1. What Is Phylogeny? The evolutionary history of a group.
Families, genera, species, genes
Phylogeny is not knowable (in most cases).
Many methods exist to estimate phylogeny.

2. Phylogenetic relationships
Two lineages are more closely related to each other than to some other lineage if they share a more recent common ancestor.
Phylogenetic hypotheses are hypotheses of common ancestry

3. Phylogenetic Trees
A CLADOGRAM

4. CLADOGRAMS AND PHYLOGRAMSE D C A B C D E H I J F G A B G I F H J
RELATIVE TIME
ABSOLUTE
TIME or
DIVERGENCE

5. Trees - Rooted and Unrooted

6. Systematics: The study of the classification of the immense diversity of life
Phylogenetic Systematics: The use of phylogenetic methodology to resolve monophyletic groups
Tree of Life

7. Reconstructing Evolutionary Trees
Phylogeny: Evolutionary history of a group.
Phylogenetic Tree: Shows evolutionary history graphically.
A phylogeny must be inferred from data
that are likely to reveal evolutionary history

8. Homology
Similar structures or behaviors in different organisms, which are supposed to represent modifications of a single evolutionary novelty in a common ancestor
Different function,
but homologous
Similar function,
but not homologous

9. Homology
Similar structures or behaviors in different organisms, which are supposed to represent modifications of a single evolutionary novelty in a common ancestor

10. Synapomorphies
Homologous traits or states that are shared among species because they share a common ancestor

11. Synapomorphies
Homologous traits or states that are shared among species because they share a common ancestor

12. Cladistics Methods of phylogeny reconstruction where monophyletic
groups are identified on the basis of shared derived characters.
Synapomorphy

13. Homoplasy
Shared derived similarities, that are not based on a singular common origin (= homology), but on an independent origin in different taxa.

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

15. 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

16. 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

17. 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

18. 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 utilizes the principle of parsimony.
Parsimony= The tree that requires the fewest number of evolutionary steps to explain the data is preferred.

19. Tree Reconstruction with Parsimony

20. Tree Reconstruction with Parsimony
Mutation=Evolutionary Step

21. Tree Reconstruction with Parsimony

22. 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)

23. 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

24. Tree 1 is favored under the criterion of Parsimony

25. How to search all possible trees?
The number of possible trees increases exponentially with the number of species making exhaustive searches impractical for many data sets
But we have a larger data set to consider, so using parsimony methodology, we need to utilize a way to search for the best tree without evaluating all possible trees.

27. Finding optimal trees: Heuristic searches
Heuristic methods are used to search tree space for most parsimonious trees by building or selecting an initial tree and swapping branches to search for better ones
The trees found are not guaranteed to be the most parsimonious-they are best guesses

28. Finding optimal trees: Heuristics
Tree bisection and reconnection (TBR)

29. Parsimony: Advantages
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