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.

Course outline
1 (Sep 15) Introduction and course organization (SYH, CNW)
2 (Sep 22) Introduction to phylogenetic analysis using genotyping and DNA sequences data (SYH)
3 (Sep 29) Molecular homology, multiple sequence alignments (SYH)
4 (Oct 6) Distance methods: models of nucleotide and protein evolution (SYH)
5 (Oct 13) Parsimony: tree length and other indices, molecular clock, substitution modeling testing, tree-searching algorithms, consensus trees (SYH)
6 (Oct 20) Maximum likelihood theory and methods; Phylip and PAUP* (SYH)
7 (Oct 27) Accuracy and performance of MP & ML; Assessment, Tree Confidence; Phylip and PAUP* (SYH)
8 (Nov 3) Bayesian methods; Introduction to MrBayes (CNW)
9 (Nov 10) Midterm examination
10 (Nov 17) Molecular divergence dating (1) (CNW)
11 (Nov 24) Molecular divergence dating (2) (CNW)
12 (Dec 1) Applications in phylogeography research (1) (CNW)
13 (Dec 8) Applications in phylogeography research (2) (CNW)
14 (Dec 15) Applications in adaptive evolution research (1) (CNW)
15 (Dec 22) Applications in adaptive evolution research (2) (CNW)
16 (Dec 29) Applications in community structure research (CLH)
17 (Jan 5) Final examination