Constructing Phylogenetic

1
Trees
Constructing Phylogenetic
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Choose the taxa

• We will study some of the major clades of
  vertebrates
• Dinosaurs and birds
• Rodents and rabbits
• Primates
• Sharks and rays
• Crocodiles and relatives
• Boney fishes
• Amphibians

3
Determine the characters

• After studying the vertebrates, we select a set
  of traits, which seem to be homologies, and build
  a data table.

4
Homology, homoplasy, or analogy?
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Determine polarity of characters

• From studying fossils and outgroups closely
  related to the vertebrate clade, we hypothesize
  that the ancestor of vertebrates had none of
  these features.

Relative to the ancestor, all these characters
are
apomorphies
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Group taxa by synapomorphies

• Since we have a good idea of what the ancestral
  characters are, this is not so hard. We might
  start out by examining the egg character. We
  group the lineages that share the synapomorphic
  form of this character, an amniotic egg (A), and
  hypothesize that they form a clade (B)

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Analyze entire table

• We go through the whole table, grouping clades
  according to synapomorphies.

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Work out conflicts that arise

• What evolutionary events might create conflicts?

We assume
Divergence
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Work out conflicts that arise

• What evolutionary events might create conflicts?

We assume
Divergence
We may see
Convergence
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Work out conflicts that arise

• What evolutionary events might create conflicts?

We assume
Divergence
We may see
Convergence
Or
Parallel Evolution
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Or even

• Reversion

12
Here are our groups
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Now, build a tree

• Based on the groupings in the table, we produce
  this tree

14
Review

• Plesio near (the beginning) primitive
• Apo away (from the beginning)
• or derived
• Syn same (as others in group)
• Aut(o) self (unique)