studying evolution through computational phylogeny€¦ · outgroup use (cont’d) da-fei feng,...
TRANSCRIPT
STUDYING EVOLUTION THROUGH COMPUTATIONAL PHYLOGENY Yulia Newton University of California Santa Cruz [email protected] 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?