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.

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

Phylogenetic Trees A CLADOGRAM

CLADOGRAMS AND PHYLOGRAMS E 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

Trees - Rooted and Unrooted

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 http://tolweb.org/tree/phylogeny.html

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

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

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

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

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

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

Homoplasy 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 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

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

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

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

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.

Tree Reconstruction with Parsimony

Tree Reconstruction with Parsimony Mutation=Evolutionary Step

Tree Reconstruction with Parsimony

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)

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

Tree 1 is favored under the criterion of Parsimony

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.

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

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

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