Evolution and Biodiversity Laboratory

Systematics and Taxonomy

by Dana Krempels and Julian Lee
Recent estimates of our planet's biological diversity suggest that the species number between 5
and 50 million, or even more. To effectively study the myriad organisms that inhabit the biosphere,
we attempt to classify organisms into groups that reflect evolutionary relationships.

I. Taxonomy
Strictly speaking, taxonomy is the science of sorting and classifying living organisms into groups
called taxa (singular = taxon). Taxonomy also includes describing and naming the members of those
taxa. A scientist who engages in taxonomy is a taxonomist.
A taxon is a group of organisms that a taxonomist has judged to represent a cohesive unit. The
criteria used to sort specimens into various taxa are not fixed, and the science of taxonomy is not
without its internal controversies.
Taxonomists often distinguish between natural and artificial taxa. A natural taxon is constructed
on the basis of evolutionary relationships. While not all taxonomists insist that taxa be natural, most
believe that taxonomic groups should consist of evolutionarily related units. The science of
determining evolutionary relationships among taxa is known as systematics, and its practitioners are
systematists. (Most systematists are also taxonomists, and vice versa.)
Since systematists are concerned not only with the ability to sort and identify organisms, but also
with determining their evolutionary relationships, taxonomy is used as a tool within systematics.
Biological nomenclature is the application of names to organisms recognized as part of a
particular taxon. From most to least inclusive, the major taxonomic ranks are shown in Figure 1.

Figure 1. The Linnaean taxonomic hierarchy.

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 Each Domain contains related Kingdoms. Each kingdom consists of related phyla. Each
phylum consists of related classes, classes of related orders, orders of related families, families of
related genera (singular: genus) and genera of related species.
(“King Philip came over from Germany stoned.”)
Between the major taxonomic ranks may be larger and smaller taxa such as subkingdoms,
superphyla, subclasses, infraorders, subspecies, etc.
Every described, named organism is nested into a complete organizational hierarchy, from
species through domain.
The scientific name of an organism (its genus and species) is always written with the genus
capitalized and the specific epithet in lower case. Because the words are Latinized, they
should be italicized.
This system of nomenclature was created by Swedish botanist Carl Linne, who published it as
Systema naturae, in 1735. Linne Latinized his own name to Carolus Linnaeus, and we remember
him today as Linnaeus, the father of modern taxonomy.
A. The Aspects of a Taxon
A taxon is generally considered to have three aspects:

1. The taxon's name.

The name of the taxon to which all flesh-eating mammals with specialized cutting teeth called
carnassials belong is Carnivora. The name of the taxon containing all domestic dogs is Canis
familiaris. You get the idea.
A scientific name has no more significance than any other convenient label used to describe a
group of similar items. Names such as "Bacteria," "Felidae" and "Oryctolagus cuniculus" are similar in
function to descriptive names of similar objects, such as "shoes" or "machines."
Don't let names confuse or intimidate. Once you know the Latin or Greek word roots, seemingly
complicated names make perfect sense and become easier to remember. For example, the name of
Eleutherodactylus planirostris, a little frog naturalized in southern Florida gardens, can be broken
down into its Greek roots: eleuthero, meaning "free," dactyl, meaning "toe," plani, meaning "flat" and
rostris, meaning "nose." Our pal is just a flat-nosed frog with unwebbed (“free”) toes!

2. The taxon's rank.

Like the taxon's name, the taxon's rank has no real biological significance. It serves only to help
the biologist locate the taxon within its hierarchy. For example, the taxon “Eukarya” is currently
assigned the rank of domain. The taxon “Mammalia” is currently assigned the taxonomic rank of
class.
A taxon’s rank can change. You may notice that a given taxon's rank may not always be the
same in every source you read. Some publications may refer to Basidiomycota (Club Fungi) as a
phylum, whereas others might refer to it as a subphylum. Classifications change as new data become
available.
The relative rank of a taxon within its larger and smaller groupings is more relevant than the rank
itself. For example, it's important to know that all members of Felis are classified within the larger
taxon "Carnivora," and that all carnivores are classified within the still larger taxon "Mammalia." It's
less important to struggle to recall that "Carnivora" is an order and "Mammalia," is a class.
Many institutions use a rankless system. In this system, a taxon is described only by its name.
The rank is left off, but tacitly understood. An author using this system will write "Mammalia" rather
than "Class Mammalia" avoiding confusion if its rank changes.

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3. The taxon's content.
All the students in your lab are (probably) members of the genus Homo and the species Homo
sapiens. To the systematist, this is perhaps the most relevant aspect of the taxon. By grouping
individuals within a single species, related species within a single genus, related genera within a
single family and so on, the systematist tells us which organisms share common evolutionary
ancestry.
Organisms are not classified randomly. The systematist uses morphological characters, DNA
sequencing, protein analysis, developmental biology, karyology, ultrastructure and other information
to determine evolutionary relationships.

B. The Taxonomic Key: A Tool for Identification

When an investigator must identify an unknown specimen, a useful tool is the taxonomic key. A
taxonomic key is constructed as a series of paired statements/descriptions based on similarities and
differences between taxa in a group being identified. Because the key branches in two at each stage,
is called a dichotomous (from the Greek dicho meaning "in two" or "split" and tom, meaning "cut")
key.
Paired statements describe contrasting characteristics found in the organisms being classified.
With the specimen at hand, the investigator chooses which of the paired statements best matches the
organism. The statement selected may immediately identify the specimen, but more often it will direct
the user to the next set of paired, descriptive statements. At the end--if an appropriate key has been
used (e.g., you wouldn't use a book called Key to the Flora of Southern California to identify an
unknown tree you've discovered in Guatemala)--the specimen is identified by name.
Sometimes a key for identification of a specimen you have at hand simply doesn't exist, and you
must go to the primary literature to see if any species descriptions match it. Identification of unknown
species can be a difficult and challenging enterprise. Fortunately, the specimens you're going to use
in today's first exercise are not only easily recognizable, but also included in a ready-made key.

Exercise I. Using a Taxonomic Key

Work in pairs for this exercise. At your station you will find several containers filled with
"species" of pasta native to the United Aisles of Publix. The noodles have an evolutionary
relationship to one another: They all are members Order Semolina, which evolved from an ancestor
resembling a soda cracker. The taxonomic key—which may or may not reflect their evolutionary
relationships—is a tool that allows identification of an individual pasta to its proper taxonomic group.
In this case, the key identifies each type of pasta to genus and species.
Let's key out (a jargon-y verb commonly used to describe the process of identifying things with a
taxonomic key) some pasta! Select one individual from each of the containers, place it in one of the
plastic cups provided, and then use the taxonomic key below to identify each pasta individual to its
correct genus and species.
A NOTE OF CAUTION: Be careful when choosing which of the two character states in the key
your pasta actually exhibits. What exactly is its skin? What is its body? What is its body form?
Confusing traits can cause incorrect identification.
This is true in real keys used to identify real organisms, too. Character states are not always
obvious, and some types of organisms (Chenopode plants!) are notoriously difficult to identify, even
with an excellent taxonomic key. So proceed with caution, and if you do make an error, go back and
start from the beginning.

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 A TAXONOMIC KEY TO THE
PASTA OF SOUTHERN FLORIDA
1a. Body tubular in shape ……...…...………………….......................……...….....….… 2
1b. Body not tubular …………….……………………….......................……........…....… 4

2a. Skin lined with small, symmetrical ridges ……....................…………...…......…… 3

2b. Skin smooth …………………………….........….....................................… Ziti edulis

3a. Anterior and posterior ends of organism slanted …............................. Penna rigata
3b. Anterior and posterior ends of organism
perpendicular to body axis …………………..........................…. Rigatonii deliciosus

4a. Skin lined with small, symmetrical ridges ……….......................… Conchus crispus
4b. Skin not lined with ridges ………………………..…….......................……………… 5

5a. Body cylindrical in overall shape ……………..............................…… Rotinii spiralis

5b. Body dorsoventrally flattened in shape ……...................................... Farfalla aurea

Write the name of each type of pasta underneath its picture below.

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Exercise II. Creating a Taxonomic Key
Work in pairs for this exercise. Now that you have seen how simple it is to use a taxonomic
key, you should be able to create one. At your station you will find a set of eight cards bearing
pictures of imaginary animals. These hypothetical animals, created and "evolved" by J. H. Camin,
Professor of Biology at the University of Kansas, are called Caminalcules. (An “animalcule” is a
small animal). Caminalcules have served as test material for a number of experiments in systematic
theory and practice. Use of imaginary organisms for such studies offers a distinct advantage over
using real groups, because preconceived notions and biases about classifications and evolutionary
relationships can be eliminated.
Create a dichotomous key of your Caminalcule species (omit the OUTGROUP, on the light gray
card; use only the numbered Caminalcules). Refer to the pasta key from the previous exercise to
guide your organization. There's no single correct way to create a taxonomic key. The one you used
to identify your pasta “species” could have been arranged in many other ways. It is not required that
a key reflect evolutionary relationships, though many keys do. Once you have completed the second
part of today’s lab (Systematics), you’ll be better prepared to create a key that reflects common
ancestry. But for now, it’s not necessary.
Use your paperback copy of A Guide to Greek and Latin Word Roots by Donald J. Borror to create
a Latinized scientific name (consisting of genus and species) for each of your species, and try to be
as descriptive as possible with the name. (Some of your individuals might be in the same genus. It's
for you to decide.) Use proper Systema naturae rules in naming your species: Genus capitalized,
species lower case, and name italicized. (If you don’t have a copy of the Borror book, you may get a
loaner from your TA, in exchange for your Cane Card. No Cane Card, no loaner.)

A Taxonomic Key for Identification of Caminalcules

1a. ……..
1b. ……..

2a. ……..
2b. ……..

3a. ……..
3b. ……..

4a. ……..
4b. ……..

5a. ……..
5b. ……..

6a. ……..
6b. ……..

7a. ……..
7b. ……..
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 Once you have finished your key, trade it AND the cards used to devise it with the lab partners
across the table from you. (Each team has a different set of Caminalcules, so you’ll need to use the
other team’s cards, too.) Using each other's keys, try to identify all of each other’s species correctly.
When you have identified them all, check with your “swap buddies” to see how well you did.

II. Systematics
Because new data constantly change our understanding of evolutionary relationships,
classifications are constantly updated and changed. The goal of most modern systematists is to
construct monophyletic taxa, which reflect true evolutionary relationships by including all
descendants of a single common ancestor. Various lines of evidence can be used to determine the
degree of common ancestry between two taxa, including comparison of morphology (at many levels,
including cellular), nucleic acid sequence, protein sequence, embryo development, etc. As new
technologies arise, our ability to study evolutionary relationships evolves.
A. Reconstructing Phylogenies
A phylogeny is a history of the evolutionary descent of extant (i.e., presently living) or extinct
(i.e., no longer living) taxa from ancestral forms. To date, about 1.4 million species (including
750,000 insects, 250,000 plants and 41,000 vertebrates) of the 5 to 50 million on earth have been
scientifically described and classified.
What is a species? Although biologists still debate the precise definition, we shall use the
biological definition of a species as a group of actually or potentially interbreeding natural
populations which are reproductively isolated from other such groups. More simply, two
organisms can be considered members of the same species if they can breed to produce fertile,
viable offspring under natural conditions.
1. Primitive vs. Derived Characters
Ever since Darwin's publication of On the Origin of Species by Means of Natural Selection, the
scientific community has labored to understand how different species arise. We know that extant
species evolved from previously existing ancestral species, and that this may involve descent with
modification of traits (= characters) from one generation to the next. Terminology:

• primitive character (plesiomorphy) shows little or no change from the same character in an
ancestor
• symplesiomorphy (literally "shared primitive character") is a primitive character shared
between two or more taxa
• derived character (apomorphy) has changed in appearance and/or function relative to the
same character in an ancestor
• synapomorphy (literally "shared derived character") is a derived character shared between
two or more taxa
All living things exhibit these most basic symplesiomorphies:
1. Organization of structure (anatomy)
2. Capacity to generate more organisms like themselves (reproduction)
3. Growth and development
4. Ability to utilize energy to do work (metabolism)
5. Response to environmental stimuli (reaction)
6. Regulatory mechanisms to keep the internal environment within tolerable limits (homeostasis)
7. Populations that change in gene composition over time (evolution)

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 Consider: Would your knowing only that a living thing has the ability to maintain homeostasis help
you distinguish it from other living things? Would knowing only that it could reproduce allow you to
tell it apart from other living things? Simple answer: NO. Shared, primitive characters are not
informative to someone trying to sort the organisms into smaller, less inclusive groups.
In classifying members of a taxon, the systematist must consider characters that make the
individuals in that taxon unique and different from members of other taxa. To achieve this end,
synapomorphies unique to that taxon are informative and useful. The next section explains why.

2. Symplesiomorphies vs. Synapomorphies

Because all living things share evolutionary history, however distantly, each taxon shares certain
very ancient (i.e., primitive, or plesiomorphic) characters with other taxa. Shared, primitive
characters cannot be used to separate members of different taxa, since everyone has them.
However, more recently evolved (i.e., derived, or apomorphic) characters can set one taxon apart
from another. Synapomorphies inherited from a common ancestor can inform the systematist about
relative recency of common descent. The more synapomorphies two taxa have in common, the
more recently they evolved from a common ancestor.
We humans share certain characters, unique to animals, with all other animals but not with plants,
fungi, protists, or bacteria. List five characters unique to humans and all other animals, but not found
in any other living things (e.g., plants, fungi):
1.
2.
3.
4.
5.
Important: the characters you listed above--exhibited by no living organisms except animals--are
considered symplesiomorphies only with respect to Animalia. But if you include all living things, then
these same animal characters become synapomorphies that set animals apart from all other living
things. A character cannot be "primitive" or "derived" in a vacuum. It can be described with these
terms only when taxa and their characters are being compared.
With this in mind, list three derived characters that set mammals apart from all other animals:
1.
2.
3.
Do you exhibit all three of the characters listed? (Good! You're a mammal!) Since you share those
characters with all your mammalian relatives, the characters are said to be primitive with respect to
all mammals, though they are derived with respect to all animals other than mammals.
See the pattern? Because you share the three characters above with all other mammals, those
characters won't help you determine how closely related you are to any other mammal groups.
Hence, we must consider synapomorphies at the next level, to separate our taxonomic group within
the rest of the mammals.
List three derived characteristics shared by all primates (Primates, of which you are a member), but
not shared by other mammals. (You might have to do some searching.)
1.
2.
3.
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 What you have listed are three synapomorphies shared by Primates that set them apart from all
other mammals. But because all primates share these three characters, they are symplesiomorphies
with respect to only primates. In other words, these three characters will not help you to determine
which primates are your closest relatives. To do that, we must find more unique derived characters.
List two derived characteristics shared by all great apes (Hominidae, of which you are a member),
but not shared by other primates. Again, you might have to do some searching. Notice that it can
become more difficult to find synapomorphies linking particular members into a single as the taxon
becomes smaller/less inclusive, because organisms that share recent common ancestry may have
more in common than not.
1.
2.

Finally, list as many derived characters as possible that make Homo sapiens different from all
other great apes. Be sure to restrict your list to truly BIOLOGICAL characters--not cultural ones.
(This is where it gets really challenging, and sometimes there is simply not a clear line to draw,
especially where cultural influences ("nurture") interact with a truly genetic and heritable ("nature")
character.)
1.
2.
3.
4.
5.

As you can see, it is not a simple task to find biological characteristics that truly separate Homo
sapiens from other species of great apes. In fact, we share more than 99% of our genes with our
closest ape relatives, the Common Chimpanzees (Pan troglodytes) and Bonobos (Pan paniscus).
Take a look back at the several lists you have made, and note how synapomorphies identified at
higher and higher resolutions help us to determine most recent common ancestry among the various
taxa. Systematists use this method to construct and revise phylogenies for all living things.

3. Homologous vs. Analogous characters

If the similarity between two characters in two separate taxa can be attributed to their presence in
a common ancestor, then those two characters are said to be homologous. For example, the
forelimb bones of all tetrapod (four-legged) vertebrates are homologous to one another, because they
all evolved from the same bones in a common tetrapod ancestor. Although the bones may have
evolved very different sizes, shapes, and functions, they all developed from the same embryonic
sources and have evolved from the same ancestral tetrapod limb bones.
List five homologous characters you share with all other vertebrates that perform a similar function
in you and all other vertebrates:
1.
2.
3.
4.
5.

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Now list five homologous characters you share with other vertebrates that have evolved to serve a
different function in you than they serve in some other vertebrates:
1.
2.
3.
4.
5.
Of the five characters you just listed, which are unique to Homo sapiens, and which are shared by at
least some other vertebrates? What does this say about the recency of your common ancestry with
those other vertebrates?

Not all physical similarities are homologous. In many cases, unrelated taxa have evolved
superficially similar morphologies in response to similar natural selection pressure. For example, a
shark and a dolphin both share a streamlined, fusiform shape well adapted for swift swimming.
However, while the shark's body evolved from a fishlike ancestor with a somewhat fusiform shape,
the dolphin's fishlike form is secondarily derived from that of a terrestrial, four-legged mammalian
ancestor.
The superficial similarity of shark and dolphin is a result of convergent evolution. Specifically,
what is meant by the term "convergent" evolution?

Characters that have evolved similar form and function from disparate ancestral sources are said
to be analogous. Analogous characters are sometimes called homoplastic characters or
homoplasies (from the Greek homo, meaning “alike” and plas, meaning “shape”).
Don’t let the similarity of the terms "homoplastic" and "homologous" confuse you! Look up their
root derivations in your Dictionary of Word Roots and Combining Forms (Donald Borror). Write their
exact, translated meanings here:
homo (Greek) =
plas (Greek) =
analog (Greek) =
List five characters you have that are analogous to characters with the same function but of different
ancestral origin in any other species.
1.
2.
3.
4.
5.

B. Modern Systematics: The Cladistic System

The Cladistic System of classification was first published by German zoologist Willi Hennig in
1950. The cladistic system is an objective and quantitative method of modern classification, and it is
to its tenets that we—and the vast majority of modern systematists--adhere.
In the Cladistic System, organisms are classified exclusively on the basis of recency of descent
from a common ancestor. Taxonomic/phylogenetic relationships are determined strictly on the basis
of synapomorphies. The presence of many shared derived characters among taxa is considered
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strong evidence of their common descent. Differences in the degree or rate of change among
branches of organisms are irrelevant to their classification. For example, the cladist recognizes that
birds--despite their plumage (modified scales homologous to reptile scales) and "warm-bloodedness"-
-share a more recent common ancestor with crocodilians than with other vertebrates. Birds and
crocodilians (and their extinct relatives) are classified together in Archosauromorpha (literally “ancient
lizard form”). In the old system (Classical Evolutionary Systematics), birds were place in their own
class (“Aves”), and crocodilians in a different class (“Reptilia”) that did not reflect their common
ancestry. Those two old names are now pretty much defunct, except when they are used as common
names.
C. Phylogenetic Trees
By considering synapomorphies and symplesiomorphies and by identifying homoplasies, the
systematist attempts to construct phylogenies that reflect natural evolutionary relationships.
Phylogenies can be represented as treelike diagrams showing how various extant taxa branched
from common ancestors and from each other. Such a diagram is called a phylogenetic tree or
evolutionary tree (Figure 2).
A phylogenetic tree shows putative evolutionary relationships. Taxa are represented as branches
that bifurcate from nodes. A node represents the hypothetical common ancestor of the taxa on the
branches above it on the tree, and it also represents the taxonomic unit (order, family, genus, etc.)
that contains the taxa represented by the branches. Nodes are considered hypothetical ancestors
(also known as hypothetical taxonomic units, or HTUs) because they cannot be directly observed.
The base or root of the tree represents the hypothetical common ancestor of all the groups (clades)
on the tree.
Phylogenetic trees may be represented in many different ways, some of which are shown in
Figure 2. But the different diagrams all provide similar essential information.

Figure 2. A phylogenetic tree. The taxa included are “human,” “zebra,” and “goldfish.” Each
node represents the common ancestor of the taxa to the right of it on the tree. All taxa
descended from a common ancestor comprise a clade. (Human and Zebra comprise a single
clade; Human/Zebra/Goldfish comprise another, more inclusive clade that will have a higher
taxonomic rank than the clade including only Human and Zebra.) Branches diverge from
nodes, and represent a genetic unit descended from the ancestor at that node. The root
represents the common ancestor of all taxa included on the tree.

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 The phylogenetic tree in Figure 2 shows only recency of common descent. It does not indicate
which species might be (subjectively) described as "primitive" or "derived" (Those terms should be
used to describe characters; they are meaningless when applied to an entire species.)
Note that two lineages branching from the same ancestor arose at the same geological time.
Many people hold the misconception that Homo sapiens is the “most highly evolved” species, or even
the most recently evolved. Neither is true. View Figure 3 below and remember the following rules.
Rule #1: The branches at every node can be rotated. The branches do not imply any sort of
order; they indicate only recency of common descent. In Figure 4, the node at Ancestor F (Figure 4a)
could be rotated so that the tree looked like the one shown in Figure 4b. The information given would
be exactly the same. Any node on the tree can be rotated in a similar fashion.
Rule #2: Two lineages branching from a single ancestral node are known as sister taxa.
Further specialization after a branch point is irrelevant. Therefore, it would be incorrect to say that
humans evolved more recently than chimpanzees, or that humans should be placed in their own
family simply because they seem so different from chimpanzees. Taxonomic groupings are based on
common ancestry only, not subjective perceptions of specialization.
Rule #3: There is no such thing as a “most highly evolved species”. All extant species are
descended from successful ancestors, and are evolved to survive and reproduce in the context of
their specific environment. Evolution is a process. It has neither a goal nor a subjective value
system.
Rule #4. No extant nor extinct taxon is considered ancestral to any other extant or extinct
taxon. Nodes represent hypothetical ancestors, not taxonomic units. When an ancestral lineage
diverges to become two separate taxa, the ancestral lineage (hypothetical ancestor) is considered
extinct, even if one of the descendant taxa is (or might be) virtually the same as that hypothetical
ancestor. This should be remembered when one hears the oft-repeated, but incorrect statement
“humans evolved from monkeys”. They did not. Humans and monkeys share a common ancestor.
That’s not the same thing.

Figure 3. Different graphic representations of phylogenies. Whether a tree is upright, on its

side, or drawn as an emerging spiral, the information is essentially the same. Nodes
represent common ancestors of taxa (branches) above them on the tree, and endpoints
represent taxa—whether extinct or extant—in the phylogeny.

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 •
•
• Figure 4a. Phylogeny of Primates. The nodes from which branches emerge represent
the hypothetical common ancestor of all taxa above that node on the tree. The
endpoints of the branches represent the descendants of that ancestor. Some
phylogenetic trees include both extinct and extant (still living) taxa. In modern
systematics, extinct taxa (represented by fossils) are treated the same way as extant
taxa, and are not considered ancestral to extant taxa.

•
• Figure 4b. Phylogeny of Primates demonstrating a rotation of the node at Ancestor G,
relative to the original drawing shown in Figure 3a. Rotating the node in this manner
does not change the phylogenetic information.

Figure 4 shows nine lineages of extant primates. Located beneath (to the left of) them on the tree
are their hypothetical ancestors.
• The Ancestral Primate gave rise to all primates.
• Ancestor A is gave rise to Tarsiers and Anthropoids, but not Lemurs and their kin.
• Ancestor E is the most recent common ancestor of all Great Apes, but not Gibbons.
• Ancestor G gave rise only to humans, chimpanzees and bonobos.

In trees such as those shown in Figure 4, the length of branches is not proportional to the degree of
change from an ancestor or from related taxa. Such a tree is said to have unscaled branches.
Time of divergence is shown by the time scale at the bottom of the diagram.

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Modern systematics is done largely with molecular data, and it is now possible to quantify the degree
of difference in DNA sequences. Scaled branches, such as those on the trees shown in Figure 5,
indicate degree of divergence between taxa. (The unit is specified by the authors. For example, one
unit might represent 1% of difference between two DNA or RNA sequences.)

Figure 5. Scaled branches (top) can be used to indicate the degree

of divergence between taxa on the tree, with respect to a particular
character. Trees with unscaled branches indicate time of divergence
with a time scale.
(Source: http://www.ncbi.nlm.nih.gov/About/primer/phylo.html)

The trees above all have a hypothetical ancestor their roots. Sometimes, however, the
hypothetical ancestor is not known, and cannot be included on a phylogenetic tree.
Rooted and Unrooted Trees
Rooting a tree is determining the location of the hypothetical common ancestor with respect to the
other taxa on the tree. Because we have seen only rooted trees so far, this might seem like a no-
brainer. But it’s not always simple. Raw phylogenetic data often yield unrooted trees.
In an unrooted tree (Figure 6) there is no hypothetical ancestor, and no directionality to the tree.
The tree shows only the putative evolutionary relationships of the taxa on the tree, without the
evolutionary directionality implied by an ancestor.

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 Figure 6. Trees can be rooted or unrooted (Source:
http://www.ncbi.nlm.nih.gov/About/primer/phylo.html)

In rooted trees, each node represents the most recent common ancestor of the taxa branching
from it. Rooted trees are directional, with all taxa evolving or radiating from that single common
ancestor at the root. In rooted trees, each ancestor is united to each node by a unique (evolutionary)
path.
Clearly, unrooted trees are not as informative as rooted trees. In order to root a tree, one must
consider a taxonomic unit that is closely related to, but phylogenetically outside, the group of taxa
being studied. This closely related group is known as the outgroup. The outgroup is known to be
more distantly related than the ingroup (the taxa of interest). It serves as a sort of “reference” group
so that primitive characters common to taxa being studied can be identified: Characters common to
both the outgroup and the taxa being classifed are considered primitive to the entire assemblage. For
example, if you were trying to determine symplesiomorphies of various species of Canidae (dog
family), you might use a bear (Ursidae) as your outgroup (Figure 7).

Figure 7. Hypothetical phylogeny of canid taxa, with member of

Ursidae (Polar Bear) as outgroup. Characters common to the bear
and the canids should be considered symplesiomorphies with
respect to the canids of interest, and not used to construct less
inclusive canid taxa.

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Monophyly, Polyphyly, Paraphyly
A phylogenetic tree is not constructed randomly. The systematist uses data on morphology,
homology of nucleic acids, congruence of similar proteins, etc. to determine recency of common
descent.
A clade is a group of species that includes an ancestral species and all of its descendants. Such
a group is said to be monophyletic. The systematist uses cladistic techniques to construct
monophyletic phylogenies that reflect true common ancestries. However, this is not always easy.
When new data become available, it is sometimes discovered that a taxon under study is not
monophyletic.
A paraphyletic taxon fails to include all descendants of a particular common ancestor. A
polyphyletic taxon includes members that have descended from more than one different ancestor,
but the common ancestor of those has not been included. These are illustrated in Figure 8.

Figure 8. Representative vertebrate taxa are grouped in monophletic (a), paraphyletic (b) and
polyphyletic (c) assemblages, shown by blue shading. Note that the paraphyletic tree (b) shows the
traditional, evolutionary system for classifying Reptilia (turtles, crocodilians, snakes, and lizards),
which does not reflect actual evolutionary relationships. Reptilia can be made monophyletic by
including Aves (birds). The polyphyletic tree (c) illustrates what can happen when organisms are
classified on the basis of superficial similarity, such as “warm bloodedness” or “four-chambered
heart”. These characters most likely evolved independently in mammals and in birds.

Using some of the characteristics of the pasta you met earlier in this exercise, we have constructed a
hypothetical phylogenetic tree showing their possible evolutionary relationships. (Figure 9) This may
not be the only possible tree. The more data used, the more likely the tree will reflect actual
evolutionary relationships. Notice that each character that sets a particular species apart from the
others appears as a hashmark on the branch of the tree leading to that taxon.

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 Figure 9. A hypothetical phylogeny of the pasta of the United
States. The hash-marks along the tree indicate the appearance of
synapomorphies found only in the taxa above that character on the
tree. A flat noodle serves as the ougroup, indicating the primitive
condition of the characters used to group the taxa.

Exercise III. Constructing a Phylogenetic Tree

Classifications should be natural, meaning that they reflect evolutionary. We do not, for example,
place slime molds and whales in the same family. Systematics, then, is a two-part endeavor. First,
one must erect an hypothesis of evolutionary relationship among the organisms of interest. Second,
one must devise a classification scheme that faithfully reflects the hypothesized relationship. We will
use our Caminalcules to create a phylogenetic tree.
Examine the Caminalcules in Figure 10. These will be your Operational Taxonomic Units (OTUs)-
-a name we use to avoid assigning them to any particular taxonomic rank (such as species). Think of
them as biological species, and refer to them by number.

Figure 10. A variety of Caminalcules, arranged in no particular order.

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Using Synapomorphies to Construct a Phylogeny
In the Cladistic System, the investigator groups OTUs together on the basis of synapomorphies.
The presence or absence of a synapomorphy in two or more OTUs is inferred to be the result of
inheritance (or lack thereof) from their common ancestor.
Results of a cladistic analysis are summarized in a phylogenetic tree called a cladogram (from
the Greek clad meaning "branch"), an explicit hypothesis of evolutionary relationships. You already
have seen an example of a cladogram, and know that monophyletic taxa are constructed on the basis
of synapomorphies unique to each group. Now you’ll get to do one yourself! Oo!

Step One. Select a series of characters that can be expressed as binary (i.e., two-state).
For example:
Character a: "eyes present" (+) versus "eyes absent" (-)
Character b: "body mantle present" (+) versus "body mantle absent" (-)
Character c: "paired, anterior non-jointed appendages present" (+) versus
"paired, anterior non-jointed appendages not present" (-)
Character d: "anterior appendages flipperlike" (+) versus
"anterior appendages not flipperlike" (-)
Character e: "eyes stalked" (+) versus "eyes not stalked" (-)
Character f: "body mantle posterior bulbous" (+) versus
"body mantle posterior not bulbous" (-)
Character g: "eyes fused into one" (+) versus "eyes separate" (-)
Character h. "forelimbs with digits" (+) versus "forelimbs without digits" (-)

Step Two. Examine all your organisms and determine which character state it exhibits. Enter the
data in a matrix like the one shown in Table 1.
Note that in this example, character a (presence or absence of eyes) and character b (presence or
absence of a body mantle) is the same in all eight OTUs. Hence, this (primitive) character is not
useful to us in finding differences between the OTUs.
Note also that only OTUs 2 and 7 share character e (stalked eyes), which is absent from all other
OTUs. This suggests that OTUs 2 and 7 both inherited this character from a common ancestor.
Likewise, OTUs 1, 4, and 6 share character f (bulbous mantle posterior), which is absent from all
others. This supports the hypothesis of common ancestry among OTUs 1, 4, and 6. The same
reasoning argues for common ancestry between OTUs 3 and 5 (character h), and so on.

Table 1. Character states of characters a - h in Caminalcules in Figure 10.

character 1 2 3 4 5 6 7 8
a + + + + + + + +
b + + + + + + + +
c + + - + - + + +
d - + - - - - + -
e - + - - - - + -
f + - - + - + - -
g + - - - - - - -
h - - + - + - - -
A cladogram consistent with the distribution of these eight characters among the eight OTUs is
shown in Figure 11.

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 This is not the only possible phylogeny consistent with the character distribution among the OTUs.
In practice, there are often several--or even many--cladograms consistent with the data. In such
cases, systematist generally applies a parsimony criterion for selecting the "best" cladogram. The
rule of parsimony states that when two or more competing hypotheses are equally consistent
with the data, we provisionally accept the simplest hypothesis. This is not to say that evolution
is always parsimonious, only that our hypotheses should be.
In the case of competing cladograms, the rule of parsimony would require that we accept the
simplest cladogram, the one with the fewest "steps" to each of the taxa on the tree. In our example,
we could hypothesize that OTU 6 is actually more closely related to OTU 1 than to OTU 4. However,
this would require that character g (fused eyes) had evolved once, and then secondarily lost in both
OTUs 4 and 6. This is less parsimonious than stating fused eyes evolved only once, in OTU 1 only.

Figure 11. A cladogram based on synapomorphies in Caminalcules 1 - 8.

Cladistics and Linnaean Classification
Given an hypothesis of evolutionary relationships, the second step in biosystematic endeavor is to
erect a classification that faithfully reflects those relationships. Because the results of a cladistic
analysis (i.e., the cladogram) are heirarchical, they can easily be incorporated into the Linnaean
hierarchy, as shown in Figure 12. (Remember Linnaeus? If not, go back and review.)
In cladistic analysis, all taxa must be monophyletic, meaning that they must include the common
ancestor (almost always hypothetical) and all descendants of that common ancestor. Thus, in the
cladogram above, OTUs 2 and 7 together with their common ancestor (at the branch point just below
them) constitute a monophyletic genus, as do OTUs 1,4,6 and 8 and their common ancestor (at the
branch point just above the appearance of character d).
A Family consisting of only OTUs 2 and 7 would not be monophyletic, because it does not include
all the descendants of the common ancestor (at the branch point just below character d). Such a
group would be considered paraphyletic (containing some, but not all, of a particular ancestor's
descendants).

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 A Family consisting of OTUs 2 and 7 plus OTUs 3 and 5 would be considered polyphyletic
(consisting of species derived from more than one most recent common ancestor). This is because
such a taxon would be made up of groups descended from both the ancestor just below the
appearance of character h, and the one just below the appearance of characters c and e.
Order Caminalcula:
Family 1
Genus 1
Species 2
Species 7
Genus 2
Species 1
Species 4
Species 6
Species 8
Family 2
Genus 3
Species 3
Species 5

Figure 12. Incorporated results of a cladistic analysis showing Linnaean relationships among
the OTUs.

Exercise: Constructing a Cladogram Based on Synapomorphies

Using the Caminalcules in the packet at your lab station, go through the steps of sample cladistic
analysis we did for the Caminalcules in Figure 10. Use the Tables 3 and 4 to list shared, derived
characters that help you group the OTUs into taxa that reflect their (hypothetical) evolutionary
relationships. Finally, in the space provided, draw a cladogram of your Caminalcules, showing the
appearance of each character, as in Figure 9. Is it rooted or unrooted? Be careful!

Outgroup Analysis: Rooting the Tree

As you may already realize, your phylogenetic tree of Caminalcules should be unrooted because
you have no way to know which character states are derived. One is tempted to automatically
assume that a more complex form is the more derived state. However, there is always the chance
that a taxon has lost an ancestral character (or character state). (Can you think of any examples in
our own species?)
To root your tree, you will need to consider the character states in an outgroup. The deck of
Caminalcule cards your team will use has an outgroup on a light grey card. Your outgroup is one
individual of a species of Caminalcules related to your ingroup (the rest of the Caminalcules on your
cards). Use the outgroup to root your tree. Note that the rooted tree may be quite different from your
unrooted one.

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Table 3. Character states in Caminalcule Packet.
character state of character if (+) state of character if (-)
a
b
c
d
e
f
g
h

Table 4. Synapomorphies in Caminalcule Packet.

OTUs
character
a
b
c
d
e
f
g
h
A Cladogram of Caminalcules:

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A Rooted Cladogram of Caminalcules:

You did it!

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