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

edge

nodes

root

clade

Roots

http://www.snowballearth.org/

Common ancestor

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

Text format representation of the tree:

(((A,C), (B,D)), (E,F))

output

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?