1. Systematics: Tree of Life http://tolweb.org/tree/phylogeny.html
1) Taxonomy: Classification and naming of organisms
Hierarchical nomenclature with taxonomic categories
(kingdom, phylum, class, order, family, genus, and species)
2) Phylogenetic analysis: The study of evolutionary relationships among species
a. Under common decent, hierarchical classification reflects true genealogical relationships
Tree of Life

2. Phylogenetic Analysis
Species 1
a b c d e f g h i j
Species 2
a b c d e f g h i j
Species 3
a b c d e f g h i j
Species 4
a b c d e f g h i j i1 j1 h1 e1
Ancestor 3
(node) d1 g1 f1 b1
shared
characters a1
Ancestor 2
(node) c1
shared derived
characters
Ancestor 1
a b c d e f g h i j

3. Phylogenetic Terms i1 j1 e1 h1 d1 g1 f1 b1 a1 c1
Species 1
Species 2
Species 3
Species 4 i1 j1 e1 h1
Ancestor 3 d1 g1 f1 b1
Ancestor 2 a1
monophyletic group: set of species that share
a common ancestor.
synapomorphy: shared derived character
state.
autapomorphy: uniquely derived character c1
Ancestor 1

4. The identification of synapomorphies help define
nested series of monophyletic groups.

5. Phylogenetic Analysis
Species 1
a b c d e f g h i j
Species 2
Species 3
Species 4
Ancestor 1
Ancestor 2
Ancestor 3 h1 g1 c1 f1 i1 j1 a1 b1 j0 e1 d1
shared
characters
shared derived
characters

6. Phylogenetic Terms i1 j0 g1 h1 h1 f1 g1 e1 d1 a1 j1 c1 b1
Species 1
Species 2
Species 3
Species 4 j0 i1 g1 h1 h1 f1
Ancestor 3 g1 e1 d1 a1
Ancestor 2 j1
homoplasy: when two species share a derived character state because of convergent evolution or evolutionary reversal, but not because of common descent.
convergent evolution: independent evolution
of a derived character state in two or more
taxa. c1 b1
Ancestor 1

7. Example: Wings in insects, birds, and bats
Types of Homoplasy
Convergence: Shared derived similarities, that are not based on common origin (i.e. homology ), but on an independent origin in different taxa.
Example: Wings in insects, birds, and bats
Reversal :The secondary presence of an apparently ”ancestral” character state.
Example: Aquatic mode of life for fish, terrestriality for tetrapods, reversal to aquatic life in whales

8. Homoplasy: Common in DNA sequence data
Homoplasy: Common in DNA sequence data. Each nucleotide position defines a separate character

9. Homoplasy - independent evolution
Loss of tails evolved independently in humans and frogs - there are two steps on the true tree
Lizard
Human
TAIL (adult)
absent
present
Frog
Dog

10. Homoplasy: Misleading evidence of phylogeny
If misinterpreted as a synapomorphy, the absence of tails would be evidence for a wrong tree: grouping humans with frogs and lizards with dogs
Human
Lizard
TAIL
absent
present
Frog
Dog

11. Homoplasy: Reversal True tree Wrong tree
Reversals are evolutionary changes back to an ancestral condition
As with any homoplasy, reversals can provide misleading evidence of relationships
True tree
Wrong tree 1 2 3 4 5 6 7 8 9 10 1 2 7 8 3 4 5 6 9 10

12. So how do we construct trees with a sample of homologous characters?
How do we sort out phylogeny from a mixture of signal (synapomorphies) and noise (homoplasy).
Cladistic methodology (Willi Hennig) utilizes the principle of parsimony.
Parsimony= The tree that requires the fewest number of evolutionary changes or steps to explain the data is preferred.

13. Tree Reconstruction with Parsimony

14. Tree Reconstruction with Parsimony
Nucleotide substitution
= evolutionary step

15. Tree Reconstruction with Parsimony

16. Tree Reconstruction with Parsimony
Character 2
Tree 1
Tree 2
Tree 3
I(A)
III(A)
I(A)
II(G)
I(A)
II(G)
II(G)
IV(G)
III(A)
IV(G)
IV(G)
III(A) or or
I(A)
III(A)
I(A)
II(G)
II(G)
IV(G)
IV(G)
III(A)

17. What to do when some characters tell you one
thing and others tell you something else
(Homoplasy)?
Parsimony with Multiple Characters
The most parsimonious pattern of character change is
noted for each character separately, for each tree.
The number of changes is summed across characters
for each tree.
The preferred tree is the one that implies the fewest
overall character changes. 1 2 3

18. Tree 1 is favored under the criterion of Parsimony

19. Parsimony Advantages: Disadvantages:
Simple method - easily understood operation
Does not seem to depend on an explicit model of evolution
Should give reliable results if the data is well structured and homoplasy is either rare or widely (randomly) distributed on the tree
Disadvantages:
Doesn’t always provide the best estimate of phylogeny
Maximum likelihood
Bayesian analysis