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04_Ward_Inferring_trees_Outline

04_Ward_Inferring_trees_Outline - BIS2C W2011 Building...

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BIS2C W2011 Lecture 4 (7 January 2011) 1 Building trees (part 2) Today’s lecture revisiting monophyly, unrooted trees, branch lengths, and step counting building trees: model-based approaches Recapping some points If terminal taxa are individual species: they may or may not be monophyletic. If terminal taxa are higher taxa (groups of species): monophyly is assumed (or else they wouldn’t be drawn as a single branch). Unrooted trees can float freely and the branches of the trees can rotate around internal nodes without changing the meaning. Unrooted trees are different when neighbors (adjacent taxa) are different. What do “steps” or “character state changes” mean? A population -level process in which one state become substituted for another. Evaluating steps (character state changes) on trees Character conflict and how to deal with it. Building trees: model-based approaches Maximum likelihood : develop a probabilistic model of character evolution; search for most likely tree (ML tree) under that model.
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