Topics - BIOS 659

Week	Day	Topic	Instructor	Assignments & lecture notes
24-Aug	Tu	Intro, syllabus, introductions	Mike	Slide Show
26-Aug	Th	Molecular Basis of Evolution and Codon Usage Bias		Slide Show

31-Aug	Tu	Evolutionary Change of Amino Acid Sequences		Slide Show
2-Sep	Th	Lab (LC 205): Discussion of neutralist/selectionist debate; practice using computer tools to explore codon usage bias and estimating amino acid substitution rates		Exercise I, Notes on selectionist/neutralist debate

7-Sep	Tu	Evolutionary Change in DNA Sequences		Slide Show
9-Sep	Th	Lab (LC 205): Discussion of sequence alignment; practice using computer tools for estimating nucleotide substitution rates		Exercise II

14-Sep	Tu	Likelihood ratio tests, determining the best nucleotide substitution model for a given data set		Slide Show, ModelTest manual, ModelTest block for PAUP
16-Sep	Th	Synonymous and Nonsynonymous Nucleotide Substitutions		Slide Show

21-Sep	Tu	More on synonymous & nonsynonymous substitutions - MLE approaches		Assignment 1
23-Sep	Th	Finish synonymous & nonsynonymous substitutions, discuss case studies		Slide Show

28-Sep	Tu	Tools of the trade: PAUP		PAUP Manual
30-Sep	Th	Phylogenetic trees, searching "treespace"		Slide Show

5-Oct	Tu	Distance-based methods for phylogenetics: NJ, UPGMA		Slide Show
7-Oct	Th	Distance methods, cot: Minimum Evolution, LS fit

12-Oct	Tu	Phylogenetic Inference: Distance & Minimum Evolution		Assignment 2
14-Oct	Th	Phylogenetic Inference: Maximum Parsimony		Slide Show

19-Oct	Tu	Phylogenetic Inference: Maximum Parsimony		Assignment 3
21-Oct	Th	Phylogenetic Inference: Maximum Likelihood		Slide Show

26-Oct	Tu	Phylogenetic Inference: Maximum Likelihood
28-Oct	Th	Hands-on		Assignment 4

2-Nov	Tu	Phylogenetic Inference: Bayesian Methods	Kelchner	Background reading Slide Show
4-Nov	Th	Hands-on	Kelchner

9-Nov	Tu	Accuracies and Statistical Tests of Phylogenetic Trees: the probability of finding the true tree		Slide Show
11-Nov	Th	More tests: bootstrap, interior branch tests		Slide Show

16-Nov	Tu	Assessing tree support: hands on		Assignment 5
18-Nov	Th	Issues for microbial phylogenetics	Sheridan

		Thanksgiving break…

30-Nov	Tu	Molecular Clocks and Linearized Trees
2-Dec	Th	Molecular Clocks and Linearized Trees

7-Dec	Tu	Population Trees from Genetic Markers
9-Dec	Th	GUEST	Matocq?	Final Exam assigned

TBA	TBA	Final Exam