Lec 4 - BIS2C Winter 2009 (Ward) Lecture 4. Building trees...

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Unformatted text preview: BIS2C Winter 2009 (Ward) Lecture 4. Building trees & tree applications Today’s lecture (9 January) • revisiting monophyly, unrooted trees, branch lengths, and step counting • building trees (cont’d) • tree applications Monday’s lecture • tree applications (cont’d) a b c d e h g f Clades (monophyletic groups) If a tree has n internal nodes, then there are n monophyletic groups in that tree (excluding terminal taxa ) . a b c d e h g f Clades (monophyletic groups) Terminal taxa are individual species: may or may not be monophyletic. Terminal taxa are higher taxa (groups of species): monophyly is assumed (or else they wouldn’t be drawn as a single branch). This phylogeny of the three domains reveals five clades: {Archaea + Eukarya} and {Bacteria + Archaea + Eukarya}, corresponding to the descendants of the two internal nodes that are marked, but also the three domains individually: Bacteria, Archaea, and Eukarya. Each of the three domains contains numerous species but in the summary tree we don’t show them. Each of the three domains contains numerous species but in the summary tree we don’t show them. There is an implied common ancestor of the species included in bacteria. Each of the three domains contains numerous species but in the summary tree we don’t show them. There is an implied common ancestor of the species included in bacteria. Ditto for Archaea and Eukarya. Unicellular eukaryotes If a multi-species group is not monophyletic then it will be depicted by multiple branches that don’t form a clade (e.g., unicellular eukaryotes). No meaning to branch lengths. Branch length is proportional to the amount of character change A C B D A C B D Cladogram Phylogram What would the equivalent unrooted trees look like for both the cladogram and the phylogram? No meaning to branch lengths. Branch length is proportional to the amount of character change A C B D A C B D Cladogram Phylogram What would the equivalent unrooted trees look like? In the equivalent unrooted trees we remove the root and straighten the branch to which the root was attached. root root No meaning to branch lengths. Branch length is proportional to the amount of character change A C B D A C B D Cladogram Phylogram In the equivalent unrooted tree we remove the root and straighten the branch to which the root was attached. A C B D A C B D No meaning to branch lengths. Branch length is proportional to the amount of character change A C B D A C B D Cladogram Phylogram A C B D A C B D No meaning to branch lengths. Branch lengths meaningful Rooted Unrooted No meaning to branch lengths. Branch length is proportional to the amount of character change A C B D A C B D Cladogram Phylogram A C B D A C B D Rooted Unrooted No meaning to branch lengths....
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Lec 4 - BIS2C Winter 2009 (Ward) Lecture 4. Building trees...

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