Looking at Evolutionary
History with Phylogenetics
and Cladistics
Fred Brown
Science Education Consultant
fredbrown3@aol.com
Emil Hans (Willi) Henning (1917-1976)
http://palaeoblog.blogspot.com/2007/04/born-this-day-willi-henning.html
German entomologist
 Henning developed a mechanism
(cladistics) to find evolutionary pathways
among related organisms
 It is based upon morphology and on many
kinds of evidence, including molecular
sequences (Old methods used only
morphology)
 The pathways are determined by shared
derived characteristics (synapomorphies)
 Rather than putting organisms into
Linnaean taxonomic “boxes,” the
cladistics process shows the evolutionary
pathways
Phylogenetic Systematics,
a.k.a. Evolutionary Trees
Phylogenetic systematics is the formal
name for the field within biology that
reconstructs evolutionary history and
studies the patterns of relationships
among organisms.
Unfortunately, history is not something
we can see. It has only happened once
and only leaves behind clues as to
what happened. Systematists use these
clues to try to reconstruct evolutionary
history.
Phylogenetic Systematics:
Definitions
 Taxonomy is the ordered division and naming of
organisms
 Phylogeny is the evolutionary history of a species or
group of related species
 The discipline of systematics classifies organisms
and determines their evolutionary relationships
 Systematists use fossil, molecular, and genetic data
to infer evolutionary relationships
 Systematists depict evolutionary relationships in
branching phylogenetic trees
Understanding Phylogenies
Understanding a phylogeny is a lot like reading a family
tree. The root of the tree represents the ancestral lineage,
and the tips of the branches represent the descendents of
that ancestor. As you move from the root to the tips, you
are moving forward in time.
Understanding Phylogenies
When a lineage splits (speciation), it is represented as
branching on a phylogeny. When a speciation event
occurs, a single ancestral lineage gives rise to two or
more daughter lineages.
Understanding Phylogenies
Phylogenies trace patterns of shared ancestry between
lineages. Each lineage has a part of its history that is
unique to it alone and parts that are shared with other
lineages.
Understanding Phylogenies
Similarly, each lineage has ancestors that are unique to
that lineage and ancestors that are shared with other
lineages — common ancestors.
Understanding Phylogenies
A clade is a grouping that includes a common ancestor
and all the descendents (living and extinct) of that
ancestor. Using a phylogeny, it is easy to tell if a group of
lineages forms a clade. Imagine clipping a single branch
off the phylogeny — all of the organisms on that pruned
branch make up a clade.
Understanding Phylogenies
Clades are nested within one another — they form a
nested hierarchy. A clade may include many thousands of
species or just a few. Some examples of clades at
different levels are marked on the phylogenies below.
Notice how clades are nested within larger clades.
The tips of a phylogeny represent descendent lineages.
Depending on how many branches of the tree you are including
however, the descendents at the tips might be different
populations of a species, different species, or different clades,
each composed of many species.
Trees, Not Ladders
Several times in the past,
biologists have committed
themselves to the erroneous idea
that life can be organized on a
ladder of lower to higher
organisms. This idea lies at the
heart of Aristotle's Great Chain of
Being (see right).
Similarly, it's easy to misinterpret
phylogenies as implying that
some organisms are more
"advanced" than others; however,
phylogenies don't imply this at all.
Trees, Not Ladders
In this highly simplified phylogeny, a speciation event
occurred resulting in two lineages. One led to the mosses
of today; the other led to the fern, pine, and rose. Since
that speciation event, both lineages have had an equal
amount of time to evolve. So, although mosses branch off
early on the tree of life and share many features with the
ancestor of all land plants, living moss species are not
ancestral to other land plants. Nor are they more primitive.
Mosses are the cousins of other land plants.
Trees, Not Ladders
When reading a phylogeny, it is important to keep three
things in mind:
1. Evolution produces a pattern of relationships A B C D
among lineages that is tree-like, not ladder-like.
Trees, Not Ladders
When reading a phylogeny, it is important to keep three
things in mind:
2.Just because we tend to read phylogenies from left to
right, there is no correlation with level of “advancement.”
Trees, Not Ladders
When reading a phylogeny, it is important to keep three
things in mind:
3. For any speciation event on a phylogeny, the choice of
which lineage goes to the right and which goes to the
left is arbitrary. The following phylogenies are
equivalent:
Biologists often put the clade they are most interested in
(whether that is bats, bedbugs, or bacteria) on the right
side of the phylogeny.
Misconceptions About Humans
The points described above cause the most problems
when it comes to human evolution. The phylogeny of
living species most closely related to us looks like this:
Misconceptions About Humans
It is important to remember that:
1.Humans did not evolve from chimpanzees. Humans and
chimpanzees are evolutionary cousins and share a recent
common ancestor that was neither chimpanzee nor
human.
2.Humans are not “higher” or “more evolved” than other
living lineages. Since our lineages split, humans and
chimpanzees have each evolved traits unique to their own
lineages.
Reading Trees: A Quick Review
A phylogeny, or evolutionary tree, represents the evolutionary
relationships among a set of organisms or groups of
organisms, called taxa (singular: taxon). The tips of the tree
represent groups of descendent taxa (often species) and the
nodes on the tree represent the common ancestors of those
descendents. Two descendents that split from the same node
are called sister groups. In the tree below, species A & B are
sister groups — they are each other's closest relatives.
Reading Trees: A Quick Review
Many phylogenies also include an outgroup—a taxon outside
the group of interest. All the members of the group of interest
are more closely related to each other than they are to the
outgroup. Hence, the outgroup stems from the base of the tree.
An outgroup can give you a sense of where on the bigger tree
of life the main group of organisms falls. It is also useful when
constructing evolutionary trees.
Reading Trees: A Quick Review
What’s the difference between a phylogeny, an
evolutionary tree, a phylogenetic tree, and a
cladogram?
For general purposes, not much. To some biologists, use of the
term “cladogram” emphasizes that the diagram represents a
hypothesis about the actual evolutionary history of a group,
while "phylogenies" represent true evolutionary history. To
other biologists, "cladogram" suggests that the lengths of the
branches in the diagram are arbitrary, while in a "phylogeny,"
the branch lengths indicate the amount of character change.
The words “phylogram” and “dendrogram” are also sometimes
used to mean the same sort of thing with slight variations.
These vocabulary differences are subtle and are not
consistently used within the biological community.
Reading Trees: A Quick Review
Evolutionary trees depict clades. A clade is a group of
organisms that includes an ancestor and all descendents
of that ancestor. You can think of a clade as a branch on
the tree of life. Some examples of clades are shown on the
tree below.
Reading Trees: Phylogenetic
Starbursts
Often, one sees phylogenies that include polytomies, nodes
with more than two descendent lineages, creating a “starburst.”
This can mean one of two things:
Lack of knowledge
Usually, a polytomy means that we don’t have enough data to
figure out how those lineages are related. By not resolving that
node, the scientists who produced the phylogeny are telling you
not to draw any conclusions—and also to stay tuned: often
gathering more data can resolve a polytomy.
Reading Trees:
Phylogenetic Starbursts
There are many ways that the polytomy above could be
resolved. Six are shown below. Only more data can help us
decide which is the most accurate representation of the
relationships between A, B, C, D, and E.
Reading Trees: Phylogenetic
Starbursts
 Rapid speciation
Sometimes a polytomy means that
multiple speciation events happened at
the same time. In this case, all the
daughter lineages are equally closely
related to one another. The researchers
who have reconstructed the tree you are
examining should tell you if they feel that
the evidence indicates that this is the
case.
The phylogeny to the right shows the
relationships among the members of a
group of fish called cichlids. Cichlid fish
speciated quickly after their home lakes
formed in Africa, resulting in several
phylogenetic polytomies.
Using Trees for Classification
Clearly, evolutionary trees convey a
lot of information about a group's
evolutionary history. Biologists are
taking advantage of this by using a
system of phylogenetic classification,
which conveys the same sort of
information that is conveyed by trees.
In contrast to the traditional Linnaean system of classification,
phylogenetic classification names only clades. For example, a
strictly Linnaean system of classification might place the birds
and the non-Avian dinosaurs into two separate groups.
However, the phylogeny of these organisms reveals that the
bird lineage actually branches off of the dinosaur lineage, and
so, in phylogenetic classification, the birds should be
considered a part of the group Dinosauria.
Advantages of Phylogenetic
Classification
Phylogenetic classification has two main advantages over
the Linnaean system.
First, phylogenetic classification tells you something
important about the organism: its evolutionary history.
Second, phylogenetic classification does not attempt to
“rank” organisms. Linnaean classification “ranks” groups of
organisms artificially into kingdoms, phyla, orders, etc. This
can be misleading as it seems to suggest that different
groupings with the same rank are equivalent. For example, the
cats (Felidae) and the orchids (Orchidaceae) are both family
level groups in Linnaean classification. However, the two
groups are not comparable.
Advantages of Phylogenetic
Classification
 One has a longer history than the other. The first
representatives of the cat family Felidae probably lived
about 30 million years ago, while the first orchids may
have lived more than 100 million years ago.
 They have different levels of diversity. There are about
35 cat species and 20,000 orchid species.
 They have different degrees of biological
differentiation. Many orchids belonging to different
genera are able to hybridize. But the same is not true of
cats — house cats (belonging to the genus Felis) and
lions (belonging to the genus Panthera) cannot form
hybrids.
Advantages of Phylogenetic
Classification
Orchids of these two different genera hybridize...
Laelia
Cattleya
...but cats of these two different genera do not.
Felis
Panthera
There is just no reason to think that any two identically ranked groups
are comparable and by suggesting that they are, the Linnaean system
is misleading. So it seems that there are many good reasons to switch
to phylogenetic classification. However, organisms have been named
using the Linnaean system for many hundreds of years. How are
biologists making the transition to phylogenetic classification?
Switching to Phylogenetic
Classification
Biologists deal with phylogenetic
classification by de-emphasizing
ranks and by reassigning names
so that they are only applied to
clades.
This means that your use of
biological names doesn't have to
change very much. In many cases,
the Linnaean names are perfectly
good in the phylogenetic system.
For example, Aves, which is the
class of birds in the Linnaean
system, is also used as a
phylogenetic name, since birds
form a clade (right).
Switching to Phylogenetic
Classification
Most of the specific names that
you are accustomed to using
(e.g., Homo sapiens, Drosophila
melanogaster) have not changed
at
all
with
the
rise
of
phylogenetic
classification.
However, there are some names
from Linnaean classification that
do NOT work in a phylogenetic
classification. For example, the
reptiles do not form a clade (and
cannot be a named group in the
phylogenetic system) — unless
you count birds as members of
Reptilia too.
Constructing Trees: Cladistics
Cladistics is a method of hypothesizing relationships among
organisms—in other words, a method of reconstructing
evolutionary trees. The basis of a cladistic analysis is data on
the characters, or traits, of the organisms in which we are
interested. These characters could be anatomical and
physiological characteristics, behaviors, or genetic sequences.
The result of a cladistic analysis is a tree, which represents a
supported hypothesis about the relationships among the
organisms. However, it is important to keep in mind that the
trees that come out of cladistic analyses are only as good as
the data that go into them. New and better data could change
the outcome of a cladistic analysis, supporting a different
hypothesis about the way that the organisms are related.
Constructing Trees: Cladistics
Assumptions
There are three basic assumptions in cladistics:
1.Change in characteristics occurs in lineages over time.
The assumption that characteristics of organisms change over time is
the most important one in cladistics. It is only when characteristics
change that we are able to recognize different lineages or groups. We
call the “original” state of the characteristic plesiomorphic and the
“changed” state apomorphic.
Constructing Trees: Cladistics
Assumptions
There are three basic assumptions in cladistics:
2. Any group of organisms is related by descent from a
common ancestor.
This assumption is supported by many lines of evidence and
essentially means that all life on Earth today is related and shares a
common ancestor. Because of this, we can take any collection of
organisms and hypothesize a meaningful pattern of relationships,
provided we have the right kind of information.
Constructing Trees: Cladistics
Assumptions
There are three basic assumptions in cladistics:
3. There is a bifurcating, or branching, pattern of lineagesplitting.
This assumption suggests that when a lineage splits, it divides into
exactly two groups.
Constructing Trees: Cladistics
What about primitive and derived characters?
You might hear people use the term “primitive” instead of
plesiomorphic and “derived” instead of apomorphic. However,
many biologists avoid using these words because they have
inaccurate connotations.
We often think of primitive things as being simpler and inferior—but in
many cases the original (or plesiomorphic) state of a character is
more complex than the changed (or apomorphic state). For example,
as they have evolved, many animals have lost complex traits (like
vision and limbs). In the case of snakes, the plesiomorphic
characteristic is “has legs” and the apomorphic characteristic is
“doesn’t have legs.”
Constructing Trees: Cladistics
What about primitive and derived characters?
You might hear people use the term “primitive” instead of
plesiomorphic and “derived” instead of apomorphic. However,
many biologists avoid using these words because they have
inaccurate connotations.
We often think of primitive things as being simpler and inferior—but in
many cases the original (or plesiomorphic) state of a character is
more complex than the changed (or apomorphic state). For example,
as they have evolved, many animals have lost complex traits (like
vision and limbs). In the case of snakes, the plesiomorphic
characteristic is “has legs” and the apomorphic characteristic is
“doesn’t have legs.”
Homologies and Analogies
Since a phylogenetic tree is a hypothesis about evolutionary
relationships, we want to use characters that are reliable indicators of
common ancestry to build that tree. We use homologous characters
— characters in different organisms that are similar because they
were inherited from a common ancestor that also had that character.
An example of homologous characters is the four limbs of tetrapods.
Birds, bats, mice, and crocodiles all have four limbs. Sharks and bony
fish do not. The ancestor of tetrapods evolved four limbs, and its
descendents have inherited that feature — so the presence of four
limbs is a homology.
Homologies and Analogies
Not all characters are homologies. For example, birds and bats both
have wings, while mice and crocodiles do not. Does that mean that
birds and bats are more closely related to one another than to mice
and crocodiles? No. When we examine bird wings and bat wings
closely, we see that there are some major differences.
Homologies and Analogies
Bat wings consist of flaps of skin stretched between the bones of the
fingers and arm. Bird wings consist of feathers extending all along the
arm. These structural dissimilarities suggest that bird wings and bat
wings were not inherited from a common ancestor with wings. This
idea is illustrated by the phylogeny below, which is based on a large
number of other characters.
Homologies and Analogies
Bird and bat wings are analogous — that is, they have separate
evolutionary origins, but are superficially similar because they
evolved to serve the same function. Analogies are the result of
convergent evolution.
Interestingly, though bird and bat wings are analogous as wings, as
forelimbs they are homologous. Birds and bats did not inherit wings
from a common ancestor with wings, but they did inherit forelimbs
from a common ancestor with forelimbs.
Constructing Trees:
A Step by Step Method
2. Determine the characters and examine each taxon to determine
the character states.

For example, you might select a suite of anatomical traits as your
characters (e.g., number of segments in the antennae, presence of
an upper vein on wing, etc.), and your character states would then
be the different anatomical characteristics that your organisms
have (e.g., has six antennal segments/has five antennal segments,
has an upper vein/does not have an upper vein).

Alternately, you might select the 362 bases in a particular gene as
your characters, and your character states would then be A, T, G,
or C for each of the 362 characters. Note that it is important to
select characters that seem to be homologies, that is, characters
that are similar because they were inherited from a common
ancestor. Analogies, characters that evolved through convergent
evolution in two separate lineages (like the dorsal fins of sharks
and dolphins), are not useful for reconstructing phylogenies.
Constructing Trees:
A Step by Step Method
3. Determine the polarity of characters — in other words, figure out
the order of evolution for each character. For example, did the
beetle species under consideration all evolve from an ancestor
with five antennal segments — and only later did six evolve, or
was it the other way around? Did a lineage with six antennal
segments evolve into a lineage with five?

Figuring out the polarity of a character can take some work. In
some situations, it is reasonable to assume that the character
states in the outgroup are the ancestral states for the taxa of
interest. In other situations, paleontologists may have fossil
evidence that indicates the probable ancestral state of the
character.

Many different methods may be used to reason about character
polarity. (Note that for some types of cladistic analysis,
determination of character polarity is not absolutely necessary.)
Constructing Trees:
A Step by Step Method
4. Group taxa by synapomorphies, not by symplesiomorphies.
Synapomorphies are derived or “changed” character states shared by
two taxa. Symplesiomorphies are original character states shared by
two taxa. So for example, imagine that we have determined that the
common ancestor of our beetle clade had five antennal segments and
passed that character state onto its immediate descendents: seven of
the modern beetle species still have that character state. However,
one lineage within the clade evolved six antennal segments and
passed that character state onto its descendents —14 of our beetle
species. According to this rule, we would group the 14 beetle species
with six segments together — but would not group the seven species
with five segments together because this is the original character
state.
Constructing Trees:
A Step by Step Method
Constructing Trees:
A Step by Step Method
5. Work out conflicts that arise by some clearly stated method,
usually parsimony (more on this later).
6. Build your tree following these rules:

All taxa go on the endpoints of the tree, never at nodes.

All nodes must have a list of synapomorphies, which are common
to all taxa above the node (unless the character is later modified).

All synapomorphies appear on the tree only once unless the
character state was derived separately by evolutionary
parallelism.
Constructing Trees:
A Step by Step Method
7. Voila! You have made a phylogeny. However, remember that this
phylogeny is a hypothesis. It is supported by the available data,
but new data or new interpretations of old data could change it! To
be confident about your hypothesis, you must scrutinize your data
by asking questions like these:

Could a supposed synapomorphy be the result of convergent
evolution?

Do your characters make sense from an evolutionary perspective?

Should you consider other characters?

Should you consider additional taxa?
Constructing Trees:
A Simple Example
Now we'll go through a simple example based on the steps just
described.
1. Choose the taxa. You decide to study the major clades of
vertebrates shown in the leftmost column of the table below. (Note
that many vertebrate lineages are excluded from this example for the
sake of simplicity.)
2. Determine the characters. After studying the vertebrates, you
select a set of traits, which seem to be homologies, and build the
following data table to record your observations. (Note that many
relevant vertebrate characters are excluded from this example for the
sake of simplicity.)
Constructing Trees:
A Simple Example
Constructing Trees:
A Simple Example
3. Determine the polarity of characters. From studying fossils and
outgroups closely related to the vertebrate clade, you hypothesize
that the ancestor of vertebrates had none of these features.
Constructing Trees:
A Simple Example
4. Group taxa by synapomorphies. Since we have a good idea of what
the ancestral characters are (see above), this is not so hard. We
might start out by examining the egg character. We focus in on the
group of lineages that share the synapomorphic form of this
character, an amniotic egg (A, below), and hypothesize that they
form a clade (B):
Constructing Trees:
A Simple Example
4. Group taxa by synapomorphies. Since we have a good idea of what
the ancestral characters are (see above), this is not so hard. We
might start out by examining the egg character. We focus in on the
group of lineages that share the synapomorphic form of this
character, an amniotic egg (A, below), and hypothesize that they
form a clade (B):
Constructing Trees:
A Simple Example
We go through the whole table like this, grouping clades according to
synapomorphies (C):
5. Work out conflicts that arise. There are no conflicts here. Every
group is a subset of another group (see C above).
6. Build your tree. Based on the groupings above, you produce this
tree:
Constructing Trees:
A Simple Example
7. Voila! You have made a phylogeny.
Of course, this was just an example of the tree-building process.
Phylogenetic trees are generally based on many more characters
and often involve more lineages. For example, biologists
reconstructing relationships between 499 lineages of seed plants
began with more than 1400 molecular characters!
Constructing Trees: Parsimony
What is parsimony?
The parsimony principle is basic to all science and tells us to
choose the simplest scientific explanation that fits the
evidence. In terms of tree-building, that means that, all other
things being equal, the best hypothesis is the one that requires
the fewest evolutionary changes.
For example, we could compare these two hypotheses about
vertebrate relationships using the parsimony principle:
Constructing Trees: Parsimony
What is parsimony?
The parsimony principle is basic to all science and tells us to
choose the simplest scientific explanation that fits the
evidence. In terms of tree-building, that means that, all other
things being equal, the best hypothesis is the one that requires
the fewest evolutionary changes.
For example, we could compare these two hypotheses about
vertebrate relationships using the parsimony principle:
Constructing Trees: Parsimony
Hypothesis 1 requires six evolutionary changes and Hypothesis 2
requires seven evolutionary changes, with a bony skeleton evolving
independently, twice. Although both fit the available data, the
parsimony principle says that Hypothesis 1 is better — since it does
not hypothesize unnecessarily complicated changes.
This principle was implicit in the tree-building process we went
through earlier with the vertebrate phylogeny. However, in most
cases, the data are more complex than those used in our example and
may point to several different phylogenetic hypotheses. In those
cases, the parsimony principle can help us choose between them.
Using Trees
Biologists use phylogenetic trees in many different ways to
solve both scientific and practical problems. The following case
studies highlight just a few of these examples:
Using trees for classification
Using trees to make predictions about fossils: The whale’s ankle
Using trees to learn about the evolution of complex features: The
striped cichlid
Using trees to make predictions about poorly-studied species: A
new drug
Using trees to learn about the order of evolution: The spider’s web
Using trees to learn about the evolution of diversity: The beetles’
diet
Using Trees for Classification
Using phylogenies as a basis for classification is a relatively
new development in biology.
Most of us are accustomed to the Linnaean system of
classification that assigns every organism a kingdom, phylum,
class, order, family, genus, and species, which, among other
possibilities, has the handy mnemonic King Philip Came Over
For Good Soup. This system was created long before scientists
understood that organisms evolved. Because the Linnaean
system is not based on evolution, most biologists are
switching to a classification system that reflects the organisms'
evolutionary history.
Using Trees for Classification
This phylogenetic classification system names only clades —
groups of organisms that are all descended from a common
ancestor. As an example, we can look more closely at reptiles
and birds.
Using Trees for Classification
Under a system of phylogenetic classification, we could name
any clade on this tree. For example, the Testudines, Squamata,
Archosauria, and Crocodylomorpha all form clades.
Using Trees for Classification
However, the reptiles do not form a clade, as shown in the
cladogram. That means that either "reptile" is not a valid
phylogenetic grouping or we have to start thinking of birds as
reptiles.
Using Trees for Classification
Another interesting thing about phylogenetic classification is
that it means that dinosaurs are not entirely extinct. Birds are,
in fact, dinosaurs (part of the clade Dinosauria). It's pretty neat
to think that you could learn something about T. rex by
studying birds!
Using Trees to Make Predictions about
Fossils: The Whale’s Ankle
Scientists used to think that whales’ ancestors were now-extinct
carnivores called mesonychids. However, based on recent
findings, scientists have hypothesized that whales are actually
more closely related to hoofed mammals like hippos and
ruminants such as cows and giraffes.
Using Trees to Make Predictions about
Fossils: The Whale’s Ankle
This hypothesized phylogeny leads us to predict that ancient whales
should share some characters with their close relatives. The close
relatives of whales have a type of ankle called a double pulley ankle,
so we would expect that ancestral whales would also have a double
pulley ankle.
Using Trees to Make Predictions about
Fossils: The Whale’s Ankle
And in fact, recent fossil discoveries have borne out that prediction.
Scientists found ancient whales with hind legs and pelvises: these
whales had the same kind of double pulley ankle bone that modern
pronghorns, camels, cows and hippos have.
Compare the ankle bones of the two ancient whales on the left and
right (the specimen on the right is missing some bones) and those of
a modern pronghorn (center). Notice the double pulley structure
boxed on all three.
Using Trees to Learn about the
Evolution of Complex Features: The
Striped Cichlid
Reconstructing ancestral characters can help us understand
how a complex feature evolved. For example, the cichlid fish
shown above and represented below vary in shape, color, and
striping patterns.
Using Trees to Learn about the
Evolution of Complex Features: The
Striped Cichlid
Researchers reconstructed the phylogeny of these fish based
on molecular data, then mapped striping patterns onto the
phylogeny. Scientists used parsimony to infer the probable
pattern of the ancestral fish. The resulting phylogeny shows
how these complex patterns evolved in different lineages.
Using Trees to Learn about the
Evolution of Complex Features: The
Striped Cichlid
This technique helped biologists figure out that evolutionary
changes in cichlid striping pattern seemed to be related to
ecological shifts—not sexual selection. Similar techniques
have been used to understand, for example, how birds evolved
the ability to fly and how tetrapods evolved to live on land.
Using Trees to Make Predictions about
Poorly-Studied Species: A New Drug
Phylogenies also allow us to generate expectations about the characteristics
of living organisms that we have not yet studied. For example, scientists
discovered that the Pacific Yew produces a compound called taxol that is
helpful in treating certain kinds of cancer, but it was difficult and expensive to
get enough of the compound out of the tree to make its use broadly feasible.
However, based on the evolutionary relationships among yew species,
biologists expected that close relatives of the Pacific Yew might produce
similarly effective compounds
Happily, they were right! They discovered that the leaves of the European
Yew contain a related compound that can also be used to efficiently produce
taxol. Taxol is now widely available for cancer treatment.
Using Trees to Learn about the Order
of Evolution: The Spider’s Web
Phylogenies can be used to test hypotheses about evolution. Before
phylogenies became a standard tool within biology, many biologists assumed
that the orb-weaving spiders, with their intricate and orderly webs, had
evolved from spiders with disorderly cobweb-like webs. However, the
cladistic analysis of these spiders showed that, in fact, orb-weaving was the
ancestral state, and that cobweb-weaving had evolved from spiders with more
orderly webs. The phylogeny caused the biologists to reject their original
hypothesis about orb-weaving evolution.
A disorderly, cobweb-like web on the left, and a neat, orderly web on the right.
Using Trees to Learn about the
Evolution of Diversity: The Beetles’
Diet
If you were to randomly pick an extant animal species, odds are that it
would be a beetle. While there are 250,000 described species of
plants, 12,000 described species of roundworms, and only 4,000
described species of mammals, there are over 350,000 beetle species
described, with many more beetles yet to be discovered!
Using Trees to Learn about the
Evolution of Diversity: The Beetles’
Diet
What accounts for all these beetles? Brian Farrell hypothesized that their
diets might have something to do with it, and he performed a phylogenetic
study to test that idea. He reconstructed the phylogeny of all the major
groups of beetles and noted their feeding characteristics. This research
allowed him to infer what the ancestral beetles were likely to have been eating
and when each lineage switched to a new type of food. His evidence suggests
that different beetle lineages switched to feeding on flowering plants
(angiosperms) several times during their evolutionary history.
To understand what happened when these switches occurred, Farrell
compared sister groups. He saw the same pattern again and again (as shown
below): the lineage that switched to angiosperms speciated frequently and
became very diverse, while the lineage that did not switch to angiosperms
had a lower rate of speciation and did not become very diverse. Feeding on
angiosperms is associated with higher rates of speciation (or lower rates of
extinction — it's hard to tell). This link between food and diversity is
particularly compelling because it has played out several times in beetle
evolution — nature replicated the same experiment over and over again.
Using Trees to Learn about the
Evolution of Diversity: The Beetles’
Diet
What remains to be discovered is why switching to angiosperm feeding is
associated with beetle radiations. One possibility is that switching to
angiosperms provided beetles an entrée to new niches. Consistent with this
explanation is the fact that once beetle lineages switched to angiosperms,
some of them diversified into lineages that specialize, feeding on different
parts of the plant (root, seed, leaf, etc.). This diversification would then
constitute an adaptive radiation. However, this explanation still needs to be
tested with more data.
What We Can and Cannot Learn from
Phylogenetic Trees
 Phylogenetic trees do show patterns of
descent
 Phylogenetic trees do not indicate when
species evolved or how much genetic
change occurred in a lineage
 It shouldn’t be assumed that a taxon
evolved from the taxon next to it
Activity 2:
“What, If Anything, Is a
*
Zebra”
* http://www.indiana.edu/~ensiweb/lessons/zebra.html#anchor980882#anchor980882
Activity 2:
“What, If Anything, Is a Zebra”*
1.
A)
B)
C)
D)
How are rabbits and rodents related?
Rabbits are rodents
Rabbits are closely related to rodents
Rabbits are not closely related to rodents
Rabbits are not related to rodents at all
2. If animals were classified according to brain size, humans and dolphins would be
classified as
“Psychozoa.”
Why? Because both have the largest brains
Why aren’t they? They aren’t, because dolphins are more closely related by descent (as
indicated by many details of their anatomy, etc.) to whales, while people are clearly more
closely related to apes (again as indicated by many details of their anatomy, molecular
biology, etc.)
3. Why aren’t children with Down’s Syndrome considered to be more closely related to each
other (due to many striking similarities) than to their parents?
Because we KNOW they are related to their parents!
Activity 2:
“What, If Anything, Is a Zebra”*
4. How many living species of zebras are there? 3
What are their common names? Burchell’s, Grevy’s, and mountain zebra
5. The genus Equus includes zebras, true horses, asses, and donkeys
6. What is “Cladistics”?
A method for establishing the pattern of branching for sets of related species.
7. What is a clade?
A branch in an evolutionary tree.
8. What are “sister groups”?
Two lineages sharing a common ancestor, from which no other lineage has sprung.
9. What is OUR sister group?
Chimps and gorillas
10. What is a “cladogram”?
A cladistic pattern; a chart of branching relationships
11. Why are orangutans, chimps, and gorillas (the “Great Apes”) not a true genealogical unit?
Orangutans are more distant from chimps and gorillas than people are.
Activity 2:
“What, If Anything, Is a Zebra”*
12. What are “shared derived characters”?
Features present only in members of immediate lineage, unique and newly evolved; must
avoid primitive characters here; [“synapomorphies” as a single answer here is insufficient]
alone.
14. What are “primitive characters”?
Features present in a distant common ancestor.
15. What are the clearest shared derived characters which chimps and gorillas share?
Chromosome inversions
16. On what does Bennett base her cladistic analysis of Equus?
Skeletal features, mostly in the skull
17. According to Bennett, are zebras a genealogical unit? No
Why? Because one zebra (the mountain zebra) is more like true horses than other zebras
18. According to chromosome analysis, are zebras a genealogical group? Yes
Why?
Because all zebras have fewer than 50 chromosome pairs (all other Equus spp. have
more than 50 chromosome pairs).
Activity 2:
“What, If Anything, Is a Zebra”*
18. Why is there “no such thing as a fish”?
Some fishes, e.g. lungfish, are closer to prehistoric amphibians, etc. than to other fish!
19. What is “phenetics”?
A theory of classification based on overall similarities, based on large number of traits,
expressed numerically; computerized
20. Why do phenetics and cladistics sometimes fail to produce identical lineages? (Answer on
back).
Real relationships are very complex; also, these classification schemes assume a constant rate
of change, but rates can vary greatly.