L41 BIOL 2970 Lecture Notes - Lecture 25: Pyrimidine, Long Branch Attraction, Upgma
25 Feb 2016
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Document Summary
Cladogram branches denote nested hierarchy of clades and homologies not the same as a phylogenetic tree. Phenogram branches show overall similarity or distance between sequences. Aligned sequences as for parsimony: calculate genetic distance for all pairs of sequences and summarize in a matrix, use algorithm (upgma, neighbor-joining) to convert the distance matrix to a phenogram, apply statistical test (bootstrapping) Homoplasy (homoplastic) character similarity that does not represent common ancestry. Number of evolutionary changes exceeds the number of derived states: parallelism lineages diverge from a common ancestor but not from each other, reversal evolutionary return to an ancestral character formerly changed or lost. Parsimony assumption constant expected rates of evolution on all branches of the tree. Lba (long branch attraction) parallelisms on long branches cause parsimony mistakenly to group them as a clade. Solution use extra information from the data to estimate branch length and model of base substitution.
