` 5.

4 Cladistics

Syllabus objectives:

Understandings:
 A clade is a group of organisms that have evolved from a common ancestor
 Cladograms are tree diagrams that show the most probable sequence of divergence in clades
 Evidence for which species are part of a clade can be obtained from the base sequence of a gene or the
corresponding amino acid sequence of a protein
 Sequence differences accumulate gradually so there is a positive correlation between the number of
differences between two species and the time since they diverged from a common ancestor
 Traits can be analogous or homologous
 Evidence from cladistics has shown that classification of some groups based on structure did not
correspond with the evolutionary origins of a group or species

Applications:
2. Cladograms including humans and other primates
3. Reclassification of the figwort family using evidence from cladistics

Skills:
 Analysis of cladograms to deduce evolutionary relationships

1|Page
Cladograms:

In phylogeny (the study of evolutionary

relationships), a diagram illustrating
evolutionary relationships between species
is called a phylogenetic tree or cladogram.
The word ‘tree’ is used because the
branching pattern shows when different
species ‘split off’ from others.

The terminal taxa at the tips of the phylogenetic tree

are connected by branches. Nodes are the branching
points, representing a common ancestor shared by
two or more taxa.

Phylogenetic trees depict the relationship among taxa.

More closely related taxa are connected by shallower
nodes (nodes near the tip of the tree.)

The graphic style of phylogenetic trees varies. For example, the tree shown below depicts the exact same pattern
of relationships among Taxa A–H as the three trees shown.

Practice questions:

1. Taxon B and Taxon C are more closely related to one another

than either is to Taxon A. How can we tell?

2. Taxa A, B and C are more closely related to each other than

they are to Taxa D, E, F, G and H. Why is this?

3. In this phylogenetic tree, what is Taxon B’s sister taxon?

4. In this phylogenetic tree, what is Taxon D’s sister taxon?

5. In this phylogenetic tree, the identified node represents the shared common ancestor of which taxa?

2|Page
Clades:

A clade is a group that includes an ancestor (node) and all of

its descendants (all shallower nodes and terminal taxa that
descend from that node).

Clades are not mutually exclusive – they form nested sets on a

tree which means that any taxon can belong to many clades.

Look at the cladogram on the top left. How many clades does Taxon B belong to?

How many clades does Taxon E belong to?

How many clades does Taxon A belong to?

How many clades does Taxon H belong to?

Practice:

Which of the highlighted area within these

cladograms on the left is a clade? Explain:

3|Page
Cladograms represent hypothesized relationships
among organisms and may include extinct species.

Early naturalists used physical characteristics and

later, fossil data, attempting to represent
evolutionary relationships among organisms.

Today, modern classification systems use fossil

data, physical characteristics and DNA/RNA
information to draw increasingly more accurate
branching diagrams.

Practice Question:

a. What is the primitive characteristic in the cladogram shown below?

b. Name the members of the mammal clade in this cladogram.

c. What is the outgroup (a group that is less closely related to the others in the cladogram) when
considering the clade of multicellular organisms?

d. Do shark eggs have a protective membrane (the amnios) around them? How can you tell?

e. Explain why there are no bacteria shown in this diagram.

4|Page
Comparative anatomy to establish phylogenetic relationships:

Most of the data used in making phylogenetic judgments have come from comparative anatomy and from
embryology; although those are rapidly being surpassed by systems constructed using molecular data.
Historically, cladograms have been constructed based on structural characteristics, however this not always a
reliable method for establishing evolutionary connections

• Related species may have distinctive (homologous) features

• Unrelated species may have similar (analogous) features

1. Homologous structures:

Revision from 5.2: What are homologous structures?

Why are homologous structures useful for constructing a cladogram?

In comparing features common to different species, anatomists try to identify homologous structures.

2. Analogous structures:

What are analogous structures?

Why are the human and the octopus’ eye an example for an analogous structure?

Problems in distinguishing between homologous and analogous structures have sometimes led to mistakes in
classification in the past. For this reason, the morphology (form and structure) of organisms is now rarely used
for identifying members of a clade and evidence from base or amino acid sequences is trusted more
5|Page
Molecular evidence helps to establish more reliable cladograms:

Look at these made-up DNA base sequences. Which two

species are the most closely related? Explain:

This cladogram is part of a molecular phylogeny of

all the living primates. It was made by comparing
34 927 base pairs sequenced from 54 genes taken
from each of a single species in each genus. The
branches on the tree are scaled so that they
reflect the amount of evolutionary change (in
other words, the number of modifications in
characteristics) that has occurred. The numbers
show the differences in base pairs between
different species.

Which organisms is the genus chimpanzee (Pan)

most closely related to? Explain your answer.

Sequence differences accumulate gradually so there is a positive correlation between the number of differences
between two species and the time since they diverged from a common ancestor

The assumption is that these changes occur at a

regular rate (which may not always be the case).

Therefore, if species A had 5 differences from

species B and 10 differences from species C, then
the lineages from A and C must have split twice as
long ago as for A and B.

6|Page
There is evidence that mutations occur at a roughly constant
rate so they can be used as a molecular clock. The number of
differences in sequence can be used to deduce how long ago
species split from a common ancestor.

• 70 000 years ago European-Japanese split

• 140 000 years ago, African- European/Japanese split
• 5 000 000 years ago, human chimpanzee split.
•

Example:
The amino acid sequence of cytochrome c has been analyzed in over 100 eukaryotic species, and the molecular
data support the notion that cytochrome c is an evolutionarily conservative protein.

Below: Alignment of human and rat cytochrome c amino acid sequences using BLAST. Sequence similarity
between the two proteins is 91%

Human Cyt C: MGDVEKGKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLHGLFGRKTGQAPGYSYTAANKNKGIIW 61

Alignment: MGDVEKGKGKKIF+ KC+QCHTVEKGGKHKTGPNLHGLHGLFGRKTGQA G+SYT ANKNKGI W
Rat Cyt C: MGDVEKGKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLHGLFGRKTGQAAGFSYTDANKNKGITW 61

Human Cyt C: GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE 105

Alignment GEDTLMEYLENPKKYIPGTKMIF GIKKK ERADLIAYLKKATNE
Rat Cyt C: GEDTLMEYLENPKKYIPGTKMIFAGIKKKGERADLIAYLKKATNE 105

Below: Alignment of human and yeast cytochrome amino acid sequences using BLAST. Sequence similarity
between the two proteins is 64%.

Human Cyt C: GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLHGLFGRKTGQAPGYSYTAANKNKGIIW 61

Alignment: G +KG +F +C QCHTVEKGG HK GPNLHGLHG+FGR +GQA GYSYT AN K ++W
Yeast Cyt C: GSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGLHGIFGRHSGQAEGYSYTDANIKKNVLW 66

Human Cyt C: EDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKA 102

Alignment: E+ + EYL NPKKYIPGTKM F G+KK+++R DLI YLKKA
Yeast Cyt C: ENNMSEYLTNPKKYIPGTKMAFGGKKEKDRNDLITYLKKA 107

Cytochrome c sequence similarity

between humans and rats (91%) is much
higher than between humans and yeast
(64%).

This indicates that the evolutionary path

leading to the human species diverged
with that of yeast far before its
divergence from rat. A comparison of
cytochrome c sequences from different
species has been used to order the
divergence of species in relative time,
shown by the graph.

7|Page
The phylogeny of the amount of change in myoglobin and cytochrome c, respectively, in 3 different species

Phylogeny based on nucleotide differences in the gene for cytochrome c

8|Page
Practice Question:

1. Find the human, rhesus monkey, kangaroo, snapping turtle, bullfrog, and tuna on the "Amino Acid
sequences in Cytochrome-C Proteins from 20 Different Species" chart and underline their names.

2. Compare the human amino acid sequence with each of these five animals by counting the number of
times an amino acid in that animal’s cytochrome c is different from the amino acid in that same position
of the human sequence. For example, the number of differences between human and dog=10.
Number of amino acid differences between...
Human and Human and Human and Human and Human and
Rhesus monkey Kangaroo Snapping turtle Bullfrog Tuna

3. The cladogram diagram below

shows the relationship of
selected animals based on their
shared anatomical features. For
example, out of seven key traits,
all of these animals have a dorsal
nerve cord, but only humans,
monkeys and kangaroos have
mammary glands.

9|Page
Record the total number of amino acid differences between humans and each animal shown below. Write your
answer in the hexagon below the arrow pointing to the name of that animal.

4. Does the data from the amino acid sequence generally agree with the anatomical data that was used to
make the cladogram?

5. Do organisms with fewer shared anatomical traits also have more amino acid differences? Explain by
reference to the cladogram above:

6. Based on the molecular data, how does the "human-monkey" relationship compare to the "duck-chicken"
relationship (which shows three amino acid differences)?

7. If the molecular data, the structural similarities, and the fossil record all support the same pattern of
relationships, can we be fairly confident that the pattern is accurate? Why or why not?

8. Chickens and turkeys are both birds and have the same sequence of amino acids in their cytochrome-c
protein. Explain how two species can have identical cytochrome-c and still be different species.

9. Neurospora (bread mold) and Saccharomyces (bakers yeast) are both fungi. Chickens and turkeys are
both birds. What can you say about the inferred evolutionary relationships between the two birds
compared to the relationship between the two fungi? Explain your reasoning.

10. Write a short paragraph summarizing the important information that can be obtained from cladograms
(not the information used to make them).

10 | P a g e
The construction of cladograms based on base and amino acid sequences only became possible towards the end
of the 20th century. Before that the sequence data was not available and computer software had not developed
to do that analysis. The construction of cladograms and identification of clades is known as cladistics.

What do the two phylogenies of the shell (Volutes) on

the right show about phylogeny based on sequence data
and phylogeny based on morphological (structure) data?

Why is classification of groups based on morphology not

always reliable, and what is the consequence?

Reptiles and their cladograms:

Reptiles, as a group, consist of the crocodilians, lizards and snakes, tortoises and turtles and tuatara.

However, reptiles are not a clade. One of them is

actually more closely related to birds. Which one?

Traditional taxonomy, based on appearance,

placed mammals, birds, and reptiles in separate
classes. However, cladistic taxonomy, based on
phylogeny, places birds in a clade called
archosaurs; along with crocodilians and
dinosaurs. These archosaurs share a more
recent ancestor than other reptiles.

11 | P a g e
Reclassification of families:

Like many families today, the Figworts have split up. Even now,
they are moving on to new families, acquiring new names.

It’s sad, but modern life is full of such scenes. What drove them
apart? Well, modern taxonomy. A major reclassification has
been carried out.

Less than half of the species have been retained in the family,
which is now only the thirty-sixth larges among the
angiosperms

Practice question:

A common way to discover how groups of living things are related is to compare the visible external features.
This approach has been used for many years in classification. These features may well represent homologous
structures – that is structures derived from a common ancestral structure.

1. Look at the diagram showing the structures found in some flowers.

2. Using these main structural features compare the eight flowers in the images below.
Plantain Snapdragon Figwort Buddleia

Foxglove Monkey flower Lopseed Speedwell

3. Record the presence of the structures in the table of results by making a X in the cells where the feature
is present.
Snapdragon

Speedwell
Foxglove
Buddleja

Lopseed
Plantain

Monkey
Figwort

flower

2 upper
lobes
3 lower
lobes
Petals form
a tube
4 or 5
petals

12 | P a g e
Remember, to build a cladogram biologists find different numbers of shared characteristics between different
groups. The different degrees of relationship between the different groups is shown in a branching tree diagram
called a cladogram. The organisms are found at the tips of each branch, and shared homologous features are
shown on the diagram as solid square boxes.
4. Create a cladogram in the space below using data from the table of flower structures.

A new method is beginning to provide a lot of new evidence about how groups of living things are related. This
method takes a few genes and compares the base sequence of these genes in several related species.
Image a single gene just a few hundred nucleotide bases long. Here is a short extract of 30 bases in 3 species.

Species A: CATCATCATCATCATCATCATCATCATCAT
Species B: CATCATTACTACTACTACCATCATCATCAT
Species C: CATCATTACTACTACTACCATCATTATCAT
In the DNA of these species there looks to have been two mutations.

• In red, CATCATCATCAT has become inverted and now reads TACTACTACTAC.

• In blue a base C has been substituted by a base T

5. Of course, both mutations could have happened in reverse. TAC could have become CAT and T could have
become C. Is it possible to identify which base sequence came first?

There are (at least) 3 possibilities. Follow the sequences of mutations in the 3 examples and identify which of
these is the simplest sequence of mutations. The simplest one is the best explanation.

13 | P a g e
In a recent study (Olmstead et al 2001) three genes totalling
4200 bases were compared across 65 species. The results were
analysed by a computer program to try to give the simplest
explanation of the differences found. This extract of the
cladogram is adapted from the data.

This is a simplified cladogram. Compare this to the first cladogram drawn from the flower features.

Which of the flowers are found in unexpected places on the DNA cladogram? Why?

What does this mean about the physical features of the flowers? Are they homologous structures
inherited from a common ancestor?

“This is the beginning of an era of great advancement in classification”, said Richard Olmstead. What was
he referring to?

14 | P a g e
Cladograms of humans & primates:

The pattern of branching in a cladogram is assumed to

match the evolutionary origins of each species.

The sequence of splits at nodes is therefore a

hypothetical sequence in which ancestors of existing
clades diverged

Although cladograms can provide strong evidence for

the evolutionary history of a group, they cannot be
regarded as proof. Cladograms are constructed on the
assumption that the smallest possible number of
mutations occurred to account for current base or
amino acid sequence differences. Sometimes this
assumption is incorrect and pathways of evolution were
more convoluted. It is therefore important to be
cautious in analysis of cladograms and where possible
compare several versions that have been produced
independently using different genes.

The closest relatives of humans are chimpanzees and bonobos. The entire genome of these three species has
been sequences giving very strong evidence for the construction of a cladogram.

15 | P a g e
Practice Question:

16 | P a g e
Practice question:

The cladogram below shows how closely related a group of species of spiders are on the Hawaiian island group. Two
of the species have not been given a scientific name. Three pairs of the spiders spin very similar webs. These
are shown on the diagram. The island on which the spider lives is also indicated.

location:

T. laboriosa - Mainland - USA

T. hawaiensis - Hawai’i

“emerald
- O’ahu
ovoid”

T. limu - O’ahu

“eurylike” - O’ahu

T. acuta - Maui

T. fliciphilia - Maui

T. stelarobusta - Maui

T. eurychasma - Maui

T. perkinsi - Hawai’i

[Source: T A Blackledge and R G Gillespie (November 2004), Proceedings of the National Academy of Sciences, 101, (46),
pages 16228 16233]

(a) Deduce whether spiders that spin similar webs or spiders that live on the same island are more closely
related.

(2)

(b) Mitochondrial DNA from the spiders was analysed to produce the cladogram. Outline the method of
analysing the DNA to produce evidence for cladograms.
(3)

17 | P a g e