STUDYING EVOLUTION THROUGH COMPUTATIONAL PHYLOGENY Yulia Newton University

STUDYING EVOLUTION THROUGH COMPUTATIONAL PHYLOGENY Yulia Newton University of California Santa Cruz ynewton@soe. ucsc. edu http: //users. soe. ucsc. edu/~ynewton/

Types of Evolution

Types of Evolution

Different Ways to Draw an Evolutionary Tree and many more …

Tree Anatomy clade edge nodes root

Roots Common ancestor http: //www. snowballearth. org/

Root Placement

Outgroup Use http: //www. cscs. umich. edu/

Outgroup Use (Cont’d) Da-Fei Feng, Glen Cho, and Russell F. Doolittle. Determining divergence times with a protein clock: Update and reevaluation, PNAS, 1997.

Cladogram • Cladogram – all taxa are at the same level • Tells us how long ago speciation for each taxa happened http: //evolution. berkeley. edu/

Phylogram • Phylogram – the length of the edge indicates how much evolution happened since the last common ancestor • Tells us how closely two species are related

Phylogram (cont’d) http: //scientopia. org/

Cladogram vs. Phylogram http: //www. mrent. org/

Cladogram vs. Phylogram

Steps for Building Phylogenetic Trees

Newick Format output Text format representation of the tree: (((A, C), (B, D)), (E, F)) input

Drawing Tree From Newick Format (((A, C), (B, D)), (E, F))

Drawing Tree From Newick Format (((A, C), (B, D)), (E, F))

Drawing Tree From Newick Format (((A, C), (B, D)), (E, F))

Drawing Tree From Newick Format (((A, C), (B, D)), (E, F))

Drawing Tree From Newick Format (((A, C), (B, D)), (E, F))

Drawing Tree From Newick Format (((A, C), (B, D)), (E, F))

Which two are the closest relatives?

Which two are the closest relatives?

Which two are the closest relatives?

Which two are the closest relatives?