Phylogenetic Trees I

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Phylogenetic Trees - I
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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.

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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.
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Phylogenetic Trees
Cladogram
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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

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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
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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).
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Cladogram / Phylogram
Cladogram
Phylogram
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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.
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Gene trees and species trees
A
a
Species tree
Gene tree
B
b
C
c
We often assume that gene trees give us species
trees
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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

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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