Introduction

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Charting the Tree of Life

Michael J. Donoghue

Joel Cracraft

Many, perhaps even most, people today are comfortable with

the image of a tree as a representation of how species are

related to one another. The Tree of Life has become, we think,

one of the central images associated with life and with science

in general, alongside the complementary metaphor of

the ecological Web of Life. But this was not always the case.

Before Darwin, the reigning view was perhaps that life was

organized like a ladder or “chain of being,” with slimy “primitive”

creatures at the bottom and people (what else!) at the

very top. Darwin (1859) solidified in our minds the radically

new image of a tree (fig. I.1), within which humans are but

one of many (as we now know, millions) of other species

situated at the tips of the branches. The tree, it turns out, is

the natural image to convey ancestry and the splitting of lineages

through time, and therefore is the natural framework

for “telling” the genealogical history of life on Earth.

Very soon after Darwin, interest in piecing together the

entire Tree of Life began to flourish. Ernest Haeckel’s (1866)

trees beautifully symbolize this very active period and also,

through their artistry, highlight the comparison between real

botanical trees and branching diagrams representing phylogenetic

relationships (fig. I.2).

However, during this period, and indeed until the 1930s,

rather little attention was paid to the logic of inferring how

species (or the major branches of the Tree of Life) are related

to one another. In part, the lack of a rigorous methodology

(especially compared with the newly developing fields of

genetics and experimental embryology) was responsible for

a noticeable lull in activity in this area during the first several

decades of the 1900s. But, beginning in the 1930s, with

such pioneers as the German botanist Walter Zimmermann

(1931), we begin to see the emergence of the basic concepts

that underlie current phylogenetic research. For example, the

central notion of “phylogenetic relationship” was clearly defined

in terms of recency of common ancestry—we say that

two species are more closely related to one another than either

is to a third species if and only if they share a more recent

common ancestor (fig. I.3).

This period in the development of phylogenetic theory

culminated in the foundational work of the German entomologist

Willi Hennig. Many of his central ideas were put

forward in German in the 1950s (Hennig 1950), but worldwide

attention was drawn to his work after the publication

of Phylogenetic Systematics in English (Hennig 1966). Hennig

emphasized, among many other things, the desirability of

recognizing only monophyletic groups (or clades—single

branches of the Tree of Life) in classification systems, and

the idea that shared derived characteristics (what he called

synapomorphies) provided critical evidence for the existence

of clades (fig. I.4).

Around this same time, in other circles, algorithms were

being developed to try to compute the relatedness of species.

Soon, a variety of computational methods were implemented

and were applied to real data sets. Invariably, given

the tools available in those early days, these were what would

now be viewed as extremely small problems.

1

2 Introduction

Figure I.1. The only illustration in Darwin’s Origin of Species (1859), which can be taken to be

the beginning of “tree thinking.”

Since that time major developments have occurred along

several lines. First, although morphological characters were

at first the sole source of evidence for phylogenetic analyses,

molecular data, especially DNA sequences, have become

available at an exponential rate. Today, many phylogenetic

analyses are carried out using molecular data alone. However,

morphological evidence is crucial in many cases, but

especially when the object is to include extinct species preserved

as fossils. Ultimately, of course, there are advantages

in analyzing all of the evidence deemed relevant to a particular

phylogenetic problem—morphological and molecular. And

many of our most robust conclusions about phylogeny, highlighted

in this volume, are based on a combination of data

from a variety of sources.

A second major development has been increasing computational

power, and the ease with which we can now manipulate

and analyze extremely large phylogenetic data sets. Initially,

such analyses were extremely cumbersome and time-consuming.

Today, we can deal effectively and simultaneously with

vast quantities of data from thousands of species.

Beginning in the 1990s these developments all came together—

the image and meaning of a tree, the underlying

conceptual and methodological developments, the ability to

assemble massive quantities of data, and the ability to quantitatively

evaluate alternative phylogenetic hypotheses using

a variety of optimality criteria. Not surprisingly, the number

of published phylogenetic analysis skyrocketed (Hillis, ch.

32 in this vol.). Although it is difficult to make an accurate

assessment, in recent years phylogenetic studies have been

published at a rate of nearly 15 a day.

Where has this monumental increase in activity really

gotten us in terms of understanding the Tree of Life? That

was the question that motivated the symposium that we organized

in 2002 at the American Museum of Natural History

in New York, and which yielded the book you have in

front of you. Although it may be apparent that there has been

a lot of activity, and that a lot can now be written about the

phylogeny of all the major lineages of life, it is difficult to

convey a sense of just how rapidly these findings have been

accumulating. Previously, there was a similar attempt to provide

a summary statement across all of life—a Nobel symposium

in Sweden in 1988, which culminated in a book titled

The Hierarchy of Life (Fernholm et al. 1989). That was an

exciting time, and the enthusiasm and potential of this enIntroduction

3

deavor were expressed in the chapters of that book. But, in

looking back at those pages we are struck by the paucity of

data and the minuscule size of the analyses that were being

performed at what was surely the cutting edge of research at

the time.

It is also clear that so much more of the Tree of Life is

being explored today than only a decade ago. Now we can

honestly present a picture of the relationships among all of

the major branches of the Tree of Life, and within at least

some of these major branches we are now able to provide

considerable detail. A decade ago the holes in our knowledge

were ridiculously obvious—we were really just getting started

on the project. There are giant holes today, which will become

increasingly obvious in the years to come (as we learn

more about species diversity, and database phylogenetic

knowledge), but we believe that it is now realistic to conceive

of reconstructing the entire Tree of Life—eventually to include

all of the living and extinct species. A decade ago, we

could hardly conjure up such a dream. Today we not only

can imagine what the results will look like, but we now believe

it is attainable.

It also has become increasingly obvious to us just how

important it is to understand the structure of the Tree of

Life in detail. With the availability of better and better estimates

of phylogeny, awareness has rapidly grown outside

of systematic biology that phylogenetic knowledge is essential

for understanding the history of character change

and for interpreting comparative data of all sorts within a

historical context. At the same time, phylogeny and the

algorithms used to build trees have taken on increasing

importance within applied biology, especially in managing

our natural resources and in improving our own health

and well-being. Phylogenetic trees now commonly appear

in journals that had not previously devoted much space

to trees or to “tree thinking,” and many new tools have

been developed to leverage this new information on

relationships.

Figure I.2. A phylogenetic tree realized by Haeckel (1866),

soon after Darwin’s Origin.

Figure I.3. Zimmermann’s (1931) tree, illustrating the concept

of “phylogenetic relationship.”

Figure I.4. The conceptual phylogenetic argumentation scheme

of Hennig (1966: 91), with solid boxes representing derived

(apomorphic) and open boxes representing primitive

(plesiomorphic) characters.

4 Introduction

In this volume we have tried, with the chapters in the

opening and closing sections, to highlight the value of the Tree

of Life, and then, in a series of chapters by leading experts, to

summarize the current state of affairs in many of its major

branches. In presenting this information, we appreciate that

many important groups are not covered in sufficient detail, and

a few not at all, and we know that in some areas information

will already be outdated. This is simply the nature of the

progress we are making—new clades are discovered literally

every day—and the sign of a healthy discipline. Nevertheless,

our sense is that a benchmark of our progress early in the 21st

century is a worthy exercise, especially if it can help motivate

the vision and mobilize the resources to carry out the megascience

project that the Tree of Life presents. This would surely

be one of the most fundamental of all scientific accomplishments,

with benefits that are abundantly evident already and

surprises whose impacts we can hardly imagine.

Acknowledgments

The rapidly expanding activity in phylogenetics noted above set

the stage for a consideration and critical evaluation of our

current understanding of the Tree of Life. This juncture in

time also coincided with the inception of the International

Biodiversity Observation Year (IBOY; available at http://

www.nrel.colostate.edu/projects/iboy) by the international

biodiversity science program DIVERSITAS (http://www.

diversitas-international.org) and its partners. Assembling the

Tree of Life (ATOL) was accepted as a key project of IBOY, and

a symposium and publication were planned. This volume is the

outgrowth of that process.

The ATOL symposium would not have been possible

without the participation of many institutions and individuals.

Key, of course, was the financial commitment received from the

host institutions, the American Museum of Natural History

(AMNH) and Yale University, and from the International Union

of Biological Sciences (IUBS), a lead partner of DIVERSITAS and

convenor of Systematics Agenda 2000 International. Assembling

the Tree of Life (ATOL) was accepted as a core project of the

DIVERSITAS program, International Biodiversity Observation

Year (IBOY). We especially acknowledge the leadership of Ellen

Futter (president) and Michael Novacek (senior vice president

and provost) of the AMNH and of Alison Richard (provost) of

Yale University for making the symposium possible. In addition,

a financial contribution from IUBS facilitated international

attendance, and we are grateful to Marvalee Wake (president),

Talal Younes (executive director), and Diana Wall (director,

IBOY) for their support.

The scientific program of the symposium was planned with

the critical input of Michael Novacek and many other colleagues,

and we are grateful for their suggestions. Ultimately, we

tried to cover as much of the Tree of Life as possible in three

days and at the same time to include plenary speakers whose

charge was to summarize the importance of phylogenetic

knowledge for science and society. We are well aware of the

omissions and imbalances that result from an effort such as this

one and which are manifest in this volume. Our ultimate goal

was to produce a single volume that would broadly cover the

Tree of Life and that would be useful to the systematics

community as well as accessible to a much wider audience. We

challenged the speakers to involve as many of their colleagues as

possible and to summarize what we know, and what we don’t

know, about the phylogeny of each group, and to write their

chapters for a scientifically literate general audience, but not at

the expense of scientific accuracy. We trust that their efforts will

catalyze future research and greatly enhance communication

about the Tree of Life.

The symposium itself could not have been undertaken

without the tireless effort of numerous people. The staff of the

AMNH and its outside symposium coordinator, DBK Events,

spent countless hours over many months facilitating arrangements

with the speakers and attendees, and not least, making

the organizers’ lives much easier. It is not possible to identify all

of those who contributed, but we would be remiss if we did not

mention the following: Senior Vice President Gary Zarr, and

especially Ann Walle, Anne Canty, Robin Lloyd, Amy Chiu, and

Rose Ann Fiorenzo of the AMNH Department of Communications;

Joanna Dales of Events and Conference Services; Mike

Benedetto of IT-Network Systems; Frank Rasor and Larry Van

Praag of the Audio-Visual Department; and Jennifer Kunin of

DBK Events.

Finally, many colleagues helped with production of this

volume. Many referees, both inside and outside of our institutions,

contributed their time to improve the chapters. Merle

Okada and Christine Blake, AMNH Department of Ornithology,

helped in many ways with editorial tasks, and Susan Donoghue

assisted with the index. Most important, we are grateful to Kirk

Jensen of Oxford University Press for believing in the project

and facilitating its publication, and to Peter Prescott for seeing it

through.

Literature Cited

Darwin, C. R. 1859. On the origin of species. John Murray,

London.

Fernholm, B., K. Bremer, and H. Jцrnvall (eds.). 1989. The

hierarchy of life. Nobel Symposium 70. Elsevier, Amsterdam.

Haeckel, E. 1866. Generelle Morphologie der Organismen:

allgemeine Grundzьge der organischen Formen-Wissenschaft,

mechanisch begrьndet durch die von Charles Darwin

reformirte Descendenz-Theorie. G. Reimer, Berlin.

Hennig, W. 1950. Grundzьge einer Theorie des phylogenetischen

Systematik. Deutscher Zentraverlag, Berlin.

Hennig, W. 1966. Phylogenetic systematics. University of

Illinois Press, Urbana.

Zimmermann, W. 1931. Arbeitsweise der botanischen

Phylogenetik und anderer Gruppierubgswissenschaften.

Pp. 941–1053 in Hanbuch der biologischen

Arbeitsmethoden (E. Abderhalden, ed.), Abt. 3, 2, Teil 9.

Urban & Schwarzenberg, Berlin.

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