Our material on phylogenetics in bioinformatics was roughly divided into five "units".  Some of the topics that you should especially focus on, with one or a few goals or questions follow each section.


1.  concepts of trees and inferences based on trees


- trees as hypotheses of evolutionary history and shared ancestory

- HOMOPLASY:  convergence, parallelism, reversal

- gene trees I:  orthology, paralogy

- monophyly

- inference of ancestral states using ACCTRAN


                  * be able to "read" a phylogenetic tree, and draw correct inferences about the monophyly of groups of organisms or sequences


                  * given a tree and a set of data for a given character, be able to infer the ancestral states of the character using the method of ACCTRAN



2.  methods of building phylogenetic trees


- parsimony, distance, likelihood compared and contrasted

- the basic approaches, similarities and differences

- standard (nonparametric) bootstrap in phylogenies: use and interpretation

- strengths and weaknesses of each of the major methods

- PHYLIP as an intro to computer programs for phylogeny


                  * be able to perform and interpret a small parsimony analysis by hand, as we did in class, or using any of the main approaches including boostrap, with PHYLIP



3.  distance models of sequence evolution


                  * contrast the different distance models for sequence (or protein) evolution.  What are some advantages and disadvantages?


4.  maximum likelihood as a general tool for hypothesis testing


                  * what is the likelihood ratio test and how is it used to test a wide variety of possible hypotheses about sequence evolution, such as:  rates of evolution, monophyly of group or sequences, similarity of branching history of two trees, etc.


                  * be able to outline or diagram the goals and basic steps in a parametric bootstrap analysis, and it's use in  hypothesis testing in sequence studies.


5.  further concepts and their application


- gene families II, reconciled gene trees

- long branch attraction conditions, causes


                  * The example given in class of phylogenetic analyses of invertebrate animals was a good example of a dataset where different methods gave different results, but exploring the different results led to a better understanding of the history of the sequences.  What were some "take home lessons" to be gained from this example?