L41 BIOL 2970 Lecture Notes - Lecture 9: Upgma, Synapomorphy, Distance Matrix
2 Nov 2016
School
Department
Course
Professor
Document Summary
Assumptions: (1) terminal addition: new characters are added to the end of ontogeny. (2) condensation: older features are compressed to earlier and shorter developmental occurrences. Process called alignment: common descent, phylogenies form dna sequences: Identify study group (=ingroup) + outgroup: obtain homologous dna sequences for all species being compared. Identify shared derived character states = parsimony informative sites . Find tree topology that requires the smallest number of evolutionary changes. Parallelism: lineages diverge from their common ancestor but not from each other: reversal: evolutionary return to an ancestral state formerly changed or lost, bootstrapping as a statistical test of branch support (parsimony, distance methods, maximum-likelihood methods) Sample sites in the alignment randomly with replacement to produce a new data set equal in size to the original. Perform phylogenetic analysis on the new data set: repeat steps 1-2 ~1000 times. For each branch, what % of trees from step 3 have the branch: distance matrix methods (upgma, neighbor-joining):
