1 The Importance of the Tree of Life to Society

Back

The affinities of all the beings of the same class have

sometimes been represented by a great tree. . . . As buds give

rise by growth to fresh buds, and these, if vigorous, branch

out and overtop on all sides many a feebler branch, so by

generation I believe it has been with the great Tree of Life,

which fills with its dead and broken branches the crust of the

earth, and covers the surface with its ever branching and

beautiful ramifications.

—Charles Darwin, On the Origin of Species (1859)

Terry L. Yates

Jorge Salazar-Bravo

Jerry W. Dragoo

Despite Darwin’s vision of the existence of a universal Tree

of Life, assembly of the tree with a high degree of accuracy

has proven challenging to say the least. Generations of systematists

have worked on the problem and debated (or

fought) about how to best approach a solution, or questioned

if a solution was even possible. Much of the rest of the biological

sciences and medicine either simply accepted decisions

of systematists without question or discounted them

entirely as lacking rigor and accuracy. Attempts at solving

the problem met with only limited success and were generally

limited to similarity comparisons of various kinds until

the convergence of three important developments: (1) conceptual

and methodological underpinnings of phylogenetic

systematics, (2) development of genomics, and (3) rapid

advances in information technology.

Convergence of these three areas makes construction of

a robust tree representing genealogical relationships of all

known species possible for the first time. This, coupled with

the fact that the current lack of a universal tree is severely

hampering progress in many areas of science and limiting the

ability of society to address many important problems and

to capitalize on a host of opportunities, demands that we

undertake this important project now and with conviction.

Although many challenges still stand before us (which themselves

represent additional opportunities), constructing a

complete Tree of Life is now conceptually and technologically

possible for the first time. It is relevant to note here that

we still had hundreds of problems to solve when we decided

to land a man on the moon, and their solution produced

hundreds of unexpected by-products. The size of this undertaking

and the human resources needed, however, require

an international collaboration instead of a competition. Assembling

an accurate universal tree depicting relationships

of all life on Earth, from microbes to mammals, holds enormous

potential value for society, and it is imperative that we

start now. This chapter, although not meant to be exhaustive,

aims to provide a number of examples where even our

limited knowledge of the tree has provided tangible benefits

to society. The actual value that a fully assembled tree would

hold for society would be limitless.

Enabling Technologies and Challenges

Despite widespread acceptance of phylogenetic systematics

during the 1980s, it was not until the advent of genomics

and modern computer technology, enabled by more efficient

and rapid phylogenetic algorithms in the 1990s, that largescale

tree assembly became possible. The rapid growth of

genomics, in particular, revolutionized the field of phylogenetic

systematics and provided a new level of power to tree

assembly. To reconstruct the evolutionary history of all organisms

will require continued advances in computer hardware

and development of faster and more efficient algorithms.

The mathematics and computer science communities are

already actively engaged in this challenge, and breakthroughs

7

8 The Importance of Knowing the Tree of Life

are occurring almost daily. For example, researchers working

on resolving the relationships of 12 species of bluebells

back to a common ancestor have used the 105 genes found

in chloroplast DNA from those species (and an outgroup

—tobacco) to reconstruct the phylogeny. The resulting analysis

examined 14 billion trees. But not only did they reconstruct

the phylogeny, they also inferred the gene order of the

105 genes found in the chloroplast genome for each ancestor

in the tree, which means 100 billion “genomes” were

analyzed. The process took 1 hour and 40 minutes using a

512-processor supercomputer (Moret et al. 2002).

Although this represents a major advancement, additional

advancements will be needed for the relationships of

the current 1.7 million known species to be reconstructed.

Necessary software tools have not been developed to take full

advantage of existing data and to permit integration with

existing biological databases. The enormous amounts of data

being generated by the enabling technologies associated with

modern genomics, although posing considerable challenges

to the computer world, will allow tree construction at a level

of detail far exceeding anything in the past.

Even in groups such as mammals that are well known relative

to invertebrates and microbes, the use of genomics in tree

construction is increasing our knowledge base at a phenomenal

rate and providing important bridges to other fields of

knowledge. Recent work by Dragoo and Honeycutt (1997),

for example, has revealed that skunks represent a lineage of

their own distinct from mustelids (fig. 1.1). Skunks historically

have been classified as a subfamily within the Mustelidae

(weasels), but genetic data suggest that raccoons are more

closely related to weasels than are skunks. Additionally, stink

badgers were classified within a different subfamily of mustelids

than skunks. Morphological and genetic data both support

inclusion of stink badgers within the skunk clade. The

skunk–weasel–raccoon relationship was based on analyses of

genes within the mitochondrial genome. However, DNA sequencing

of nuclear genes has provided support for this hypothesis

as well (Flynn et al. 2000, and K. Koepfli, unpubl.

obs.). This discovery is already proving valuable to other fields

such as public health and conservation.

These types of advances are producing major discoveries

across the entire tree, but nowhere is it more evident than

in the microbial world. New discoveries using genomics and

phylogenetic analysis have led to the discovery of entire new

groups of Archaea (DeLong 1992) that will prove critical to

our understanding of the functioning of the world’s ecosystems.

Others using similar techniques are discovering major

groups of important microbes living in extreme environments

(Fuhrman et al. 1992) that could lead to discovery of important

new classes of compounds. In fact, the number of new

species of bacteria being discovered with these methods, as

noted by DeLong and Pace (2001), is expanding almost exponentially.

It is not only new species that are being discovered

but also new kingdoms of organisms within the domains

Bacteria and Archaea.

Human Health

Ten people died in April through June 1993 as a result of an

unknown disease that emerged in the desert Southwest of

the United States. Approximately 70% of the people who ac-

Figure 1.1. Phylogenetic

relationship of skunks with

relation to weasels as well as

other caniform carnivores;

modified from Dragoo and

Honeycutt (1997). The arrow

indicates a sister-group

relationship between weasels

(Mustelidae) and raccoons

(Procyonidae) to the exclusion

of skunks. Skunks thus were

recognized as a distinct family,

Mephitidae.

Mephitidae

Mustelidae

Procyonidae

Pinnipedia

Ursidae

Canidae

Feliformia

Hog-nosed Skunk

Striped Skunk

Spotted Skunk

Stink Badger

Small- clawed Otter

River Otter

Sea Otter

Zorilla

Mink

Long- tailed Weasel

Ferret

Wolverine

Marten

European Badger

American Badger

Ringtail

Raccoon

Kinkajou

Walrus

Sea Lion

Seal

Bear

Coyote

Gray Fox

Ocelot

Mongoose

The Importance of the Tree of Life to Society 9

quired this disease died from the symptoms. No known cure

or drugs was available to treat this disease, nor was it known

if the disease was caused by a virus or bacterium or some

other toxin. Later, a previously unknown hantavirus was

determined to be the cause and was described as Sin Nombre

virus (SNV; Nichol et al. 1993), and it was discovered that

the reservoir for this virus was the common deer mouse

(Childs et al. 1994).

Phylogenetic analyses of viruses in the genus Hantavirus

suggested that this new virus was related to Old World hantaviruses.

However, the virus was different enough in sequence

divergence to suggest that it was not a result of an introduction

from the Old World, but rather had evolved in the

Western hemisphere. Phylogenetic analyses of both murid

rodents and known hantaviruses indicated a high level of

agreement between host and virus trees (fig. 1.2), suggesting

a long history of coevolution between the two groups

(Yates et al. 2002). This information allowed researchers to

predict that many of the murid rodent lineages may be associated

with other lineages of hantaviruses as well.

Predictions made from analyses of these phylogenetic

trees have been supported with the descriptions of at least

25 new hantaviruses in the New World since the discovery

of SNV (fig. 1.3). More than half (14) of these newly recognized

viruses have been detected in Central and South

America. Additionally, many of the viruses are capable of

causing human disease. It is likely that many more yet unknown

hantaviruses will be discovered in other murid hosts

not only in North and South America but also in other countries

around the world. The poorly studied regions of such

countries as African and Asia quite probably contain many

such undescribed viruses.

Further studies enabled by findings of coevolutionary

relationships have allowed the development of models that

are able to predict areas and times of increased human risk

to disease far in advance of any outbreaks (Yates et al. 2002,

Glass et al. 2002). Knowledge of phylogenetic relationships

of these organisms has thus proven critical for our understanding

of diversity of these pathogens and how to predict

the risk to humans. An understanding of these relationships

also will be critical for us to determine if we are under attack

from introduced pathogens.

In 1999 several people were diagnosed with or died from

symptoms of a viral infection similar to that caused by the

St. Louis encephalitis virus (Flaviviridae). The virus was determined

to be transmitted by mosquitoes and not only affected

humans but also was killing wild and domestic birds.

Phylogenetic analyses using RNA sequencing from this virus

as well as other flaviviruses were conducted to determine

that the disease causing agent was actually the West Nile virus

(Jia et al. 1999, Lanciotti et al. 1999). This virus was determined

from those analyses to be closely related to strains

found in birds from Israel, East Africa, and Eastern Europe

(fig. 1.4; Lanciotti et al. 1999). The information obtained

from those studies provided the basic biology needed to allow

health officials to effectively treat this new outbreak of

West Nile virus as well as make predictions about the spread

of the virus using the known potential avian hosts. Advance

knowledge of where it might spread next was critical in preventing

human and animal infection. West Nile virus has

currently spread as far west in the United States as California

and has resulted in numerous human and animal deaths.

Conservation

Conservation biology is quite likely the area of science most

heavily affected (and will continue to be so) by a better knowledge

of the Tree of Life. A more complete Tree of Life will

mean that more species are identified. Currently, one of the

Figure 1.2. Coevolution of New World

murid rodents (solid lines) and

hantaviruses (dotted lines) based on

comparison of each independent

phylogeny; modified from Yates et al.

(2002).

Rattus norvegicus

Microtus pennsylvanicus

Peromyscus maniculatus(grass)

Peromyscus maniculatus (forest)

Peromyscus leucopus(NE)

Peromyscus leucopus(NW)

Peromyscus leucopus(SW)

Reithrodontomys megalotis

Reithrodontomys mexicanus

Sigmodon hispidustexensis

Sigmodon hispidus

Sigmodon alstoni

Oryzomys palustris

Oligoryzomys flavescens

Oligoryzomys chacoensis

Oligoryzomys longicaudatus(N)

Oligoryzomys longicaudatus(S)

Oligoryzomys microtis

Calomys laucha

Akodon azarae

Bolomys obscurus

Seoul

Prospect Hill

SinNombre

Monongahela

New York

Blue River (IN)

Blue River (OK)

El Moro Canyon

Rio Segundo

Muleshoe

Black Creek Canal

Caсo Delgadito

Bayou

Lechiguanas

Bermejo

Oran

Andes

Rio Mamore

Laguna Negra

Pergamino

Maciel

10 The Importance of Knowing the Tree of Life

most important issues in conservation biology is the question

of how many species are out there (Wheeler 1995).

Although no single value can be used with any level of confidence,

a figure often cited is 12.5–13 million species (e.g.,

Singh 2002); Cracraft (2002) estimated (admittedly roughly)

that only a very small fraction—in the order of 0.4%—of this

figure [or some 50–60 (103 taxa)] are included in any sort of

phylogenetic analysis. A more developed, inclusive Tree

of Life would help identify, catalog, and database elements

of biodiversity that may not have been included until now.

A more developed Tree of Life would help incorporate

an evolutionary framework with which to base conservation

strategies. Two major questions in conservation biology are

how variation is distributed in the landscape, and how it came

about. Conservation planners, too, need to highlight these

spatial components for conservation action. Erwin (1991)

convincingly argued for the need to incorporate phylogenies

and evolutionary considerations in conservation efforts.

Desmet et al. (2002), Barker (2002), and Moritz (2002) have

proposed methodological and practical applications for this

strategy. For example, Barker (2002) reviewed and expanded

on some of the properties of phylogenetic diversity measures

to enable capturing both the phylogenetic relatedness of

species and their abundances. This measure estimates the

relative diversity feature of any nominated set of species by

the sum of the lengths of all those branches spanned by the

set. These branch lengths reflect patristic or path-length distances

of character change. He then used this method to

address a number of conservation and management issues

(from setting priorities for threatened species management

to monitoring biotic response to management) related to

birds at three different levels of analyses: global, New Zealand

only, and Waikato specifically.

An improved Tree of Life would allow for rigorous testing

of old premises in evolutionary theory. For more than 40 years,

the premise that shrinking and expanding of tropical forests

in the neotropics and elsewhere has become a paradigmatic

force invoked to explain the diversity of species in these

biodiverse areas of the world (but see Colinvaux et al. 2001).

Research centered on the phylogenies and phylogeographic

patterns of various taxa in several tropical areas of the world

has now made it clear that the refuge hypothesis (see Haffer

1997, Haffer and Prance 2001) of Amazonian speciation does

not explain the patterns of distribution of many taxa. In fact,

Figure 1.3. Newly discovered

hantaviruses since 1993;

modified from Centers for

Disease Control and Prevention

(2003). Viruses prefixed by an

asterisk represent strains known

to be pathogenic to humans.

Figure 1.4. Phylogenetic relationship of New York (*) strain of

the West Nile virus compared with other strains worldwide;

modified from Lanciotti et al. (1999).

CaсoDelgadito

*Sin Nombre

RнoSegundo

El Moro Canyon

*Andes

*Bayou

*Black Creek Canal

RнoMamorй

*Laguna Negra

Muleshoe

*New York

*Orбn

Pergamino

Maciel

*HU39694

*Lechiguanas

Isla Vista

Bloodland Lake

Prospect Hill

Bermejo

*Juquitiba

*Monongahela

Blue River

*Choclo

Calabaso

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

Kunjin1966-91

India 1955- 80

The Importance of the Tree of Life to Society 11

Glor et al. (2001), Moritz et al. (2000), and Richardson et al.

(2001) have demonstrated that some of the most specious

tropical groups have patterns of diversification that resulted

during or after the unstable period of the Pleistocene, suggesting

a more recent evolutionary history. Phylogenetic patterns

indicate that heterogeneous habitats account for more biodiversity

than does the accumulation of species through time

in an unperturbed environment.

These studies and others (e.g., Moritz 2002) have shown

that it is possible to incorporate the knowledge obtained by

phylogenetic analyses (i.e., applied phylogenetics of Cracraft

2002) and the distribution of genetic diversity into conservation

planning and priority setting for populations within

species and for biogeographic areas within regions. Moritz

(2002) suggests that the separation of genetic diversity into

two dimensions, one concerned with adaptive variation and

the other with neutral divergence caused by isolation, highlights

different evolutionary processes and suggests alternative

strategies for conservation that need to be addressed in

conservation planning.

The main tenet in conservation biology is that the “value

of biodiversity lies in its option value for the future, the

greater the complement of contemporary biodiversity

conserved today, the greater the possibilities for future

biodiversity because of the diverse genetic resource needed

to ensure continued evolution in a changing and uncertain

world” (Barker 2002:165). We cannot conserve what we do

not know.

Agriculture

The potential value to agriculture of a fully assembled Tree

of Life is enormous. The existence of an accurate phylogenetic

infrastructure will enable directed searches for useful

genes in ancestors of modern-day crop plans, as opposed

to the random explorations of the past. Being able to follow

individual genes through time armed with knowledge

of their ancestral forms will allow a determination of how

the function of these genes has changed through time. This

knowledge will, in turn, allow selective modification of new

generations of plants and animals in a much more precise

way than selective breeding alone. For example, a group of

researchers working on the Tree of Life for green plants

(Oliver et al. 2000) has identified and traced the genes responsible

for desiccation tolerance from ancient liverworts

to modern angiosperms (fig. 1.5). Given the rate of desertification

occurring globally and the rapid increases in human

populations, these data may prove invaluable in helping to

sustain our global agriculture.

However, our knowledge of the relationships of wild

relatives to many important agricultural crops still is limited.

Understanding the origins and relationships should help with

further improvement of many of the world’s crop plants.

Recently, however, research on major grain crops such as

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

Manihot (a major source of starch in South America) has provided

insight into the origins of these economically important

agricultural products. But, relationships of many other

important food and fiber plants, which large parts of our

populations worldwide depend on, still remain virtually

unknown. These relationships must be understood if we

hope to make future genetic improvements, especially because

many of the wild progenitors are at risk of extinction

and we have yet to study them.

One good example of how phylogenetic relationships

may help us to generate an improved crop is seen in corn

(Zea mays mays). This is a crop of enormous economic importance,

and if it is to be used to assist in sustaining human

populations, it is imperative that we be able to make continued

improvements in disease and/or drought resistance. Corn

is a grass with a unique fruiting body commonly referred to

as the “corn cob.” This is not typically seen in wild grasses,

so there have been assorted hypotheses regarding the relationships

of corn to other species. Potential relatives to corn

are the grasses from Mexico and Guatemala known as teosintes.

Recently, Wang et al. (2001) used molecular techniques

to conclude that two annual teosinte lineages may actually

be the closest relative to corn (fig. 1.6).

These researchers have demonstrated that the origin of

this agricultural product probably occurred 9000 years ago

in the highlands of Mexico. Additionally, it was determined

that the allele responsible for the cob was a result of selection

on a regulatory gene rather than a protein-coding gene

(Wang et al. 2001). Modern cultivated corn has the poten-

Figure 1.5. Phylogeny of major groups of land plants; modified

from Oliver et al. (2000). Asterisks indicate clades that contain

desiccation-tolerant species. Oliver et al. (2000) suggest that

desiccation tolerance is a primitive state in early land plants that

was lost before the evolution of Tracheophytes and then

reappeared in at least three major lineages. Additionally, the

genes reevolved independently within eight clades found in

angiosperms.

Angiosperms*

Gnetophytes

Conifers

Cycads

Gingko

Ferns*

Equisetum

Selaginella*

Isoetes

Lycopodium

Mosses*

Hornworts*

Liverworts*

Land Plants

Tracheophytes

Seed Plants

12 The Importance of Knowing the Tree of Life

tial to interbreed with several teosinte grasses, so it may be

possible to incorporate new traits from these species to improve

existing strains of corn crops. These studies illustrate

how important it is to protect not only wild species and lineages

of teosinte grass but also the habitats in Mexico where

they are found.

Invasive Species

Invasive species have become an enormous problem worldwide

and cause billions of dollars in damage each year while

doing irreparable harm to many native species and ecosystems.

Phylogenetic analysis is an important tool in the battle

for identifying invasive species and for determining their

geographic origin. Recent examples include the West Nile

virus example described above and an invasive alga in California.

In the latter example, scientists were able to use phylogenetic

analysis of DNA sequences to identify the Australian

alga species Caulerpa taxiflora in California waters. This finding

led to an immediate eradication program that, if successful,

may save the United States billions of dollars.

In addition, understanding the evolutionary associations

of invasive species in the context of closely affiliated groups

of species such as host plants or animals is critical for predicting

their spread and implementing successful control

measures. Wang et al. (1999) performed a phylogenetic

analysis to examine relationships of potential pest species of

longhorn beetles (Cerambycidae) and found that beetles in

certain clades were not likely to become pests, whereas beetles

in two other clades could become pests outside of their native

Australia. Another clade in this group, the Asian longhorn

beetle (Anoplophora gladripennis), has been recently

introduced into the United States in hardwood packing

materials and has already spread from points of introduction

to many new areas, killing native hardwood trees as it invades

(Meyer 1998). Knowledge of the phylogenetic relationships

of trees that this beetle attacks in its native range could prove

valuable in predicting the North American trees most likely

at risk and could help model its future spread. Likewise, an

understanding of the phylogenetic affinities of natural enemies

of longhorn beetles in Asia will be critical if biological

controls for this pest are to be considered in North America.

Invasive ant species have become enormous problems

worldwide. The ant Linepithema humile has been particularly

problematic and has been particularly damaging to native

species in Hawaii. Tsutsui et al. (2001) used phylogenetic

analyses to trace the origin of this pest to Argentina. Another

invasive ant, the fire ant (Solenopsis invicta), has caused billions

of dollars of damage in the southern United States and

has even caused human and animal deaths. Like other eusocial

insects, such as Asian termites, fire ants are extremely difficult

to control using chemical and other standard methods.

Efforts to date in the latter case have been largely ineffective

and have led several authors (Morrison and Gilbert 1999,

Porter and Briano 2000) to suggest the need for the introduction

of biological control agents from the original range of these

ants in South America. In particular, these authors have suggested

the possible use of host-specific ant-decapitating flies

that lay their eggs in the heads of these ants, where the developing

larvae eventually kill the ants. Such introductions

are always risky but would be extremely so without detailed

knowledge of the Tree of Life for the groups in question.

According to Rosen (1986), “Reliable taxonomy is the basis

for any meaningful research in biology.” It is essential also

to understand the evolutionary histories of both target pest

and natural enemy to predict the possible effects of using one

to “control” the other.

Human Land Use

A well-resolved Tree of Life has important implications for

disciplines as apparently disparate from biology as the study

of human land use patterns, especially when they integrate

with other disciplines. For example, phylogenetic analysis

was used to discover that two closely related species of

rodents in the genus Calomys exist in eastern Bolivia (Salazar-

Bravo et al. 2002, Dragoo et al. 2003), each harboring a specific

arenavirus (fig. 1.7). In the Beni Department of Bolivia,

Calomys species harbor the Machupo virus (MACV), the etiological

agent of Bolivian hemorrhagic fever (BHF), whereas

in the Santa Cruz Department, Calomys callosus harbors the

nonpathogenic Latino virus (LAT). MACV occurs in the

Amazon drainage, whereas LAT is found along the drainage

of the Parana River. Additionally, it has been found that

Calomys from each region, despite their genetically based

species specificity, will hybridize in the laboratory and create

fertile hybrids. It follows that there exists not only the

risk of species invasion into a previously isolated ecological

zone, but also the risk of hybrids carrying the pathogenic

virus into the new region, the possibility of dual arenavirus

infection in such rodents, and the chance that virus recombination

with unknown consequences might occur.

In the early 1960s MACV produced several outbreaks in

northeastern Bolivia, with infection rates of 25% in some towns

Figure 1.6. Phylogenetic relationship of corn to other

teosintes; modified from Wang et al. (2001). This relationship

helps explain the morphological variation seen in domestic

corncob.

Zea perennis

Zea diploperennis

Zea maysmexicana

Zea mays parviglumis

Zeamaysmays

(domestic corn)

Teosintes

The Importance of the Tree of Life to Society 13

and mortality rates approaching 45%. Johnson et al. (1972)

noted two distinct phenotypic reactions to infection with

MACV and suggested that there may be a genetic component.

A Calomys species has been reported to express two different

immune responses when infected with MACV but not with

LAT (Webb et al. 1975). Some individuals become chronically

infected, do not produce antibodies, shed large amounts of

virus in urine, become infertile, and are the principal vectors

of BHF. Others produce an antibody response and all but clear

the virus. Although these individuals remain chronically infected,

they can reproduce (Justines and Johnson 1969).

There is growing concern in the Bolivian health community

about the unintended consequences of an all-weather road

connecting Trinidad and Santa Cruz, the capital cities of the

Beni and Santa Cruz Departments, respectively, that has been

in service for several years. This road breaches a forested natural

barrier between biomes of the respective rodents and viruses.

That barrier contains the north–south continental divide of

South America (Salazar-Bravo et al. 2002). The new road linking

the two home ranges of the virus–rodent pairs is bringing

human development to the fringes of both areas along its

course. Human populations in both departments are booming.

Thirty-five years ago Trinidad and Santa Cruz had about

6000 and 60,000 persons, respectively. Today those numbers

have increased 10-fold. Agricultural development has kept

pace, especially in the Santa Cruz Department. Therefore, a

major concern is whether the rodent and its virus from the

north may be now moving, abetted by human commerce, into

the southern department. The potential public health risk

posed by construction of new roads and new development in

the Beni and Santa Cruz Departments makes monitoring this

situation essential.

To make predictions about the evolution and spread of

arenaviruses, we need to understand the evolutionary history

of the rodent reservoirs. The significance of understanding in

greater detail evolutionary histories at the population level as

well as at the subfamily level goes beyond the importance of

prevention and treatment of BHF. The observed patterns of

infection and distribution of MACV exhibit a striking number

of similarities with not only other arenaviruses but with

hantaviruses as well. In addition to the apparent connection

to rodent population density and human ecology, these viruses

with few exceptions share a common host family of rodents,

suggesting a long common evolutionary history.

Economics

Many of the examples presented above will have economic

benefits for society. Understanding the Tree of Life also can

lead to discovery of new products that can be derived from

closely related taxa. These products can be used to affect other

areas such as biological control of pest organisms, agricultural

productivity, and medicinal necessities. For example,

in 1969 a new genus and species of bacterium, Thermus

aquaticus, was described (Brock and Freeze 1969), which later

revolutionized much of the way molecular biology is conducted

when the DNA polymerase from this organism was

used for the polymerase chain reaction (PCR; Saiki et al.

1988). PCR is a multimillion dollar a year industry that

should top $1 billion by the year 2005. This technology has

greatly benefited not only systematics and taxonomy but also

many other biological sciences, including health and forensics.

Discovery of T. aquaticus and use of the Taq DNA polymerase

has spawned many additional technologies. A cursory

view of any molecular supply catalog will show numerous

chemicals and kits designed for use with PCR technology.

Furthermore, such hardware as DNA thermocyclers and

automated sequencers also has been developed.

Additionally, DNA polymerases from other closely related

thermally stable organisms have been isolated with

Figure 1.7. Summary cladogram of four closely related taxa of

vesper mice (Calomys); modified from Salazar-Bravo et al.

(2002). Cb, Calomys species from the Beni Department of

Bolivia; Cf, C. fecundus; Cv, C. venustus; Cc, C. callosus. The

white arrow points to the forested area that separates the Llanos

de Moxos from the Chaco region. Vegetation is as follows: LM;

Llanos de Moxos, SEC; Southeast Coordillera, CH; Chaco, EP

Espinal.

LM

SEC

CH

EP

Cb

Cc

Cv

Cf

14 The Importance of Knowing the Tree of Life

varying properties such as increased half-life at higher temperatures,

decreased activity at lower temperatures, and

3'-5' exonuclease activity. As a result of PCR and the search

for new DNA polymerases, many new life forms have been

discovered. For example, the thermally stable microbes

from which Taq was recovered were thought to comprise a

tight cluster of a few genera that metabolized sulfur compounds

(Woese 1987, Woese et al. 1990). Most of these organisms

had to be cultured in the lab in order to be studied

(DeLong 1992, Barns et al. 1994). However, PCR technology

has allowed for a more in-depth study of these Archaea

by using in situ amplification of uncultivated organisms that

occur naturally in hot springs found in Yellowstone National

Park. We now know that the Crenarchaeota display a wide

variety of phenotypic and physiological properties in environments

ranging from low temperatures in temperate and

Antarctic waters to high-temperature hot springs (Barns

et al. 1996, and citations therein). In fact, PCR coupled with

phylogenetic analysis has allowed the discovery of not only

new life forms within the kingdom Crenarchaeota but also

new kingdoms within the domain Archaea (fig. 1.8; Barns

et al. 1996).

Many new DNA polymerases have been discovered and

patented and are now commercially available as a result

of some of these discoveries. According to Bader et al.

(2001:160), “Simple identification via phylogenetic classification

of organisms has, to date, yielded more patent filings

than any other use of phylogeny in industry.” Patents also

have been filed for vaccines associated with various viruses,

such as porcine reproductive and respiratory syndrome virus

and human immunodeficiency virus, that can target specific

closely related virus populations based on phylogenetic

analyses (citations within Bader et al. 2001).

Other economically important uses of a well-defined Tree

of Life include discovery of biological control organisms as

well as chemicals that target specific metabolic pathways of

related taxa. Phylogenetic analyses of root-colonizing fungi

revealed a group of nonpathogenic fungi that could serve as

a biological control against pathogenic fungi (Ulrich et al.

2000). Phylogenetic studies are being conducted on numerous

organisms for biological control, including nematodes

and associated symbiotic bacteria and target moth, fly, and

beetle pests (Burnell and Stock 2000); intracellular bacteria

Wolbachia, parasitic wasps, and flies (Werren and Bartos

2001); and insect controls of thistles (Briese et al. 2002). In

fact, Briese et al. (2002:149) state, “[G]iven the improved state

of knowledge of plant phylogenies and the evolution of host

use, it is time to base testing procedure purely on phylogenetic

grounds, without the need to include less related test

species solely because of economic or conservation reasons.”

Other forms of control include using chemicals to attack

specific metabolic pathways found in one clade of organisms

but not in another. Two such pathways that occur in microbes

and/or plants but not mammals are the shikimate pathway and

the menevalonant pathway. The chemical glyphosate has been

used commercially as an herbicide/pesticide for its ability to

disrupt the shikimate pathway in algae, higher plants, bacteria,

and fungi but theoretically does not have harmful effects

on mammals (Roberts et al. 1998). Another pathway for consideration

for an antimicrobial target is the mevalonate pathway.

This is one of two pathways that convert isopentenyl

diphosphate to isoprenoid found in higher organisms but is

the only pathway found in many low-G+C (guanine + cytosine)

gram-positive cocci. Phylogenetic analyses indicate that the

genes found in these bacteria are more closely related to higher

eukaryotic organisms and are likely a result of a very early horizontal

gene transfer between eukaryotes and bacteria before

the divergence of plants, animals, and fungi (Wilding et al.

2000). This pathway therefore represents a means for control

of the gram-positive bacteria.

Another economic value to society may lie in DNA/RNA

vaccines. Knowing the phylogenetic relationships of target

organisms may allow for the development of broad-scale vaccines

or “species”-specific vaccines. DNA vaccines are relatively

easy to make and can be produced much quicker than conventional

vaccines (Dunham 2002). Although there still are

several safety issues to address before wide-scale use of nucleic

acid vaccines (Gurunahan et al. 2000), this technology can be

used to treat several wildlife diseases (Dunham 2002) and can

be used potentially as a defense against a bioterrorist attack.

Conclusions

Assembling the Tree of Life will be a monumental task and

possibly one of the greatest missions we as a society could

Figure 1.8. Newly discovered organisms of Archaea; modified

(reduced tree) from Barns et al. (1996). Taxa labeled “pJP”

represent new life forms discovered using ribosomal RNA

sequences amplification from uncultured organisms. New taxa

were found within two kingdoms representing Crenarchaeota

and Euryarchaeota as well as the new kingdom Korarchaeota

(pJP78 and other similar rDNA sequences).

Desufurococcus mobilis

pJP74

Sulfolobus aciducaldarius

pJP7

Pyrodictium occultum

pJP8

Pyrobaculum islandicum

Pyrobaculum aerophilum

Thermoproteus tenax

pJP6

Thermofilum pendens

pJP81

pJP33

Methanopyrus kandleri

Theromococcus celer

Archaeoglobus fulgidus

pJP9

pJP78

Crenarchaeota

Euryarchaeota

Korarchaeota

The Importance of the Tree of Life to Society 15

hope to achieve. It will require numerous collaborations of

multiple disciplines within the scientific community. The

Tree of Life has already provided many benefits, not only to

science but to humanity as well. These benefits are but a small

fraction of what a fully assembled tree would have to offer.

In many respects, the power of a complete Tree of Life compared

with the partial one we have now is analogous to the

breakthroughs made possible by a complete periodic table

compared with a partial one. Imagine chemists trying to predict

the structure and function of new compounds armed

with the knowledge of only 10% of the periodic table. The

Tree of Life will form the critical infrastructure on which all

comparative biology will rest. Once completed, this infrastructure

will fuel scientific breakthroughs across all of the

life sciences and many other fields of science and engineering

and will foster enormous economic development.

Constructing the Tree of Life will create extraordinary

opportunities to promote research across interdisciplinary

fields as diverse as genomics, computer science and engineering,

informatics, mathematics, earth sciences, developmental

biology, and environmental biology. The scientific and

engineering problem of building the Tree of Life is complex

and presents many challenges, but these challenges can be

accomplished in our lifetime. Already, the international

genomics databases [GenBank (http://www.ncbi.nih.gov/

Genbank/index.html), EMBL (http://www.ebi.ac.uk/embl/),

and DDBJ (http://www.ddbj.nig.ac.jp/)] grow at an exponential

rate, with the number of nucleotide bases doubling approximately

every 14 months. Currently, there are more than

17 billion bases from more than 100,000 species listed by

the National Center for Biotechnology Information (available

at http://www.ncbi.nlm.nih.gov/). Data from nongenomic

sources, such as anatomy, behavior, biochemistry, or physiology,

also have been collected on thousands of species, and

many thousands of phylogenies have been published for

groups widely distributed across the tree. To truly benefit

industry, agriculture, and health and environmental sciences,

the overwhelming amount of data required to construct the

Tree of Life must be appropriately organized and made

readily available.

Cracraft (2002) considered the question “What is the

Tree of Life?” to be one of seven great questions of systematic

biology. In many respects, the answer to that question

is fundamental to all the others and will enable their resolution.

Even fundamental questions such as what a species is

and how many there are will be facilitated by assembling the

tree. It should be noted that addressing the latter question

and assembling the Tree of Life go hand-in-hand and form a

positive feedback loop. Discovery of new species will provide

new information that will enhance tree assembly, and

at the same time tree assembly will provide the information

necessary for the discovery of new species.

The other great questions listed by Cracraft (2002) actually

require a tree for their resolution. As addressed in this

chapter, however, great questions from other disciplines also

require a highly resolved tree for their solution. In fact, the

answer to few scientific questions offers the potential to fuel

as many major discoveries in other disciplines as does resolution

of the Tree of Life. Fields such as evolution and development,

medicine, and bioengineering will immediately

be able to rapidly address questions not before possible

without the phylogenetic infrastructure provided by the

tree. These discoveries will in turn fuel economic development,

inform land management decisions, and protect the

environment.

Assembly of the Tree of Life on this scale, however, will

require the development of innovative database structures

(both hardware and software) that support relational authority

files with annotation of both genetic and nongenetic

information. Unprecedented levels and methods of computational

capabilities will need to be developed as genomic

information from the “wet” studies in the laboratory and field

is analyzed in the “dry” environments of computers. Already

a new field of phyloinformatics and computational phylogenetics

is emerging from these efforts that promise to harness

phylogenetic knowledge to integrate and transform data

held in isolated databases, allowing the invention of new

information and knowledge.

What is needed is an international effort to coordinate

tree construction, facilitate hardware and software design,

promote collaboration among researchers, and facilitate database

design and maintenance and the creation of a center

to help coordinate and facilitate these activities. Owing to

fundamental theoretical advances in manipulating genomic

and other kinds of data, to the availability of major new

sources of data, and the development of powerful analytical

computational tools, we now have the potential (given sufficient

resources and coordination) to assemble much of the

entire Tree of Life within the next few decades, at least for

currently known species. The potential of building a Tree

of Life extends far beyond the basic and applied biological

sciences and promises to provide much value to society.

Building an accurate, complete Tree of Life depicting the

relationships of all life on Earth will call for major innovation

in many fields of science and engineering similar to those

derived from sending a man to the moon or sequencing the

entire human genome. The benefits to society from such an

undertaking are enormous and may well extend beyond the

many provided by these two successful efforts.

Acknowledgments

We thank the Centers for Disease Control and Prevention, the

U.S. National Science Foundation, and the National Institutes of

Health for previous financial support for many of the discoveries

reported here. We especially thank the National Science

Foundation for providing the leadership for the initiation of this

critical effort. We also thank the Museum of Southwestern

Biology of the University of New Mexico (UNM) and the

Department of Biology (UNM) for their support.

16 The Importance of Knowing the Tree of Life

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