Phylogenetics explores how organisms, genes, and traits have evolved, and seeks to represent the history of life’s divergence through the use of phylogenetic trees. Phylogenetics has contributed to a wide variety of research especially in the fields of systematics, biogeography (phylogeography), adaptive evolution, and community structure. Lectures will emphasize the logical basis and computational details of various tree-building algorithms and associated methods of hypothesis testing, as well as application of next-generation sequencing data in phylogenetic tree building. In general, this course will focus on the use, interpretation, and methods of reconstructing evolutionary trees.
1 (Feb 19) Introduction and course organization
2 (Feb 26) Introduction to phylogenetic analysis using genotyping and DNA sequences data
3 (March 5) Molecular homology, multiple sequence alignments
4 (March 12) Distance methods: models of nucleotide and protein evolution
5 (March 19) Parsimony: tree length and other indices, molecular clock, substitution modeling testing, tree-searching algorithms, consensus trees
6 (March 26) Maximum likelihood theory and methods; Phylip and PAUP*
7 (April 2) No class
8 (April 9) Accuracy and performance of MP & ML; Assessment, Tree Confidence; Phylip and PAUP*
9 (April 16) Midterm examination
10 (April 23) Bayesian methods; Introduction to MrBayes
11 (April 30) Molecular divergence dating (1)
12 (May 7) Molecular divergence dating (2)
13 (May 14) Applications in phylogeography research (1)
14 (May 21) Applications in phylogeography research (2)
15 (May 28) Applications in adaptive evolution research (1)
16 (June 4) Applications in adaptive evolution research (2)
17 (June 11) Applications in community structure research
18 (June 18) Final examination