An Introduction to Cladistics

This module provides a brief introduction to the philosophy, methodology, and

implications of cladistic analysis. Many of the terms that you will see along the way are
high-lighted, e.g., evolution, which means that they are included in the UCMP Glossary
of Phylogenetic Terms. Each of these terms can be clicked on for a brief definition.
After you've read through the pages on the implications and methodologies, you will be
armed in the ways of cladistics. Therefore, if you dare, you can take a journey into the
real world of cladistics. Should you choose to venture on this journey, pray you are well-
armed with good luck and wits!
Synapomorphies are the basis for cladistics
Cladistics is a particular method of hypothesizing relationships among organisms. Like
other methods, it has its own set of assumptions, procedures, and limitations. Cladistics
is now accepted as the best method available for phylogenetic analysis, for it provides
an explicit and testable hypothesis of organismal relationships.
The basic idea behind cladistics is that members of a group share a common
evolutionary history, and are "closely related," more so to members of the same group
than to other organisms. These groups are recognized by sharing unique features which
were not present in distant ancestors. These shared derived characteristics are called
synapomorphies.
Note that it is not enough for organisms to share characteristics, in fact two organisms
may share a great many characteristics and not be considered members of the same
group. For example, consider a jellyfish, starfish, and a human; which two are most
closely related? The jellyfish and starfish both live in the water, have radial symmetry,
and are invertebrates, so you might suppose that they belong together in a group. This
would not reflect evolutionary relationships, however, since the starfish and human are
actually more closely related. It is not just the presence of shared characteristics which
is important, but the presence of shared derived characteristics. In the example above,
all three characteristics are believed to have been present in the common ancestor of all
animals, and so are trivial for determining relationships, since all three organisms in
question belong to the group "animals." While humans are different from the other two
organisms, they differ only in characteristics which arose newly in an ancestor which is
not shared with the other two. As you shall see on the next page, chosing the right
characters is one of the most important steps in a cladistic analysis.
What assumptions do cladists make?
There are three basic assumptions in cladistics:
1. Any group of organisms are related by descent from a common ancestor.
2. There is a bifurcating pattern of cladogenesis.
3. Change in characteristics occurs in lineages over time.
The first assumption is a general assumption made for all evolutionary biology. It
essentially means that life arose on earth only once, and therefore all organisms are
related in some way or other. Because of this, we can take any collection of organisms
and determine a meaningful pattern of relationships, provided we have the right kind of
information. Again, the assumption states that all the diversity of life on earth has been
produced through the reproduction of existing organisms.
The second assumption is perhaps the most controversial; that is, that new kinds of
organisms may arise when existing species or populations divide into exactly two
groups. There are many biologists who hold that multiple new lineages can arise from a
single originating population at the same time, or near enough in time to be
indistinguishable from such an event. While this model could conceivably occur, it is not
currently known how often this has actually happened. The other objection raised
against this assumption is the possibility of interbreeding between distinct groups. This,
however, is a general problem of reconstructing evolutionary history, and although it
cannot currently be handled well by cladistic methods, no other system has yet been
devised which accounts for it.
The final assumption, that characteristics of organisms change over time, is the most
important assumption in cladistics. It is only when characteristics change that we are
able to recognize different lineages or groups. The convention is to call the "original"
state of the characteristic plesiomorphic and the "changed" state apomorphic. The
terms "primitive" and "derived" have also been used for these states, but they are often
avoided by cladists, since those terms have been much abused in the past.
Continue your journey by selecting one of the topics below.
Introduction to Cladistics
Methodology of Cladistics
Implications of Cladistics
The Need for Cladistics
For additional reading:
Brooks, D.R., and D.A. McLennan. 1991. Phylogeny, Ecology, and Behavior.
University of Chicago Press, Chicago. 434 pp.
Eldridge, N., and J. Cracraft. 1980. Phylogenetic Patterns and the Evolutionary
Process. Columbia University Press, New York, USA. 348 pp.
Harvey P.H., and M.D. Pagel. 1991. The Comparative Method in Evolutionary
Biology. Oxford University Press, Oxford and New York. 239 pp.
Maddison, W.P., and D.R. Maddison. 1992. MacClade: Analysis of phylogeny
and character evolution. Version 3.0. Sinauer Associates, Sunderland, MA.
D.L. Swofford. 1991. Phylogenetic Analysis Using Parsimony (PAUP), version
3.0s. Illinois Natural History Survey, Champaign, IL.
Wiley, E.O., D. Siegel-Causey, D.R. Brooks, and V.A. Funk. 1991. The Compleat
Cladist: A primer of phylogeny procedures. University of Kansas Press, Museum
of Natural History, Special Publication no. 19. 1158 pp.
More information concerning cladistics on the internet can be found in UCMP's list of
phylogenetics resources.
Still confused? Try our illustrated introduction to cladistics in the educational module,
"What Did T. rex Taste Like?"
Methodology of a Cladistic Analysis
HOW TO CONSTRUCT CLADOGRAMS
Here is an outline of the steps necessary for completing a cladistic analysis. Don't be
fooled, however, by the simplicity of these steps. Seeing a real cladistic analysis out to
fruition can be a difficult and time consuming task.
1. Choose the taxa whose evoutionary relationships interest you. These taxa must
be clades if you hope to come up with plausible results.
2. Determine the characters (features of the organisms) and examine each taxon to
determine the character states (decide whether each taxon does or does not
have each character). All taxa must be unique.
3. Determine the polarity of characters (whether each character state is original or
derived in each taxon). Note that this step is not absolutely necessary in some
computer algorithms. Examining the character states in outgroups to the taxa you
are considering helps you determine the polarity.
4. Group taxa by synapomorphies (shared derived characteristics) not
plesiomorphies (original, or "primitive", characteristics).
5. Work out conflicts that arise by some clearly stated method, usually parsimony
(minimizing the number of conflicts).
6. Build your cladogram, which is NOT an evolutionary tree, following these rules:
o All taxa go on the endpoints of the cladogram, never at nodes.
o All cladogram nodes must have a list of synapomorphies which are
common to all taxa above the node (unless the character is later
modified).
o All synapomorphies appear on the cladogram only once unless the
character state was derived separately by evolutionary parallelism.
To accomplish the task of creating a good cladogram, you must use your judgement.
Ask yourself the following questions and answer them carefully.
Could a supposed synapomorphy be the result of independent evolutionary
development?
Are your characters chosen well?
Should you consider other characters?
Should you consider additional taxa?
Continue your journey by selecting one of the topics below.
Implications of Cladistics
UNDERSTANDING BRANCHING DIAGRAMS
The output from a phylogenetic analysis is a hypothesis of
relationship of different taxa. This hypothesis can be
represented as a cladogram, a branching diagram. Cladograms
bear a lot in common with the notion of family trees. In a family
tree we trace back our ancestry. For example, in the family tree
on the right, the ancestors of all the rest of the family are the
initial black dot and yellow square. These ancestors give rise to
three children, one of which mates and has two children. We
can all trace our lineages back to one set of ancestors.
All species have ancestors too. So, for example, sometime in the past an ancestral
species (father) of Homo sapiens walked the earth. This ancestor went extinct (died),
but left descendent species (children).
In family trees, we can talk coherently about real ancestors. In biology, the ancestors
are often gone sometimes without a trace. All we have left are the children. Reading
cladograms is much like reading a family tree. Both are rich in information. Cladograms,
like family trees, tell the pattern of ancestry and descent. Unlike family trees, ancestors
in cladistics ideally give rise to only two descendent species. Also unlike family trees,
new species form from splitting of old species. In speciation, it does not take two to
tango. The formation of the two descendent species is called a splitting event. The
ancestor is usually assumed to "die" after the splitting event.
In the first tree, labelled Cladogram A, notice the small
circles. These mark the nodes of the tree. The stems of the
tree end with the taxa under consideration. At each node a
splitting event occurs. The node therefore represents the
end of the ancestral taxon, and the stems, the species that
split from the ancestor. The two taxa that split from the
node are called sister taxa. They are called sister taxa
because they are like the siblings from the parent or
ancestor. The sister taxa must each be more closely related
to one another than to any other group because they share a close common ancestor.
In the same way, you are most closely related to your siblings than to anyone else since
you share common parents. Lets focus on node C in Cladogram A. At the node, the
ancestor goes extinct but leaves two siblings hypothesized to be humans and gorillas.
Humans and gorillas are sister taxa and are more closely related to one another than
either is to chimpanzees or baboons.
Working down the tree we come to node B. At this node the ancestor of the humans
and gorillas split from the chimpanzees. Therefore the chimpanzees sister taxon is the
human/gorilla ancestor. A sister taxon can be an ancestor and all its descedents. We
call an ancestor plus all its descendents a clade. A cladogram shows us hypothesized




clades.
Finally we come to node A. Here, we find the splitting
event that led to the baboons and the ancestor to the
chimpanzees, humans and gorillas. By working our way
down the cladogram we have learned the pattern of
splitting. We have found out that chimpanzees, humans
and gorillas are more closely related to each other than
to baboons. In this example, baboons are the outgroup.
Now, how in the world did we manufacture Cladogram
A? We mentioned that it was a hypothesis. What if it we
chose another hypothesis like Cladogram B or
Cladogram C? We would change the pattern of
speciation events. In Cladogram B, humans and
chimpanzees are sister taxa and in Cladogram C, chimps
and gorillas are sister taxa.
Which of the three cladograms presented above is
correct? None of the cladograms can be proved correct, but Cladogram B is the best
supported of the three based on character data and is therefore hypothesized to best
reflect the true branching pattern.
Manufacturing cladograms which show hypotheses of ancestry and descent requires
that we analyze characters and find those characters that unite clades.
Continue your journey by selecting one of the topics below.



Why Do Biologists Need Cladistics?
Cladistics is useful for creating systems of classification.
Cladistics is now the most commonly used method to classify organisms. Why do we
need to classify organisms? Well, consider the bewildering variety of organisms that
have ever lived on Earth, from jellyfish to bacteria that's what paleontologists do for a
living. How is it possible that paleontologists, let alone other biologists, are able to
communicate their ideas about such a diverse topic as the history of life? Well, it's
obvious that a system of classification is needed. That is, we need words like beetle or
conifer so that we can talk about many organisms at one time. In fact, the history of
formal classification schemes in biology is long, dating from the 1700s, well before
Darwin proposed his theory of natural selection. Today, cladistics is the method of
choice for classifying life because it recognizes and employs evolutionary theory.
Cladistics predicts the properties of organisms.
As with any other system in science, a model is most useful when it not only describes
what has been observed, but when it predicts that which has not yet been observed.
Cladistics produces hypotheses about the relationships of organisms in a way that,
unlike other systems, predicts properties of the organisms. This can be especially
important in cases when particular genes or biological compounds are being sought.
Such genes and compounds are being sought all the time by companies interested in
improving crop yield or disease resistance, and in the search for medicines. Only an
hypothesis based on evolutionary theory, such as cladistic hypotheses, can be used for
these endeavours.
Cladistics helps to elucidate mechanisms of evolution.
Unlike previous systems of analyzing relationships, cladistics is explicitly evolutionary.
Because of this it is possible to examine the way in which characters change within
groups over time the direction in which characters change, and the relative frequency
with which they change. It is also possible to compare the descendants of a single
ancestor to look at patterns of origin and extinction in these groups, or to look at relative
size and diversity of the groups. Perhaps the most important feature of cladistic is its
use in testing long-standing hypotheses about adaptation. For many years, since even
before Darwin, it has been popular to tell "stories" about how certain traits of organisms
came to be. With cladistics, it is possible to determine whether these stories have merit,
or whether they should be abandoned in favor of a competing hypothesis. For instance,
it was long said that the orb-weaving spiders, with their intricate and orderly webs, had
evolved from spiders with cobweb-like webs. The cladistic analysis of these spiders
showed that, in fact, orb-weaving was the primitive state, and that cobweb-weaving had
evolved from spiders with more orderly webs. This situation has been repeated in many
groups with many traits, including studies of parasitism, geographic distribution, and
pollination.
This concludes the module on Cladistics. Revisit any page; additional references can be
found on the Introduction page.