studying evolution through computational phylogeny€¦ · outgroup use (cont’d) da-fei feng,...
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STUDYING EVOLUTION THROUGH COMPUTATIONAL PHYLOGENY Yulia Newton University of California Santa Cruz [email protected] http://users.soe.ucsc.edu/~ynewton/
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Types of Evolution
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Types of Evolution
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Different Ways to Draw an Evolutionary Tree
and many more …
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Tree Anatomy
edge
nodes
root
clade
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Roots
http://www.snowballearth.org/
Common ancestor
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Root Placement
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Outgroup Use
http://www.cscs.umich.edu/
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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.
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Cladogram • Cladogram – all taxa are at the same level
• Tells us how long ago speciation for each taxa happened
http://evolution.berkeley.edu/
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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
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Phylogram (cont’d)
http://scientopia.org/
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Cladogram vs. Phylogram
http://www.mrent.org/
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Cladogram vs. Phylogram
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Steps for Building Phylogenetic Trees
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Newick Format
Text format representation of the tree:
(((A,C), (B,D)), (E,F))
output
input
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Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))
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Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))
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Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))
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Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))
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Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))
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Drawing Tree From Newick Format (((A,C), (B,D)), (E,F))
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Which two are the closest relatives?
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Which two are the closest relatives?
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Which two are the closest relatives?
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Which two are the closest relatives?