32 The Tree of Life and the Grand Synthesis of Biology

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David M. Hillis

545

In the 1980s, there was rapid growth of the field of phylogenetics.

The developments were so extensive that at the

1988 Nobel symposium titled “The Hierarchy of Life”

(Fernholm et al. 1989), one participant wondered aloud if

young biologists could be attracted into the field given that

“all the big questions have been answered.” I doubted that

pronouncement; from my view, the field of phylogenetics

was still in its nascent stages. I thought most of the big and

interesting questions, as well as the major challenges,

awaited us in the future. Morris Goodman agreed, and he

described his vision for “a new age of exploration that promises

to bring to fruition Darwin’s dream of reconstructing

the true genealogical history of life” (Goodman 1989:43).

In many ways, that symposium did represent a turning

point for phylogenetics, and the symposium that represents

the subject of this book shows just how far we have come

since the 1980s. The advances in progress on the Tree of

Life have been greater in the 1990s than in all previous years

combined, and the prognosis for the future has never been

brighter.

A few comparisons between the 1988 Nobel symposium

and the present symposium, “Assembling the Tree of Life,”

demonstrate just how much progress we have made. The

description of PCR (polymerase chain reaction) had only

been published the year before the Nobel symposium (Mullis

and Faloona 1987), and DNA sequencing data were just

beginning to have a major impact on the field of phylogenetic

analysis. Statistical analysis of phylogenetic trees was

in its infancy in 1988, although several of the papers published

in the proceedings of that symposium discussed

emerging methods for assessing the strength of support for

inferred trees. Even though data sets in 1988 were rather

small by today’s standards, computational resources (both

software and hardware) were already limiting. Maximum likelihood

analyses were virtually unmentioned at the 1988 symposium,

and the computational constraints of such analyses

made their application to large problems impractical. Therefore,

systematists were severely limited by lack of data, weakly

developed statistical methodology, and computational constraints.

However, the stage was set for all of these bottlenecks

to be removed or reduced.

In figure 32.1, I show an analysis of papers in the Science

Citation Index for the past two decades (1982–2001). In 1982,

there were 186 papers in the Science Citation Index that had

the word “phylogeny” (or its derivative “phylogenetic”) in the

title, abstract, or key words. This means that it was possible to

read about one paper every other day, and still read virtually

all the literature on phylogenetics published worldwide. As I

said above, the growth of the field through the 1980s was

impressive: by the end of the decade, there had been more than

a doubling of papers on phylogeny (393 papers in 1990), and

in that year it would have been necessary to read more than a

paper a day to read all the papers in the field. However, the

real growth of the field of phylogenetics (at least in terms of

number of papers published, and therefore in the number of

phylogenetic trees presented) occurred throughout the 1990s.

546 Perspectives on the Tree of Life

In 2001, almost 5000 papers were published on phylogeny.

The total number of papers in the Science Citation Index, across

all fields of science, was 999,618 in 2001. That means that a

staggering 1 paper out of every 200 published in all fields of

science was on phylogeny! Today, when I pick up a journal in

almost any biological field, I expect to see some kind of phylogenetic

analysis in at least one of the articles. If one wanted

to attempt to read all the papers on phylogeny, that would

require reading about 100 papers a week.

Recent progress on the Tree of Life has not resulted just

because phylogenies are so much easier to infer now than

they were a decade or so ago. The importance of understanding

the relationships among the subjects of their studies finally

became widely accepted (by biologists, of all fields) in

the 1990s, as well. As phylogenies for many groups (as well

as genes) became widely available, the power of comparative

analyses became apparent in all areas of biology. Until

phylogenies were widely available, biologists were likely to

view objects of study in biology much as a chemist would

view atoms in a chemical equation. Every hydrogen atom (of

the same isotope) can be treated like all others. However,

virtually nothing in biology is like hydrogen atoms. Every

gene, every individual, every species, and every clade is more

closely related (and more similar) to some genes, individuals,

species, and clades than it is to others. This makes biology

difficult, but not impossible. However, it does mean that

every biologist must think at some level about phylogeny to

put his or her work in the context of the rest of biology.

As I watched the presentations in this symposium, I was

awed in two ways. First, the progress on reconstructing the

Tree of Life has been nothing short of phenomenal. Our annual

progress on understanding new relationships within

the Tree of Life is now much greater than all the accumulated

knowledge on relationships that we had in the late

1980s. The applications of the Tree of Life to problems as

diverse as forensics, origins of new diseases, ecology, behavior,

development, molecular evolution, and assessment

of global biodiversity is astonishing, and it is hard to keep

up with all the new developments. Second, and despite all

the recent progress, I was struck with the view that we are

on the brink of yet another turning point: as the Tree of

Life becomes more complete, its applications are also expanding

exponentially. A complete Tree of Life would allow

analyses that we would never contemplate today. Even

the goal of discovering all the species on Earth is much more

likely to be achieved if we have a complete Tree of Life for

all the known species. A complete Tree of Life would allow

us to catalog and organize all the species we know about,

greatly increasing the potential to automate the discovery

and description of the remaining unknown species. Fields

such as ecology could move from treating communities as

unknown “black boxes” to understanding their complexity

and differences, perhaps allowing ecology to emerge as

a truly predictive science. With phylogeny as a framework,

molecular biology could move from a largely descriptive

science to a field of explanation and prediction. The Tree

of Life would also allow us to organize, connect, and

synthesize all the information on all the species of Earth.

A grand, web-based “encyclopedia of life” would result,

and the field of biology would be immediately transformed.

After that point, any information that anyone collected

on any species would contribute to the understanding

of all of life. In short, the Tree of Life represents the

first (and most critical) step in the Grand Synthesis of

biology.

Will someone writing an overview of the 2022 Tree of

Life Symposium see the trend shown in figure 32.1 continue?

My guess is that the trend will continue for at least a

few years, but perhaps not decades, if the phylogenetic revolution

is to be truly successful. The term “phylogeny” is now

emphasized in papers that use phylogenetic methods in part

because the approach is still considered innovative in many

fields. However, in the future, if the Tree of Life initiative

is truly successful, people will not think to distinguish their

papers in this way. If all of biology is connected through a

Tree of Life, then studying biology in a phylogenetic context

should become almost transparent. People will include

phylogenetic analyses as a matter of ordinary operating procedure.

So, the best measure of the success of the phylogenetic

revolution will come when analyzing biological data

in a phylogenetic context merits as much of an emphasis

in a paper as using a computer to analyze data does today,

namely, something that virtually everyone does as a matter

of necessity. And as with computers, new students in biology

won’t even be able to imagine how we ever got along

without phylogenetic analysis.

Figure 32.1. Numbers of papers in the Science Citation Index that

include the words “phylogeny” or “phylogenetic” in the title,

abstract, or key words, published from 1982 through 2001.

1982 1991 2001

Year of Publication

No. Papers on Phylogeny in Science Citation Index

1000

2000

3000

4000

5000

6000

0

The Tree of Life and the Grand Synthesis of Biology 547

Literature Cited

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

hierarchy of life: molecules and morphology in phylogenetic

analysis. Excerpta Medica (Elsevier Science), Amsterdam.

Goodman, M. 1989. Emerging alliance of phylogenetic

systematics and molecular biology: a new age of exploration.

Pp. 43–61 in The hierarchy of life: molecules and

morphology in phylogenetic analysis (B. Fernholm, K.

Bremer, and H. Jцrnvall, eds.). Excerpta Medica (Elsevier

Science), Amsterdam.

Mullis, K. B., and F. A. Faloona. 1987. Specific synthesis of

DNA in vitro via a polymerase catalyzed chain reaction.

Methods Enzymol. 155:335–350.

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