C h apte r
12
chapter outline
Taxonomy: Nomenclature and Classification
Cladistics
Molecular Systematics
The Major Groups of Organisms: Bacteria, Archaea,
and Eukarya
Origin of the Eukaryotes
The Protists and Eukaryotic Kingdoms
Life Cycles and Diploidy
I n the previous section, we considered the mechanisms by
which evolutionary change occurs. Now we turn our attention
to the products of evolution—that is, to the multitude of dif-
ferent kinds, or species, of living organisms that share our bio-
sphere today. It is estimated that there are perhaps 10 million
eukaryotic species and an unknown number of prokaryotic ones.
The scientific study of this biological diversity and its evolu-
tionary history is called systematics. The overall goal of sys-
tematists is to discover all the branches of the phylogenetic tree
of life, the family tree depicting the genealogic relationships of
organisms, with a single, ancestral species at its base.
Taxonomy: Nomenclature
and Classification
An important aspect of systematics is taxonomy, which involves
the identifying, naming, and classifying of species. The modern
234
Systematics:
The Science of
Biological Diversity
A large, diverse family
 Bittersweet nightshade (Solanum
dulcamara), shown here, is a widespread weed poisonous
to humans but not as toxic as deadly nightshade (Atropa
belladonna), which can be fatal. Both poisonous species belong
to the Solanaceae, a family that includes important agricultural
crops, such as potatoes, tomatoes, eggplants, and chili peppers.
system of naming living things began with the eighteenth-
century Swedish naturalist Carl Linnaeus (Figure 12–1), whose
ambition was to name and describe all of the known kinds of
plants, animals, and minerals. In 1753, Linnaeus published a
two-volume work entitled Species Plantarum (“The Kinds of
Plants”) in which he described each species in Latin, in a sen-
tence limited to 12 words. He regarded these descriptive Latin
phrase names, or polynomials, as the proper names for the spe-
cies, but in adding an important innovation devised earlier by
Caspar Bauhin (1560–1624), Linnaeus made permanent the
binomial (“two-term”) system of nomenclature. In the margins
of Species Plantarum, next to the “proper” polynomial name of
each species, Linnaeus wrote a single word. This word, when
CHEC K POINTS
After reading this chapter, you should be able to answer the following:
1. Describe the binomial system of nomenclature.
2. Why is the term “hierarchical” used to describe taxonomic
categories? Name the principal categories between the levels of
species and kingdom.
3. What is cladistic analysis? What does a cladogram represent?
4. What evidence is there for the existence of the three major
domains, or groups, of living organisms?
5. Name the three kingdoms of multicellular eukaryotes, and give
the major identifying characteristics of each.

12–1  Carl Linnaeus (1707–1778)  A professor, physician, and
naturalist, Linnaeus devised the binomial system for naming
species of organisms and established the major categories that are
used in the hierarchical system of biological classification. When
he was 25, Linnaeus spent five months exploring Lapland for the
Swedish Academy of Sciences. He is shown here wearing a version
of the traditional Lapp outfit and holding a sprig of twinflower
(Linnaea borealis), a species that is named after him.
combined with the first word of the polynomial—the genus
(plural: genera)—formed a convenient “shorthand” designation
for the species. For example, for catnip, which was formally
named Nepeta floribus interrupte spicatus pedunculatis (mean-
ing “Nepeta with flowers in an interrupted pedunculate spike”),
he wrote the word “cataria” (meaning “cat-associated”) in the
margin of the text, thus calling attention to a familiar attribute of
the plant. Linnaeus and his contemporaries soon began calling
this species Nepeta cataria, and this Latin name is still used for
this species today.
The convenience of this new system was obvious, and
the cumbersome polynomial names were soon replaced by
binomial names. The earliest binomial name given to a par-
ticular species has priority over other names applied to the
same species later. The rules governing the scientific names
of plants, photosynthetic protists, and fungi are embodied in
Taxonomy: Nomenclature and Classification 235
the International Code of Botanical Nomenclature. Codes also
exist for animals and nonphotosynthetic protists (International
Code of Zoological Nomenclature), as well as for microbes
(International Code of Nomenclature of Bacteria).
The Species Name Consists of the Genus Name Plus
the Specific Epithet
A species name consists of two parts. The first is the name of
the genus—also called the generic name—and the second is
the specific epithet. For catnip, the generic name is Nepeta,
the specific epithet is cataria, and the species name is Nepeta
cataria.
A generic name may be written alone when one is refer-
ring to the entire group of species making up that genus; Figure
12–2 shows three species of the violet genus, Viola. A specific
epithet is meaningless, however, when written alone. The spe-
cific epithet biennis, for example, is used in conjunction with
dozens of different generic names. Artemisia biennis, a kind of
wormwood, and Lactuca biennis, a species of wild lettuce, are
two very different members of the sunflower family, and Oeno-
thera biennis, an evening primrose, belongs to a different family
altogether. Because of the danger of confusing names, a spe-
cific epithet is always preceded by the name or the initial letter
of the genus that includes it: for example, Oenothera biennis or
O. biennis. Names of genera and species are printed in italics or
are underlined when written or typed.
If a species is discovered to have been placed in the wrong
genus initially and must then be transferred to another genus,
the specific epithet moves with it to the new genus. If there is
already a species in that genus that has that particular specific
epithet, however, an alternative name must be found.
Each species has a type specimen, usually a dried plant
specimen housed in a museum or herbarium, which is desig-
nated either by the person who originally named that species
or by a subsequent author if the original author failed to do so
(Figure 12–3). The type specimen serves as a basis for com-
parison with other specimens in determining whether they are
members of the same species.
The Members of a Species May Be Grouped into Subspecies
or Varieties
Certain species consist of two or more subspecies or variet-
ies (some botanists consider varieties to be subcategories of
subspecies, and others regard them as equivalent). All of the
members of a subspecies or variety of a given species resem-
ble one another and share one or more features not present in
other subspecies or varieties of that species. As a result of these
subdivisions, although the binomial name is still the basis of
classification, the names of some plants and animals may con-
sist of three parts. The subspecies or variety that includes the
type specimen of the species repeats the name of the species,
and all the names are written in italics or underlined. Thus the
peach tree is Prunus persica var. persica, whereas the nectar-
ine is Prunus persica var. nectarina. The repeated persica in
the name of the peach tree tells us that the type specimen of
the species P. persica belongs to this variety, abbreviated “var.”
(see Figure 12–2b, c for other examples).
236 C ha p t e r 1 2    Systematics: The Science of Biological Diversity

(a) (b) (c)

12–2  Three members of the violet genus  (a) The common blue violet, Viola sororia, which grows
in temperate regions of eastern North America as far west as the Great Lakes. (b) Viola tricolor var.
tricolor, a yellow-flowered violet representing a mostly perennial species native to western Europe.
(c) Pansy, Viola tricolor var. hortensis, an annual, cultivated strain of the wild species represented
in (b). These taxa differ in flower color and size, leaf shape and margin, and other features that
distinguish the species of this genus, even though there is an overall similarity among all of them.
There are about 500 species of the genus Viola.

Organisms Are Grouped into Broader Taxonomic Categories

Arranged in a Hierarchy
Linnaeus (and earlier scientists) recognized three kingdoms—
plant, animal, and mineral—and until recently, the kingdom
was the most inclusive unit used in biological classification. In
addition, several hierarchical taxonomic categories were added
between the levels of genus and kingdom: genera were grouped
into families, families into orders, and orders into classes. The
Swiss-French botanist Augustin-Pyramus de Candolle (1778–
1841), who invented the word “taxonomy,” added another cat-
egory—division—to designate groups of classes in the plant
kingdom. Hence, the divisions became the largest inclusive
groups of the plant kingdom. At the XV International Botanical
Congress in 1993, however, the International Code of Botanical
Nomenclature made the term phylum (plural: phyla) nomencla-
turally equivalent to division. “Phylum” has long been used by
zoologists for groups of classes and has been adopted for use in
this book.
In this hierarchical system—that is, of groups within groups,
with each group ranked at a particular level—the taxonomic
group at any level is called a taxon (plural: taxa). The level at
which it is ranked is called a category. For example, genus and

12–3  Type specimen  The type specimen of the angiosperm

Mikania citriodora (family Asteraceae), which is found in Brazil.
This specimen was collected by W. C. Holmes and described by
him in a paper published in the journal Phytologia (volume 70,
pages 47–51, 1991).
 Taxonomy: Nomenclature and Classification 237

species are categories, and Prunus and Prunus persica are taxa
within those categories.
Regularities in the form of the names for the different taxa
make it possible to recognize them as names at that level. For
example, names of plant families end in -aceae, with a very few
exceptions. Older names are allowed as alternatives for a few
families, such as Fabaceae, the pea family, which may also be
called by the older name, Leguminosae. Other examples are
Apiaceae, the parsley family (also known as Umbelliferae), and
Asteraceae, the sunflower family (also known as Compositae).
Names of plant orders end in -ales.
Sample classifications of maize (Zea mays) and the com-
monly cultivated edible mushroom (Agaricus bisporus) are
given in Table 12–1.
Many Different Classifications of Plants Have Been
Proposed
The earliest classifications were based on the appearance, or
the habit, of the plant. For instance, Theophrastus (370–285
b.c.e.), a student of Aristotle’s and known as the Father of
Botany, classified all plants on the basis of form: trees, shrubs,

Biological Classification. Notice how much you can tell about an organism when you know its place
Table 12-1 in the system. The descriptions here do not define the various categories but tell you something
about their characteristics. The kingdoms Plantae and Fungi belong to the domain Eukarya.
Category Taxon Description

Maize
Kingdom Plantae Organisms that are primarily terrestrial, with chlorophylls
a and b contained in chloroplasts, spores enclosed in
sporopollenin (a tough wall substance), and nutritionally
dependent multicellular embryos

Phylum Anthophyta Vascular plants with seeds and flowers; ovules enclosed in
an ovary, pollination indirect; the angiosperms

Class Monocotyledoneae Embryo with one cotyledon; flower parts usually in threes;
many scattered vascular bundles in the stem; the monocots

Order Poales Monocots with fibrous leaves; reduction and fusion in

flower parts

Family Poaceae Hollow-stemmed monocots with reduced greenish flowers;

fruit a specialized achene (caryopsis); the grasses

Genus Zea Robust grasses with separate staminate and carpellate

flower clusters; caryopsis fleshy

Species Zea mays Maize, or corn

Edible Mushroom
Kingdom Fungi Nonmotile, multinucleate, heterotrophic, absorptive organ-
isms in which chitin predominates in the cell walls

Phylum Basidiomycota Dikaryotic fungi that form a basidium bearing four spores
(basidiospores); subphyla Agaricomycotina, Pucciniomyco-
tina, and Ustilaginomycotina

Class Agaricomycetes Fungi that produce basidiomata, or “fruiting bodies,” and

club-shaped, aseptate basidia that line gills or pores; the
hymenomycetes

Order Agaricales Fleshy fungi with radiating gills or pores

Family Agaricaceae Agaricales with gills

Genus Agaricus Dark-spored soft fungi with a central stalk and gills free from
the stalk

Species Agaricus bisporus The common edible mushroom

238 C ha p t e r 1 2    Systematics: The Science of Biological Diversity
undershrubs, and herbs. Linnaeus used the “sexual system,”
by which plants were classified into 24 classes based on the
number and arrangement of the stamens in each flower. Such
systems of classification are referred to as artificial systems,
because they classify organisms primarily as an aid to identifi-
cation and generally by means of one or a few characters.
For Linnaeus and his immediate successors, the goal of
taxonomy was the revelation of the grand, unchanging design
of creation. After publication of Darwin’s On the Origin of
Species in 1859, however, differences and similarities among
organisms came to be seen as products of their evolutionary
history, or phylogeny. Biologists now wanted classifications to
be not only informative and useful but also an accurate reflec-
tion of the evolutionary relationships among organisms. Such
classifications are referred to as natural classifications. The
evolutionary relationships among organisms have often been
diagrammed as phylogenetic trees, which depict the genea-
logic relationships between taxa as hypothesized by a particular
investigator or group of investigators.
Traditionally, the classification of a recently discovered
organism and its phylogenetic relationship to other organisms
was based on its outward similarities to other members of that
taxon. Phylogenetic trees constructed by traditional methods
rarely included detailed considerations of comparative infor-
mation. Although this approach produced many useful results,
it was based primarily on the investigator’s opinion regarding
which factors were most important in determining the classi-
fication. Therefore, it is not surprising that very different clas-
sifications were sometimes proposed for the same groups of
organisms.
In a Classification Scheme That Accurately Reflects
Phylogeny, Every Taxon Should Be Monophyletic
A monophyletic group (also called a clade) is composed of
an ancestor and all its descendants; none of its descendants
are excluded (Figure 12–4). Thus, a genus should consist of all
species descended from the most recent common ancestor—
and only of species descended from that ancestor. Similarly, a
12–4  Monophyletic, paraphyletic, and polyphyletic groups  A monophyletic group, or clade, includes
the common ancestor 1 and all of its descendants (species A, B, and C). A paraphyletic group includes the
common ancestor 2 of some (species D, E, and F), but not all, of its descendants (species G is not included).
A polyphyletic group has two or more ancestors; species D, E, F, and G share common ancestor 2, but
species C has a different one, ancestor 1.
family should consist of all genera descended from a more dis-
tant common ancestor—and only of genera descended from that
ancestor. Simply stated, a monophyletic group is one that can
be removed from a phylogenetic tree by one “cut” of the tree.
A phylogenetic classification attempts to give formal taxonomic
names only to groups that are monophyletic, although not every
monophyletic group may need a name.
As new information becomes available, researchers some-
times find that current taxonomic groups are not monophyletic.
There are two such groups: paraphyletic and polyphyletic (Fig-
ure 12–4). A paraphyletic group is one consisting of a common
ancestor, but not all descendants of that ancestor. In phylogenetic
classification, paraphyletic groups are not given formal names. A
polyphyletic group is a group with two or more ancestors, but
not including the true common ancestor of its members.
Homologous Features Have a Common Origin, and
Analogous Features Have a Common Function but Different
Evolutionary Origins
Systematics is, to a great extent, a comparative science. It groups
organisms into taxa from the categorical levels of genus through
phylum, based on similarities in structure and other characters.
From Aristotle on, however, biologists have recognized that
superficial similarities are not useful criteria for taxonomic deci-
sions. For example, birds and insects should not be grouped
together simply because both have wings. A wingless insect
(such as a silverfish) is still an insect, and a flightless bird (such
as the kiwi) is still a bird.
A key question in systematics is the origin of a similarity
or difference. Does the similarity of a particular feature reflect
inheritance from a common ancestor, or does it reflect adapta-
tion to similar environments by organisms that do not share a
common ancestor? And a related question arises concerning dif-
ferences between organisms. Does a difference reflect separate
evolutionary histories, or does it reflect instead the adaptations
of closely related organisms to very different environments?
As we will see in later chapters, foliage leaves, cotyledons,
bud scales, and floral parts have quite different functions and
 Cladistics 239

B C on ver gent Ev ol u tion

Comparable selective forces, acting on
plants growing in similar habitats but differ-
ent parts of the world, often cause totally un-
related species to assume a similar appear-
ance. The process by which this happens is
known as convergent evolution.
Let us consider some of the adaptive
characteristics of plants growing in desert
environments—fleshy, columnar stems
(which provide the capacity for water stor-
age), protective spines, and reduced leaves.
Three fundamentally different families of
flowering plants—the spurge family (Eu-
phorbiaceae), the cactus family (Cactaceae),
and the milkweed family (Apocynaceae)—
have members with these features. The
cactuslike representatives of the spurge and
milkweed families shown here evolved from
leafy plants that look quite different from
one another.
Native cacti occur (with the exception of
one species) exclusively in the New World.
The comparably fleshy members of the
spurge and milkweed families occur mainly
in desert regions in Asia and especially Afri-
ca, where they play an ecological role similar
to that of the New World cacti.
Although the plants shown here—
(a) Euphorbia, a member of the spurge fam-
ily; (b) Echinocereus, a cactus; and (c) Hoodia,
a fleshy milkweed—have CAM photosynthe-
sis (page 145), all three are related to and de-
rived from plants that have only C3 photosyn-
thesis. This indicates that the physiological
adaptations involved in CAM photosynthesis
also arose as a result of convergent evolution.

(a) (b) (c)

appearances, but all are evolutionary modifications of the same
type of organ, namely, the leaf. Such structures, which have a
common origin but not necessarily a common function, are said
to be homologous (from the Greek homologia, meaning “agree-
ment”). These are the features on which evolutionary classifica-
tion systems, ideally, are constructed.
By contrast, other structures, which may have a similar
function and superficial appearance, have an entirely different
evolutionary background. Such structures are said to be analo-
gous and are the result of convergent evolution (see the essay
above). Thus, the wings of a bird and those of an insect are
analogous, not homologous. Similarly, the spine of a cactus (a
modified leaf) and the thorn of a hawthorn (a modified stem)
are analogous, not homologous. Distinguishing between homol-
ogy and analogy is seldom so simple, and it generally requires
detailed comparison as well as evidence from other features of
the organisms under study.
Cladistics
The most widely used method of classifying organisms today
is known as cladistics, a form of phylogenetic analysis that
explicitly seeks to understand phylogenetic relationships. The
approach focuses on the branching of one lineage from another
in the course of evolution. It recognizes a monophyletic group,
or clade, by its shared derived characters (synapomorphies).
Synapomorphies are character states that arose in the com-
mon ancestor of the group and are present in all of its members.
Character states are two or more forms of a particular feature,
such as the presence or absence of wood or flowers.
To develop an evolutionary tree, one must determine
which changes are more recent and which occurred farther
back in the past; that is, the tree must have direction—it must
be rooted. By arranging the characters in a specific direction,
rooting makes it possible to recognize shared derived character
states that define monophyletic taxa.
Outgroups are used to root a tree. An outgroup is a taxon
that is closely related to but not a member of the study group
(the ingroup) under investigation. Character states possessed
by the closest outgroups are considered to be ancestral, while
those present in the ingroup, but absent in the nearest out-
groups, are considered to be derived.
The result of cladistic analysis is a cladogram, which
provides a graphical representation of a working model, or
hypothesis, of the phylogenetic relationships among a group of
organisms. These hypotheses can then be tested by attempting
to incorporate additional species or characters that may or may
not conform to the predictions of the model.
To see how a cladogram is constructed, let us consider four
different groups of plants: hornworts (see Figure 16–29), ferns,
pines, and oaks. For each of the plant groups, we have selected
four homologous characters to be analyzed (Table 12–2). To
240 C ha p t e r 1 2    Systematics: The Science of Biological Diversity
Table 12-2 Selected Characters Used in Analyzing the
Phylogenetic Relationships of Four Plant Taxa
Characters*
Xylem and
Taxon Phloem Wood Seeds Flowers
Hornworts – – – –
Ferns + – – –
Pines + + + –
Oaks + + + +
**The character state “present” (+) is the derived condition; the character state
“absent” (–) is the ancestral condition.
keep matters simple, the characters are considered to have only
two different states: present (+) and absent (–).
Through their possession of embryos, hornworts are
known to be related to the other three plant groups, which also
have embryos. However, hornworts lack many features that the
other three groups share—for example, xylem and phloem, and
many characters not shown in the table. The hornworts can be
used as the outgroup and can be considered to have diverged
earlier than the other taxa from a common ancestor. Accord-
ingly, the hornworts can be used to determine whether features
shared among ferns, pines, and oaks can potentially be used
to define a clade. For example, seeds are not present in horn-
worts, and therefore seeds can be hypothesized to be a poten-
tial shared derived feature that would support uniting pines and
oaks as a monophyletic group. Applying this argument to our
few characters results in the “absent” character state being con-
sistently recognized as the ancestral condition and the “present”
character state as the derived condition.
Figure 12–5a shows how one might sketch a cladogram
based on the presence or absence of the vascular tissues xylem
and phloem. Inasmuch as ferns, pines, and oaks all have xylem
and phloem, they can be hypothesized to form a monophyletic
group. Figure 12–5b shows how further resolution is obtained
as information about other features is added.
How does one interpret the cladogram in Figure 12–5b?
To begin, note that cladograms do not indicate that one group
gave rise to another, as in many phylogenetic trees constructed
by the traditional method. Rather, they imply that groups termi-
nating in adjacent branches (the branch points are called nodes)
shared a common ancestor. Such groups are said to be sister
groups, or closest relatives. The cladogram of Figure 12–5b
tells us that oaks shared a more recent common ancestor with
pines than with ferns, and that they are more closely related to
pines than to ferns. The relative positions of the various plants
on the cladogram indicate their relative times of divergence.
A fundamental principle of cladistics is that a cladogram
should be constructed in the simplest, least complicated, and
most efficient way. This principle is called the principle of
parsimony. When conflicting cladograms are constructed from
12–5  Cladograms  These cladograms show the phylogenetic
relationships among ferns, pines, and oaks, indicating the shared
characters that support the patterns of relationships. (a) A cladogram
based on the presence or absence of xylem and phloem. (b) Further
resolution of the relationships, based on additional information on
the presence or absence of wood, seeds, and flowers.
the data at hand, the one with the greatest number of statements
of homology and the fewest of analogy is preferred.
Molecular Systematics
Before the advent of molecular systematics, classification by
any methodology was based largely on comparative morphol-
ogy and anatomy, but plant systematics has been revolutionized
by the application of molecular techniques. The techniques most
widely used are those for determining the sequence of nucleo-
tides in nucleic acids—sequences that are genetically determined
(see Chapter 10). Molecular data are different from data obtained
from traditional sources in several important ways: in particu-
lar, they are easier to quantify, they have the potential to provide
many more characters for phylogenetic analysis, and they allow
comparison of organisms that are morphologically very different.
With the development of molecular techniques, it has become
possible to compare organisms at the most basic level—the gene.
Analysis of nucleic acid sequences provides powerful data
for understanding evolutionary relationships. Many different
genes, with varying rates of change, can be used to study evolu-
tion in different lineages. Much of the variation in the homolo-
gous genes of different groups of organisms is due to neutral
mutations that have accumulated at a nearly constant rate over
evolutionary time. This variation is not the result of a selec-
tion process. Instead, it represents the differences in the num-
ber of nucleotide changes that have occurred in homologous