Reconstructing Phylogenetic Trees

• character polarity


  outgroup comparison, choosing a monophyletic group, and comparing characteristics in each group
• outgroup is always primitive
• autapomorphies


  distinct feature, derived trait, that is unique to a certain taxon
• the principle of parsimony


  of many explanations fir the observed pattern, the simplist should be preferred
• most real life datasets are too complex for by-hand analysis
• most datasets contain conflicting characters
• number of possible trees rise rapidly with the number of taxa
• algorithmic approaches uses principle of parsimony to compare different trees
• each tree forces assumptions of character change to fit data
• the most parsimonious tree is the most likely
• homoplasy


  conflict between characters, similarity not due to common ancestor
• homoplasy can be because of convergent evolution or reversals
• reversals


  derived state revives the lost character states