis (Western Harvest Mouse)

Reithrodontomys mexicanus (Mexican Harvest Mouse)

Sigmodon hispidus (Hispid Cotton Rat)

Sigmodon hispidus (Hispid Cotton Rat)

Sigmodon alstoni (Alston’s Cotton Rat)

Oryzomys palustris (Marsh Rice Rat)

Oligoryzomys flavescens (Yellow Pygmy Rice Rat)

Oligoryzomys chacoensis (Chacoan Pygmy Rice Rat)

Oligoryzomys longicaudatus (Long-tailed Pygmy Rice Rat)

Oligoryzomys longicaudatus (Long-tailed Pygmy Rice Rat)

Oligoryzomys microtis (Small-eared Pygmy Rice Rat)

Calomys laucha (Small Vesper Mouse)

Akodan azarae (Azara’s Grass Mouse)

Bolomys obscurus (Dark Bolo Mouse)

Mammalian Host Species Distribution of 

Host Species and

Hantavirus Strain

phylogeny of rodent host species

phylogeny of hantavirus species

Korea

United States

United States, 

Mexico,

Central America

United States

Venezuela

United States

Argentina

Argentina, Chile

Peru, Bolivia

Paraguay

Argentina

Tree of Life research is being

used to discover new species

of both viruses and their

hosts, which increases our

ability to predict, diagnose

and treat new diseases.

Predicting Disease Outbreaks: Hantavirus
A

phylogenetic tree for a group of species is derived from 

a comparison of their characteristics. This hierarchical 

pattern of similarity (for example, vertebrates share

characters not found in other animals, mammals share similarities

absent in other vertebrates, and primates share features lacking

in other mammals) provides a powerful comparative framework

for interpreting, manipulating, and predicting biological information about organisms. 

A key promise of phyloinformatics is that it can provide the

tools to exploit this hierarchy of relationships for data mining.

Phyloinformatic data mining will use the hierarchy implied by

trees to conduct node-based searches across many kinds of

databases (figure below). A search using node 2, for example,

would simultaneously retrieve information from databases for

groups A, B, and C, and would combine and synthesize those

data in ways not currently possible. Tree-oriented navigation 

and data mining having this power and sophistication make use

of the predictive capabilities of phylogenetic trees to integrate 

biological information in new ways, and thus create new associations and new knowledge.

Phyloinformatics: A Comparative Framework for

Exploring Biological Databases

Phyloinformatics

K

nowledge of the Tree of Life has advanced considerably

over the past 10 years, and accompanying this has been a 

near-exponential growth in the amount of data (genetic

and otherwise) that have been used to build our current picture

of life’s history. For society and science to reap the benefits of

the powerful predictive capabilities of the Tree of Life, new

technologies and analytical techniques will have to be developed

to cope with our growing information about trees and their

associated data. The emerging discipline being created to meet

these new challenges is called phyloinformatics.

The systematics community’s vision of phyloinformatics is

expansive, encompassing the development of new informatics tools

to archive, synthesize, and retrieve the data used to build trees, and

also of novel approaches for visualizing and searching trees and the

information associated with them. Scientific innovations that will

emerge from phyloinformatics will spawn a host of benefits to

educational institutions, to students, and the public at large.

7

Groups of

Organisms

Nodes/hierarchy

Specimens/Collections

Geo-referenced data

Associated biological data

Associated literature, etc.

Node-based Search and Data Mining

Genetic/Genomic Geological

Geographic

Ecological

Human health Agricultural

Developmental Land use

Economic/trade

ABCD

1

2

3

Phyloinformatics: 

A Vision for Comparative Biology

Databases

S

pecimen collections housed in museums, herbaria, and seed

banks comprise a permanent, verifiable record of Earth’s

biological diversity. Information about species — including

genomic, anatomical, ecological, and other data — increases in 

reliability when it is linked to properly identified voucher specimens

in collections. Thus, capturing the information associated with

specimens in natural history collections is of crucial importance

for building the Tree of Life.

Natural history collections are essential

for Tree of Life research

Phyloinformatics and Predictivity
B

uilding a Tree of Life for Earth’s species, living and

extinct, is a megascience initiative that already has 

produced numerous benefits for science and society.

Meeting the challenges of constructing this Tree will create

unprecedented opportunities to foster interdisciplinary research

across fields as diverse as genomics, computer science and 

engineering, informatics, mathematics, Earth sciences, developmental biology, and environmental biology. 

The scientific problem of building the Tree of Life is 

enormous because life itself is so diverse and complex.

Collecting the necessary genomic, anatomical, and behavioral

data on all species with which to determine the Tree will

require a significant commitment of human resources and 

technological innovation. Yet, the challenges can be met. Already,

for example, the genomics database, GenBank, has information

on nearly 100,000 species, and this database is growing exponentially, and will keep doing so as new sequencing technologies

are developed. Having genomic information on all of Earth’s

species is no longer a dream. Nongenomic data — anatomical,

behavioral, biochemical, or physiological — have also been 

collected on many thousands of species, but if a comprehensive

understanding of life’s complexity over time is to be

developed, those data will have to be greatly

expanded, databased, and then integrated

with genomic information.

The burgeoning information

used to construct the Tree of

Life will have numerous

applications within industry, agriculture, the

health sciences, and in

environmental management — but only if

that information is

organized and available.

Science now has the ability to create huge databases, but much

of this information is not organized and integrated in such a

way as to create new knowledge. This must change if the full

benefits of Tree of Life research are to be achieved. 

The organizational and comparative power of phylogenetic

relationships is creating the new field of phyloinformatics,

which will harness phylogenetic knowledge to integrate and

transform data held in isolated databases, thereby inventing

new information and new knowledge. Realizing the broad

vision of phyloinformatics will require innovative approaches

to data mining, as well as to the visualization and interpretation of its results. The complex computational problems associated with constructing trees and manipulating different kinds

of data are attracting the attention of computer scientists who

are creating new algorithms for building trees and comparing

data. The computational advances underlying phyloinformatics

will contribute solutions to similar problems in other disciplines and will generate applications far beyond the field of

phylogenetic research.

Assembling the Tree of Life is as grand and important a

mission as scientists have ever tackled. Much like the mission

to place a man on the moon, or to decipher the

human genome, constructing a comprehensive

Tree of Life will promote intellectual

achievement across the sciences.

Considering the significant benefits that have already flowed

from current knowledge

about life’s history,

expanding the effort to

build a comprehensive

Tree of Life over the

next several decades is

vitally important, and

it can be accomplished.

8

Challenges and Research Needs
Credits

Front Cover:

Earth from space: NASA; deep space shot: NASA; big phylogenetic tree: courtesy 

of David Hillis; spider: American Museum of Natural History Library (AMNH);

beetle: AMNH; fish: AMNH; corn: Hugh Iltis; water lily: Joel Cracraft; jellyfish:

Joel Cracraft; archaeobacteria: Norman Pace; fungi: Joel Cracraft; parrots: Joel

Cracraft; forest antelope: Joel Cracraft; frog: Joel Cracraft; mosquito: courtesy of

Barry J. Beaty; alga: courtesy of Alexandre Meinesz

Inside Front Cover:

Tree of Life from the 19th century: E. Haeckel. 1866. 

Allgemeine Entwickelungsgeschichte der Organismen. Berlin: Georg Reimer.

Page 1:

Tree courstesy of David Hillis

Page 2:

Archaeobacterial tree: modified from Barnes, S. M., C. F. Delwiche, J. D. Palmer, 

and N. R. Pace. 1996. Perspectives in archael diversity, thermophily and monophyly

from environmental rRNA sequences. Proc. Natl. Acad. Sci. 93:9188-9193.;

Yellowstone thermophilic bacteria: Norman R. Pace; Yellowstone thermal pool: 

Joel Cracrat; fungus: Joel Cracraft

Page 3:

Corn tree: courtesy of John Doebley; teosinte and maize fruiting stalks/cobs: 

John Doebley; maize diversity: Hugh Iltis, courtesy of John Doebley. HOX gene

phylogeny: modified from Peterson, K. J. and E. H. Davidson. 2000. Regulatory 

evolution and the origin of bilaterians. Proc. Natl. Acad. Sci 97:4430-4433; 

courtesy of Kevin Peterson 

Page 4:

Elapid snake phylogeny based on ongoing work by Scott Keogh, John Scanlon, 

and Michael Lee. Keogh, J. S., R. Shine, and S. Donnellan. 1998. Phylogenetic 

relationships of terrestrial Australo-Papuan elapid snakes (subfamily Hydrophiinae)

based on cytochrome b and 16S rRNA sequences. Mol. Phylogen. and Evol.,

10:67-81. Keogh, J. S., I. A. W. Scott, and J. D. Scanlon. 2000. Molecular 

phylogeny of viviparous Australian elapid snakes: affinities of Echiopsis atriceps

(Storr, 1980) and Drysdalia coronata (Schlegel, 1837), with description of a new

genus. Journal of Zoology 252:317-326; and Lee, M. S. Y. 1997. Phylogenetic

relationships among Australian elapid snakes: The soft anatomical data reconsidered.

Herpetological Journal 7:93-102. Antivenin data based on Mirtschin, P. and R.

Davies. 2000. Dangerous snakes of Australia. Sydney: Ure Smith Press. 

Snake photographs: Mark Hutchinson; Invasive alga Caulerpa taxifolia: Alexandre

Meinesz, information provided by Rachel Woodfield; California coast: Joel Cracraft

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West Nile Virus tree: modified from Lanciotti et al. 1999. Origin of the West Nile

Virus responsible for an outbreak of encephalitis in the northeastern United States.

Science 286:2333-2337; flamingo: Joel Cracraft; mosquitos: courtesy of Barry J.

Beaty; HIV tree: modified from Ou et al. 1992. Molecular epidemiology of HIV

transmission in a dental practice. Science, 256:1165-1171

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Rodent/virus coevolution tree: modified from Smith, M. F. and J. L. Patton. 1999.

Phylogenetic relationships and the radiation of Sigmodontine Rodents in South

America: evidence from cytochrome b. Journal of Mammalian Evol., 6(2):89-128,

and Plyusnim, A. and S. P. Morzunov. 2001. Virus evolution and genetic diversity of

hantaviruses and their rodent hosts. Pages 47-75 In Hantaviruses (C. S. Schmaljohn

and S. T. Nichol. eds.). Springer, New York. Deer Mouse photograph: Richard Forbes,

courtesy of Jerry Dragoo and Terry Yates.

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Data mining/phyloinformatic tree: Cracraft, J. 2002. The seven great questions of

systematic biology: an essential foundation for conservation and the sustainable use

of biodiversity. Annals of the Missouri Bot. Garden, 89:127-144. Bird collection:

courtesy of George Steinmetz (www.GeorgeSteinmetz.com)

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Museum supercomputer: AMNH