Chapter 3. Substitution Patterns

Patterns of Substitutions withing Genes: Mutation rates, functional constraint, synonymous vs. nonsynonymous substitutions, Indels and pseudogenes, substitutions vs. mutations, fixation

Estimating substitution numbers: Juke-Cantor model, Kimura's two-parameter model, models with more parameters, substitutions between protein sequences

Variations in Evolutionary rates between genes

Molecular clock, relative rate test, causes of rate variation in lineages

Evolution in Organelles

Chapters 4. Distance-Based Methods of Phylogenetics

Advantages to molecular phylogenies

Phylogenetic trees and terminology: terminal nodes, internal nodes, inferred ancestors, Newick format, bifurcating, multifurcating, scaled trees, unscaled trees, rooted and unrooted trees (number of trees), Gene vs. Species trees, character and distance data, Pheneticists, and Cladists

Distance Matrix methods: UPGMA, estimation of branch lengths, transformed distance method,

and the general idea without the details of neighbor's relation method, neighbor-joining methods

Maximum likelihood approaches - general concept

Multiple sequence alignment and how it relates the phylogenetic analysis