Phylogenetic Trees - I
Phylogenetic Tree
- phylogenetic relationships are normally displayed
in a tree-like diagram (phylogenetic tree/cladogram)
- a cladogram is a branching diagram describing
the phylogenetic relationships of the taxa under
investigation.
- a phylogenetic tree graphically represents a
hypothetical evolutionary process.
- phylogenetic trees are subjected to revision as
additional data becomes available.
- evolutionary tree is used synonymously as
phylogenetic tree.
Phylogenetic Tree
- a cladogram consists of two major elements:
nodes and branches.
- a node represents a taxon; a branch
represents evolutionary event(s).
- the branching pattern of a cladogram is called
the topology.
Phylogenetic Trees
Cladogram
Clade
- a clade is an ancestor species with all its
descendants.
- a monophyletic group is a clade.
- There are three ways to define a clade for use in a
cladistic taxonomy
i) Node based
ii) Stem based
iii) Apomorphy based
Clade
Node-based
the most recent common ancestor
of A and B along with all of its
descendants
Stem-based
all descendants of the oldest
common ancestor of A and B that is
not also an ancestor of Z
Apomorphy-based
the most recent common ancestor
of A and B, along with all of its
descendants, possessing a certain
derived character. This definition is
generally discouraged by most
cladists
Cladogram / Phylogram / Phenogram
- A cladogram/phylogram displays branching
information to explain the evolutionary
relationships.
- A phylogram has additional information: the
length of branches according to the amount of
changes (evolutionary process).
Cladogram / Phylogram
Cladogram
Phylogram
Cladogram / Phylogram / Phenogram
- A phenogram is generated from phenetic analysis
(numerical taxonomy). It does not necessary
explain the ancestor-descendant relationships of
the taxa in the investigation.
Gene trees and species trees
Gene tree
a
A
b
B
c
C
Species tree
We often assume that gene trees give us
species trees
Characters and Character States
• Organisms comprise sets of features
• When organisms/taxa differ with respect to
a feature (e.g. its presence or absence or
different nucleotide bases at specific sites
in a sequence) the different conditions are
called character states
• The collection of character states with
respect to a feature constitute a character
Homoplasy
• Homoplasy is similarity that is not homologous
(not due to common ancestry)
• It is the result of independent evolution
(convergence, parallelism, reversal)
• Homoplasy can provide misleading evidence of
phylogenetic relationships (if mistakenly
interpreted as homology)
• homoplasy can be common in DNA data
– There are a limited number of alternative
character states (e.g. Only A, G, C and T in
DNA)
– Rates of evolution are sometimes high