PART II

Construction of
Taxonomic/Phylogenetic tree
Taxonomic /Phylogenetic Trees
There are different ways of drawing
a tree:

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Inbuilding a tree, we organize species into
nested groups based on shared derived
traits

In a phylogenetic tree, the species of

interest are shown at the tips of the tree's
branches.

The branches themselves connect up in a

way that represents the evolutionary
history of the species

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At each branch point lies the most
recent common ancestor shared by
all of the species descended from
that branch point.

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 Review these terms:
Plesiomorphy: The ancestral state or
primitive character states.
Apomorphy: A derived character used
to define specific clades.
Synapomorphies: These are shared
apomorphy.
Autapomorphy: A derived character
states that found in only one evolutionary
line.
Symplesiomorphies: Are
plesiomorphies shared by two or more
taxa. 5
Outgroup: Group outside the one
being studied. Used to root the
tree.
Ingroup: Group being
studied/group of interest

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Construction of Phylogenetic tree

The starting point is a set of data

on traits of a group of related
species. The traits could be physical
traits, genetic traits, or both .

The next step is deciding which

traits were inherited from the
common ancestor and which traits
evolved only in a descendant
species after splitting off from the
common ancestor. 7
Traitsinherited from a common
ancestor are called ancestral
traits.

Traitsthat evolved since two

groups shared a common ancestor
are called derived traits

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In this cladogram, the ancestor species has
traits A, B, and C, so these are ancestral
traits. During the process of evolution,
trait A evolves to trait a and trait B evolves
to trait b. These new traits (a and b) are 9
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Consider the following
Figures:

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 Root: the common ancestor of all taxa

 Thenodes of a cladogram represent the

common ancestry of the organisms.

A node splits into two branches and indicates

a divergence or speciation event.

 Thenode itself represents the common ancestor

of any descendants that branch off of it.

 The two taxa that branch off at a node are

called sister taxa. They share an immediate
common ancestor. In this phylogeny, taxa B and
C are sister taxa. They are both equally related
to taxon A. 13
Systematists use outgroup
comparison to differentiate between
shared derived characters and
shared primitive characters

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A character is a trait (morphological,
physiological, biochemical, molecular, etc.)
used by a systematist to determine
evolutionary relationships between
different taxa.

The specific value of a particular character

is known as its character state.

Character states are traits derived

through the process of natural selection,
adaptation and inherited variance that lead
to biodiversity in life.
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The characters that are relevant to
phylogeny, of course, are the
homologous ones.

Thus “Character” here refers to any

feature that a particular taxon
possesses.

After systematists have separated

homologous from analogous similarities;
they must sort through the homologies
the difference between shared primitive
and shared derived characters.
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For example, all mammals share the
homologous character of a backbone.
However, the presence of a backbone
does not distinguish mammals from other
vertebrates because non-mammalian
vertebrates such as fishes and reptiles
also have backbones.

Therefore; the backbone is considered a

shared primitive character because it
evolved in the ancestor common to all
vertebrates.
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The backbone is a homologous
structure that predates the branching
of the mammalian clade from the other
vertebrates; it is a shared primitive
character (symplesiomorphies)

In contrast, hair, a character shared by

all mammals but not found in non-
mammalian vertebrates, is a shared
derived character,
(synapomorphies) an evolutionary
novelty unique to a particular clade in
this case, the mammalian clade
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In building the tree, we normally
use an approach called parsimony.

Parsimony means choosing the

simplest explanation from among all
possible explanations.

In cladistics, parsimony usually

means choosing the cladogram with
the fewest branching points.

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The first step in cladistic classification
is to list shared characteristics of
organisms. The best cladogram
provides the maximum possible
number of shared homologies.

The validity of cladistic in

classification depends on the
assumption that if two organisms
share a homologue they must be
related, for example frog and a sheep
have a backbone.
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The method involves the
constriction of groups (clades)
comprising organisms which share
a unique homologue.

For example birds form a clade

sharing the unique homologue
feathers and mammals form a
clade by possessing mammary
glands.
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Consider the table below:
Feature Lamprey Antelop Bald Alligator Sea
s s e eagle buss

Lungs 0 1 1 1 0

Jaws 0 1 1 1 1

Feather 0 0 1 0 0
s

Gizzard 0 0 1 1 0

Fur 0 1 0 0 0

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The lamprey, a jawless fish that lacks
a true skeleton, is outgroup.

As shown in the table, the lamprey

lacks all of the listed features: it has
no lungs, jaws, feathers, gizzard, or
fur.

Based on this information, we will

assume that absence of these features
is ancestral, and that presence of
each feature is a derived trait.
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A cladogram is:

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Example 2: Use the following
information to construct the
phylogenetic tree, (0 indicates
character is absent and 1 indicates that a
character is present )
Vertebr Four Amniotic Egg Hair/
ae limbs egg shells Fur

Frog 1 1 0 0 0

Rode 1 1 1 0 1
nt
Lizar 1 1 1 1 0
d
Gorill 1 1 1 0 1
a
Fish 1 0 0 0 0

Bird 1 1 1 1 0
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Answer:

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Example 3: Consider character table below:
0 indicates that a character is absent and 1 indicates that a character is
present

Hair Amnioti Four Hinged Vertebra

c egg legs jaws l column

Lancelet 0 0 0 0 0
Lamprey 0 0 0 0 1
Tuna 0 0 0 1 1
Salamand 0 0 1 1 1
a
Turtle 0 1 1 1 1
Leopard 1 1 1 1 1

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From the table, let us arrange five
vertebrates; a leopard, turtle,
salamander, tuna, and lamprey (a
jawless aquatic vertebrate) into a
cladogram.

A good choice of an outgroup for our

example is a lancelet, a small animal
that lives in mudflats and (like
vertebrates) is a member of the
phylum Chordata, but does not have a
backbone.
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We can begin building our cladogram by
comparing the ingroup with the outgroup.

In our study case, an example of such a

character is a structure called a
notochord, a flexible rod running the
length of the animal.

Lancelets have notochords throughout

their lives, but in vertebrates the
notochord is present only in embryos and
is replaced later in development by the
backbone.
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Note that all the vertebrates in the
ingroup have backbones; this is a
shared primitive character that was
present in the ancestral vertebrate,
though not in the outgroup.

Now note that hinged jaws are a

character absent in lampreys but
present in other members of the
ingroup; this character helps us identify
an early branch point in the vertebrate
clade.
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A cladogram

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Practice 1: Use the following information to
construct the a cladogram, (0 indicates
character is absent and 1 indicates that a
character is present )
1 2 3 4 5 6

Outgrou 0 0 0 0 0 0
p
A 1 0 0 0 0 1

B 1 1 0 0 0 1

C 1 1 1 0 0 1

D 1 1 1 1 0 1

E 1 1 1 1 1 1

F 1 1 1 1 1 0

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Practice 2

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Practice 3

From the table above draw a

cladogram 34
Practice 4
Characters
1 2 3 4 5 6 7 8 9 10
Out 0 0 0 0 0 0 0 0 0 0
group

A 1 0 0 0 1 1 0 0 0 1
B 1 0 0 0 1 0 0 0 0 1
C 0 0 0 0 0 0 0 0 1 1
D 0 1 1 0 0 0 1 1 0 1
E 0 1 1 1 0 0 0 1 0 1

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To determining plesiomorphic and
derived characters; Outgroup
comparison method is used, Consider
the following:

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The data in the table below shows
presence or absence of observed character
states in a group of studied plant species.
Characters
Species 1 2 3 4

Outgroup Present Present Present Present

A Absent Present Absent Absent

B Absent Absent Present Absent

C Absent Absent Absent Present

D Absent Present Present Present

Draw a table to show whether the character state is

derived or primitive in each species and construct the
most parsimonious cladogram. 37
 Character table
Characters

Species 1 2 3 4

Outgroup 0 0 0 0
A 1 0 1 1
B 1 1 1 1
C 1 1 0 0
D 1 0 1 0

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From the table, draw the most
parsimonious cladogram

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Hennig argumentation consider the
information provided by each
characters one at a time to
construct a cladogram. Consider the
following example;

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The information in character 1
unites taxa A, B and C, because
they share the apomorphic state.

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Character 2: The derived state is
found only in taxon B. It is therefore
an autapomorphy of that taxon.

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Character
3: is also
autapomorphy for taxon C.

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Character 4: This derived state is
an synapomorphy that unites
taxa B and C.

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Character
5: The derived state is
autapomorphy for taxon A.

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This is the most parsimonious
cladogram.

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Practice 5: Draw a table to show whether the
character state is derived or primitive in each species
and construct the most parsimonious cladogram.

1 2 3 4 5 6 7 8 9 10

Out - - - - - - + - - -
grou
p
A + + + + + + + + + -

B + + + - - + + + - -

C + + + + - + + + - +

D + + - - - + - - - -

E + + - - - - + - - -

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