Organisms – A 3.

2 HL Classification & Cladistics

Guiding Questions

“Species are named and classified using an internationally agreed system”

Syllabus objectives:

A3.2.1 Classification is needed because of the immense diversity of species. After

Need for classification of organisms
AHL classification is completed, a broad range further study is facilitated.
The traditional hierarchy of kingdom, phylum, class, order, family, genus
A3.2.2 Difficulties classifying organisms into the traditional
and species does not always correspond to patterns of divergence
AHL hierarchy of taxa
generated by evolution.
The ideal classification follows evolutionary relationships, so all the
A3.2.3 Advantages of classification corresponding to members of a taxonomic group have evolved from a common ancestor.
AHL evolutionary relationships Characteristics of organisms within such a group can be predicted because
they are shared within a clade.
The most objective evidence for placing organisms in the same clade
A3.2.4 Clades as groups of organisms with common
comes from base sequences of genes or amino acid sequences of proteins.
AHL ancestry and shared characteristics
Morphological traits can be used to assign organisms to clades.
This method of estimating times is known as the “molecular clock”. The
Gradual accumulation of sequence differences as the
A3.2.5 molecular clock can only give estimates because mutation rates are
basis for estimates of when clades diverged
AHL affected by the length of the generation time, the size of a population, the
from a common ancestor
intensity of selective pressure and other factors.
A3.2.6 Base sequences of genes or amino acid sequences of Examples can be simple and based on sample data to illustrate the tool.
AHL proteins as the basis for constructing cladograms
Students should be able to deduce evolutionary relationships, common
A3.2.7 ancestors and clades from a cladogram. They should understand the terms
Analysing cladograms
AHL “root”, “node” and “terminal branch” and also that a node represents a
hypothetical common ancestor.
A case study of transfer of plant species between families could be used to
Using cladistics to investigate whether the
A3.2.8 develop understanding, for example the reclassification of the figwort
classification of groups corresponds to evolutionary
AHL family (Scrophulariaceae). However, students are not required to
relationships
memorize the details of the case study.
A3.2.9 Classification of all organisms into three domains This is the revolutionary reclassification with an extra taxonomic level
AHL using evidence from rRNA base sequences above kingdoms that was proposed in 1977.

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The need to classify organisms:

Organisms are classified by organizing them

according to shared traits and features.

Biologists group organisms to represent similarities and proposed relationships. Classification systems change
with expanding knowledge about new and well-known organisms.

Humans naturally like to arrange things in groups

to make it easier to study them. It also helps to
make predictions (e.g. classifying clouds help to
make predictions about the weather.)

Two central pillars are forming the basis of modern classification in biological sciences. Which ones?

Taxonomy is classification by using hierachical taxa (sgl.

taxon) such as the ones shown on the right. The taxonomic
scheme classifies species into groups with shared traits
belonging to more comprehensive groups.

Four examples of species and their taxonomic classification.

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The biologist Carl
Linnaeus developed a
system of classification
based on morphology
(structural features).

When proceeding down

the taxonomic hierarchy
from kingdom to species,
the number of animals in
each group decreases
and the similarities
between them increase.

How or when can this system of classification become problematic or difficult to apply?

Sometimes it is difficult to classify organisms according to the hierachical taxa – even if taxonomists have agreed
on the traits and the corresponding ranks that organisms should have.

These uncertainties are the result of the evolution by gradual divergence of species over time. As species diverge
from each other there will eventually be sufficient diversity for the genus to be divided into two or more separate
genera. The exact point of when this happens cannot be determined.

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Advantages of classification corresponding to evolutionary relationships:

Instead of only looking at morphology

to classify organism, scientists have
developed systems to categorize them
using molecular differences in proteins
sequences and DNA. This shows how
closely related organism are.

By comparing the genetic profiles of different species a phylogenetic tree can be developed.

Biologists agree that classification should mirror the evolutionary origins of species instead of looking at the
morphology. What is the name for the study of the evolutionary past of a species?

What are the advantages of a system reflecting evolutionary relationships?

Clades as groups of organisms with common ancestry and shared characteristics

Cladistics is a system of classification for grouping taxa based on the characteristics

that have evolved most recently. A diagram illustrating evolutionary relationships
between species is called a phylogenetic tree or cladogram.

The concept of common descent is crucial in determining on the grouping of an

organism.

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.

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 Look at the cladogram to the right. 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?

Clades are sometimes difficult to read:

Practice:

Which of the highlighted area within these cladograms on the left is a clade? Explain:

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Gradual accumulation of sequence differences as the basis for estimates of when clades diverged from a
common ancestor:

Base and amino acid sequences are evidence for members of a clade and are used to establish cladograms.
Look at these made-up DNA base sequences. Which two species are the most closely related? Explain:

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).

There is evidence that mutations in DNA or amino acid

sequences 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.

If species A had 5 differences from species B and 10 differences from species C, then how much longer ago
must A and C have split?

Members of the hominoids: Orang Utan, Gorilla, Chimpanzee, Bonobo, Human

Which of these non-human members of the family hominidae shown in the image above are most closely
related according to the cladogram?

Which hominoids are most closely related to European, African and Japanese ?

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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.

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

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Analysing cladograms:

Cladograms represent hypothesized relationships among

organisms and may include extinct species. To establish
cladograms organisms are grouped into categories that
represent common ancestries, not just physical similarities.

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 on the
right 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?

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Deeper nodes are
older than shallower
nodes to which they
are connected, this
indicates more
distant relationships
among the terminal
taxa they connect.
Along branches,
hereditary genetic
changes are
accumulation.

Practice Question:

a. What is the primitive (as in, the most basic) 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

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Activity:
1. Open the Nova Labs Evolution site (and use your google
account to log in or use the guest pass):
https://www.pbs.org/wgbh/nova/labs/lab/evolution/
2. Watch the Video Intro
3. Play the game (click on the orange button)

Morphological classification, 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.

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Practice:
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.

(a) Deduce whether spiders that spin similar webs or

spiders that live on the same island are more closely
related.

(a) Mitochondrial DNA from the spiders was analysed to

produce the cladogram. Outline the method of analysing
the DNA to produce evidence for cladograms.

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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

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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.

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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?

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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.

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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).

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