Subsections
[Cr:4, Lc:4, Tt:0, Lb:0]
- Introduction: Revision of Natural Selection, Hardy-Weinberg Equilibrium, Random Genetic Drift and
Effective Population Size.
- Manipulating sequences: Mutations; Rates of Mutations; Recombination; Indels; Aligning Sequences;
Calculating Evolutionary Distances among Sequences; Corrections and Models of Sequence Evolution.
and.
- Natural Selection: Rates, Clocks, and the Neutral Theory: Selection at the Molecular Level; The
Neutral and Nearly-neutral Theories of Molecular Evolution; Molecular Clocks and the Relative Rates
Test; Codon Bias; Variations in Substitution Rates and their Causes in Nuclear, Organellar, and Viral
DNA; Tests of Positive Selection (McDonald Kreitman, Ka/Ks, Tajimas D Statistics, etc.).
- Genome Evolution: Genome Duplication in Eukaryotic Evolution; Evolution of Gene Families; Chro-
mosome Evolution; Endosymbiosis and Lateral Gene Transfer.
- Introduction to Systematics and Phylogenetics: Taxonomy as the most Fundamental Biological Science;
Nomenclature and Classification.
- Phylogenetic Trees: Kinds of Trees; Rooting; Clades; Reconstructing Character Evolution, Consensus
Trees, Phylogenetic Hypothesis Testing; Gene Trees and Species Trees.
- Methods for Inferring Phylogenetic Trees: Parsimony, Minimum Distance, Maximum Likelihood and
Bayesian Methods; Statistical Robustness of Trees; Introduction to some Software for Building Trees
and Molecular Population Genetic Tests.
- Using Phylogenetic and Molecular Evolutionary Tools to Answer Biological Questions: Speciation;
Phylogeography; Biogeography; Infectious Diseases.
- Fundamentals of Molecular Evolution, Dan Graur & Wen-Hsiung Li, Sinauer Associates, 2nd Edition,
1999.
- Molecular Evolution: A Phylogenetic Approach, Roderick D.M. Page, Wiley-Blackwell, 1998.
- The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing,
Philippe Lemey, Cambridge University Press, 2009.
- Tree Thinking: An Introduction to Phylogenetic Biology, David Baum & Stacey Smith, Roberts and
Company Publishers, 2012.
