BIOL 4753-5753

	A	B	C	D	E
1	PART I: Phylogenetic Inference
2	Week	Date	Lecture topic	Practical topic	Notes
3	1	19-Aug	Introduction to phylogenetics and tree thinking
4	1	21-Aug	Introduction to phylogenetics and tree thinking (cont.)
5	2	26-Aug	Introduction to phylogenetics and tree thinking (cont.)	File formats and regular expressions (RegEx)
6	2	28-Aug		Unix basics, remote access & running jobs in OSCER (by Dr. Henry Neeman)
7	3	2-Sep	No class - Labor Day Holiday	No class - Labor Day Holiday
8	3	4-Sep	Tree space & optimality criteria
9	4	9-Sep	Tree space & optimality criteria
10	4	11-Sep	Distance methods
11	5	16-Sep	Models of molecular evolution
12	5	18-Sep	Multiple sequence alignment	Multiple sequence alignment
13	6	23-Sep	Maximum likelihood, bootstrap & hypothesis testing
14	6	25-Sep	Maximum likelihood, bootstrap & hypothesis testing	ML (RAXML) & bootstrap
15	7	30-Sep	Model selection; rate heterogeneity	Model selection & rate heterogeneity: PartitionFinder
16	7	2-Oct	Model selection; rate heterogeneity (cont.)	Model selection & rate heterogeneity: PartitionFinder	Graduate students: deadline to submit outline for final project
17	8	7-Oct	Bayesian inference
18	8	9-Oct	Bayesian inference	Bayesian inference and ML. Molecular clocks: BEAST tutorial	Undergraduates: deadline to send three papers for final presentation
19	9	14-Oct	Molecular clocks	Molecular clocks: BEAST tutorial
20	9	16-Oct	Gene trees & species trees	Gene trees & species trees inference
21	10	21-Oct	Midterm exam (phylogenetic inference)		Starting Monday (12:01 am); due Sunday October 27 (11:59 pm)
22	10	23-Oct	Midterm exam (cont.)
23	11	28-Oct	Exam revision. Gene trees & species trees (cont.)
24	PART II: Phylogenetic Comparative Methods
25	11	30-Oct		R basics. Introduction to reading, writing, manipulating, and visualizing trees in R
26	12	4-Nov	Introduction to the phylogenetic comparative method
27	12	6-Nov		Phylogenetically independent contrasts in R
28	13	11-Nov	Estimating speciation and extinction rates using phylogenies
29	13	13-Nov	Models of continuous trait evolution on trees	Estimating speciation and extinction rates using phylogenies
30	14	18-Nov	Models of continuous trait evolution on trees (cont.)	Phylogenetic signal & fitting models of continuous trait evolution
31	14	20-Nov	Discrete trait evolution & ancestral state reconstructions	Fitting models of discrete character evolution
32	15	25-Nov	Undergrad presentations. 3:00 to 5:30 pm. All students must be present.
33	15	27-Nov	No class - Thanksgiving	No class - Thanksgiving
34	16	2-Dec		Ancestral state reconstructions (work from home)
35	16	4-Dec		Visualizing phylogenies and comparative data in R (work from home)
36	17	9-Dec	No class
37	17	10-Dec	Graduate presentions. 4:30-6:30 pm. All students must be present.
38	17	13-Dec			Deadline to submit term paper (11:59 pm)
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