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Evolution and Systematics
(Read the section quot;Phylogenyquot; in Chapter 1 in the Kardong textbook.)
T he fact that there are different names for organisms indicates that we can tell the
kinds of organisms apart. There are different structures, shapes and sizes, but still
there are similarities. This analysis of similarities and differences is called the
comparative method. Organisms look different because of evolutionary change mostly,
and these differences are tracks of their evolutionary history. By studying the diversity
of morphology or the comparative anatomy of these, we can learn something about
their evolutionary history.
Evolution
Evolution is the history of descent with modification. Often, evolution is defined as a
change in gene frequency in a population. It is true that evolution ultimately involves a
change in gene frequencies, but this is not all there is to evolution. Evolution produces
observable patterns among organisms that can be studied without reducing evolution
only to gene frequencies.
Lineages are central to the concept of evolution. A lineage is a series of ancestor-
descendant relationships among some entities (such as organisms or populations)
through time. Descent with modification results in descendants being different from
their ancestors because the descendants have acquired evolutionary novelties not
found in their ancestors, and these novelties are passed on further to descendants.
Consider a particular nucleotide of DNA in one of your genes. If it is a cytosine (C),
then most probably it was a cytosine in your parents and in their parents. However, at
some point in the past, there is a chance that the cytosine nucleotide was a thymine (T).
The change from thymine to cytosine (T to C) is a mutation. It is also an example of an
evolutionary novelty. Evolutionary novelties arise in an individual and may spread
and become fixed in the population, and in other populations of the species. Eventually,
enough mutations can affect a number of genes such that genetically based changes in
the development, physiology, behavior, or anatomy of an organism result. In general,
change within a lineage is called anagenesis. The splitting of lineages is cladogenesis
(see Species below).
Natural Selection
One nonrandom way in which evolutionary novelties become fixed in populations and
species is by natural selection. Natural selection is the differential
survival/reproduction of different classes of self-reproducing entities (genes,
genotypes, populations, or species) that differ in a heritable characteristic. Natural
selection affects the individual organisms that differ in phenotype because of genotype
differences. Fitness is measured by how successful one genotype is at being carried into

2. Fall 2001 page 2
the next generation, relative to other genotypes. By definition, natural selection operates
when genotypes differ in fitness. The phrase quot;survival of the fittestquot; is often misused.
The estimate of fitness changes depending on the environment, so there is no ideal goal
or preferred direction in evolution; in this sense, fitness is not predictive. Natural
selection is not a force, good or evil, of any sort. It does not prevent the extinction of
populations or species. It is simply the observation that the proportion of the different
classes of individuals changes.
Adaptation
Adaptation is a process of genetic change in a population because of natural selection,
in which a feature becomes quot;improvedquot; relative to a particular function. As a noun, an
adaptation is an adaptive feature. Adaptation is often poorly defined; an organism may
become better adjusted to its environment (for example, when New Yorkers acclimate
to Texas summers), but this is not in itself adaptation. Not all features of organisms are
adaptations; the new feature has to provide an improvement in function. This demands
that one 1) identify where in the phylogeny the new trait evolved, and 2) demonstrate
that the new feature increases fitness. We will talk about adaptation in more detail later.
Historically, biologists have viewed evolution as a slow, steady process; this model of
evolution is called gradualism. An alternative view is that change occurs sporadically
and suddenly; long periods of stasis are punctuated by abrupt changes; this model is
punctuated equilibrium. In many cases the fossil record seems to suggest the latter
model, because there appear to be large gaps in the fossil record. However, the gaps
may occur because geological processes that produce fossils are themselves sporadic,
and the fossil record is an uneven sample of organism diversity over time.
Stasis
Time
Anagenesis
Cladogenesis
Morphological Divergence
Gradualism Punctuated Equilibrium
Species
In comparative anatomy, similarities and differences generally are assessed among
species. A species can be thought of as a lineage of organisms connected through time
by ancestor-descendant relationships; the components (populations) of a species

3. Fall 2001 page 3
exchange genes among themselves through interbreeding, but there is no gene flow to
other units considered to be species. This concept of species is the evolutionary species
concept.
Once these lineages are on their own evolutionary pathway, they are said to be new
species, and speciation has occurred. Often, this evolutionary independence is
accompanied by the acquisition of novel features; that is, the new species is
diagnosable. The concept that insists that species be diagnosable is the phylogenetic
species concept. Usually, these new species will become reproductively isolated from
each other; the biological species concept holds that reproductive isolation is the
necessary criterion for status as species. Under this concept, the one usually used by
most textbooks, a species is a group of individual organisms that are capable of
interbreeding with each other and that have fertile offspring.
Systematics
Systematics is the study of the evolutionary relationships among organisms. One of the
major reasons for studying the morphology of organisms is to understand their
relationships to one another. The goal of most modern systematists is to discover the
evolutionary history, or phylogeny, of the group, and to construct a taxonomy or
classification scheme that reflects that phylogeny. Because evolution is a kind of history,
it follows that there is only one phylogeny of life. That is, all species are related to each
other in a unique set of relationships. There is a natural order, and one of the goals of
students of comparative anatomy is to discover this natural order.
Taxa
The two descendant lineages of an ancestor lineage are sister-groups; or conversely,
two groups that uniquely share a common ancestor are sister-groups. A monophyletic
group (=clade) consists of an ancestor and all of its descendants. A paraphyletic group
consists of an ancestor and some of its descendants. In a polyphyletic group, at least
one of the common ancestors of any two species in the group is not part of the group. A
taxon is a species or a group of species. A taxon may or may not be given a name. If a
taxon is named, the name is a proper noun. As a historical entity, a taxon can be
regarded as an individual. Paraphyletic and polyphyletic groups, however, are not
individuals but classes. They are defined not by genealogical relationships but by the
possession of certain attributes (see Taxonomy).

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A B C D E A B C D E A B C D E
Monophyly Paraphyly Polyphyly
Characters
If taxa acquire evolutionary novelties and pass them on to descendants, then we should
be able to recover evolutionary history by examining the features of the descendants.
We may group taxa together because they share some feature, such as having hair vs.
being hairless, but this is not enough. In order to be able to understand phylogeny
(evolutionary relationships), we must use features that represent evolutionary novelties,
that is, features that delineate monophyletic groups or clades.
The way in which evolutionary trees are reconstructed is described below under
Phylogeny Reconstruction. Having reconstructed or estimated an evolutionary tree, we
can group taxa together because they share an evolutionary novelty, or derived state of
a particular character. A derived state is called an apomorphy; a primitive state is a
plesiomorphy. A synapomorphy is a derived character-state that suggests that the
several taxa that share it are closest relatives. A symplesiomorphy is a primitive state
that is shared by several taxa; the taxa that share a symplesiomorphy are not necessarily
each other’s closest relatives.
Similarity
A B C D E A B C D E A B C D E
8
10
7 9 lost
5,6
10
2,3,4 Reversal
Character 1 9
Synapomorphy Symplesiomorphy Convergence
Homology
Structures in two different species are homologous (i.e., they are homologs) if they can
be traced back to a structure in the most recent common ancestor of the two species.
Homology is similarity due to common ancestry, but the homologous structures need

5. Fall 2001 page 5
not have the identical appearance or function. Two structures that have the same
function but are not homologous are called analogs.
Two structures that are similar but not homologous are called homoplastic (regardless
of their function). Homoplasies include convergences (or parallelisms) and reversals.
Most books treat convergence and parallelism as different things in theory, but in
practice it is almost impossible to distinguish them. Structures (characters) in two taxa
are convergent if the common ancestor of the two did not possess the structure. As the
name implies, a reversal exists when a character in a taxon is not the same as that in its
immediate ancestor, but rather resembles that of a more distant ancestor. Example: the
absence of limbs in snakes is a reversal to the condition observed in fishes, because the
immediate ancestor of snakes had limbs. Although the absence of limbs in snakes and
fish is a similarity, it is a homoplasy, specifically a case of reversal.
• The members of a monophyletic group are united by homologous similarity
called synapomorphy.
• The members of a paraphyletic group are usually united by homologous
similarity called symplesiomorphy.
• The members of a polyphyletic group are usually (mistakenly) grouped
according to nonhomologous similarity called convergence.
Taxonomy
After a phylogeny is established, how is it communicated to others? The practice of
taxonomy is the naming of taxa. A particular taxonomy is a way of expressing
relationships among organisms; the word is often used as a synonym for classification.
One can visualize taxa as nested entities. Generally, systematists group species into
genera, into families, orders, classes, phyla, and kingdoms. This arrangement is called
the Linnean hierarchy and is based on Carl von Linné (Carolus Linnaeus), and the
tenth edition (1758) of Linné's book Systema Naturae. The different named levels (e. g.,
genus) of the hierarchy are categories. Categories are hierarchically arranged; that is,
they have ranks; it is possible to have taxonomies that are unranked.
Historically, systematists have made taxonomies based on some characters or attributes
by which organisms are similar or different, regardless of their phylogenetic
relationships. More recently, the emphasis is placed on taxonomies that directly reflect
phylogenetic relationships by recognizing only monophyletic groups. In the past, some
taxa were grouped together into paraphyletic groups because they shared a primitive
state or symplesiomorphy. For example, in the symplesiomorphy figure above, taxa A,
B, and C might be grouped together because they share the primitive state of a
character, and taxa D and E grouped together because they share the derived state. The
problem with grouping A, B, and C is that these taxa are not each other’s closest
relatives. Specifically, C is more closely related to D and E than to A or B, and so placing
A, B, and C in a paraphyletic higher taxon misleads us about the relationships of those
taxa.
If grouping taxa on the basis of symplesiomorphy misleads us about evolutionary
relationships, then why do it at all? The reason is that some evolutionary biologists felt
that degree of difference was also an important criterion for grouping taxa. Consider,
for example, vertebrates and invertebrates. The presence of vertebrae was considered to

6. Fall 2001 page 6
be an evolutionarily important character, and thus vertebrates had reached a certain
evolutionary level of organization, or grade. The lack of vertebrae was therefore
considered to be equally important, because quot;Invertebrataquot; were still at a lower grade or
level of evolution. Often, this distinction is based on a certain amount of anagenesis.
However, invertebrates are not a monophyletic group; some protochordates are more
closely related to vertebrates (craniates) than to other invertebrates. quot;Invertebrataquot; is
paraphyletic.
Terminology for Phylogenetic Trees
The terms cladogram, tree and phylogeny are often used interchangeably, but there are
subtle distinctions in their meaning. A tree or dendrogram is a very general word for a
branching diagram. A cladogram is a tree that shows a hierarchical distribution of
synapomorphies among taxa. A phylogeny is perhaps a more informative cladogram
that also conveys information about ancestors, descendants and their taxonomy. But for
the purposes of this course we can consider the terms to be equivalent.
The intersection of branches of a tree is called a node. Cladograms are made up of
terminal nodes representing terminal taxa, and internal nodes representing ancestors.
Reading and understanding cladograms can be tricky. The arrangement of terminal
taxa from left to right does not mean anything special. Any two sister-groups can be
rotated around their ancestral node. The lengths of branches may be proportional to
geological time, to the number of synapomorphies on that branch, or may mean
nothing.
Usually, there are only two descendants of an ancestor; this is a dichotomy. If there are
more than two descendants we call this a polytomy. Usually, a polytomy means that
the relationships among the branches that participate in the polytomy are unresolved.
An alternative, less-frequent interpretation is that there was multiple speciation at that
node.
Most of the trees we will see in the course are rooted trees; that is, they have an obvious
base, which is the root. This imparts to the tree a direction for evolutionary change.
Unrooted trees have no explicit direction of evolutionary change. For any given number
of terminal taxa, there are a certain number of possible dichotomous trees. For 3 taxa
there are 3 possible rooted trees. For 4 taxa there are 15 rooted trees. For 5 taxa there are
105 rooted trees. For 50 taxa there are more rooted trees than there are electrons in the
universe!
Phylogeny reconstruction
In phylogeny reconstruction we attempt to recover or estimate the past history by
examining the characters in the taxa we have at hand, given that we don't know what
the real tree or its synapomorphies are. One attempts to find the one (or several) of the
many possible trees that best fits the available character data. One criterion for quot;best fitquot;
is that the number of evolutionary changes in the characters is minimized or made as
small as possible. Parsimony is the name for this criterion. There are other possible
criteria for choosing among trees, such as maximum likelihood or compatibility, but

7. Fall 2001 page 7
these will not be considered in this course.
In actual practice phylogeny reconstruction is done using specialized software on a
computer. However, it is possible to reconstruct simple trees by hand. Two of the
assumptions about the characters are that they have some genetic basis (heritability)
and that they do not provide redundant information (independence). In the most
general form of tree-making, we assume that each character is equally important and
that characters can change their states in either direction (assuming there are only two
states for a character). Under the criterion of parsimony, we also assume that characters
have not changed unless their present distribution among the taxa indicates that change
must have occurred.
Usually there are two discrete conditions or states of the character, but there may be
more. If we examined the evolution a character on a rooted tree, we will see that one
state of the character was present in time before the other. The earlier state is the
primitive or plesiomorphic state (more general) of the group, and the other represents
the evolutionary novelty and is a derived or apomorphic (less general) state.
For each character, we can reconstruct a tree that best conveys the phylogenetic
information of the character. We then combine these several trees into one that best
summarizes the character information under the criterion of parsimony. In practice we
use computer software to find the best trees for a data set; it is very slow to do this by
hand, and for large numbers of taxa, it is almost impossible to find the best-fitting tree,
but we can often get close.
We will construct a tree from the following data matrix:
Characters Amphioxus Lamprey Shark Mudpuppy Snake Cat
1 Vertebrae no yes yes yes yes yes
2 Muscular heart no yes yes yes yes yes
Paired appendages
3 no no yes yes yes yes
in embryo
4 Hyomandibula no no yes yes yes yes
5 Bone no no no yes yes yes
6 Jaws no no yes yes yes yes
7 Lungs no no no yes yes yes
8 Radius/ ulna no no no yes no yes
9 Fin rays no yes yes no no no
10 Amnion no no no no yes yes
11 Metanephric kidney no no no no yes yes
The figure below gives various resolutions of the taxa for different characters. In all
cases, Amphioxus is assumed to be the outgroup. Which of the trees provides the best
fit (in terms of parsimony) to the character matrix?
Last updated by David Cannatella 9 Sep 2001.

8. Fall 2001 page 8
Amphioxus Amphioxus Amphioxus
Lamprey Lamprey Lamprey
Shark Shark Shark
1
2 3
Mudpuppy Mudpuppy Mudpuppy
4 5
6
7
Snake Snake Snake
Cat Cat Cat
Amphioxus Amphioxus Amphioxus
Lamprey Lamprey Lamprey
Shark Shark Shark
9
Mudpuppy Mudpuppy Mudpuppy
8
10
Cat
Snake Snake
11
Cat Snake Cat
Amphioxus Amphioxus Amphioxus
Lamprey Lamprey Lamprey
Shark
Shark Shark
Mudpuppy Mudpuppy Mudpuppy
Cat Snake Snake
Snake Cat Cat