Powerpoints from Lectures:
Wed. Jan 18
Introduction to Phylogenetics
Reading: Goldman and Yang 2008
Fri Jan 20
Lab: Data file formats, tree file formats, data editing and file conversion tools
Mon. Jan 23
Homology and sequence alignment
Wed. Jan 25
Approaches to sequence alignment
Friday, Jan 27
Lab: BLAST, sequence alignment
Parsimony Analysis (JBW)
Mon. Jan. 30
Basic parsimony analysis.
Wed. Feb 1
Character optimization and models of character state change
Fri. Feb. 3
Lab: Parsimony analysis, character optimization
Advanced Parsimony Analysis (JBW)
Mon Feb 6
Strategies and algorithms for heuristic parsimony analysis
Reading: Goloboff 1999
One-page proposal for Final project due.
Wed Feb 8
Resampling methods, Bremer Support
Fri Feb 10
Lab: Advanced parsimony analysis
Distance-Based Methods (JBW)
Mon Feb 13
Measures of molecular distance.
reading from text: 4. Genetic distances and nucleotide substitution models
Wed Feb 15
reading from text: 5. Phylogenetic inference based on distance methods
Fri Feb 17
Lab: Phenetic analysis of molecular data, MEGA/PAUP*
Model-Based Methods: Maximum Likelihood Methods (MM)
Mon Feb 20
Substitution rate matrices, nucleotide frequencies, other model parameters.
Wed Feb 22
Fri Feb 24
Draft Alignment for final project due
Model-Based Methods: Maximum Likelihood Methods continued (MM)
reading from text: 6 Phylogenetic inference using maximum likelihood methods
Mon Feb. 27
Implementing a Maximum Likelihood analysis
Wed Feb 29
Different algorithms and ML programs
Fri Mar 2
Lab: Implementing a Maximum Likelihood analysis (Paup, PhyML, RAxML and GARLI)
Model-Based Methods: Bayesian Analysis (MM)
reading from text: 7 Bayesian phylogenetic analysis using MRBAYES
Mon Mar 5
Bayesian inference methods in phylogenetics.
Wed Mar 7
Bayesian methods, continued
Fri Mar 9
Lab: Implementing a Bayesian analysis; MrBayes.
Spring Break (NO CLASSES)
Data Partitions (MM)
Mon Mar 19
Wed Mar 21
Fri Mar 23
Ecological Integration Symposium (no lab)
Week 10 Gene Trees vs. Species Trees (MM) Lecture 14 Mon Mar 26 Gene trees vs. species trees, deep coalescence and lineage sorting, the "anomaly zone" Wed Mar 28 Analytical approaches to gene tree discordance Fri Mar 30 Lab: Species tree analyses (BEST, *Beast, BUCKy)
Testing Hypotheses: comparative analyses (JBW)
Mon Apr 2
Use of phylogenetic frameworks for hypothesis testing, Independent Contrasts.
Reading: Garland et al. 2005
Wed Apr 4
Fri Apr 6
Reading day: no classes
Testing Hypotheses: Topology Comparisons and Molecular Clock (MM)
Mon Apr 9
Topology Comparisons: AU test and SOWH test
Wed Apr 11
Fri Apr 13
Lab: Topology comparisons
Week 13 Rate Heterogeneity and the Molecular Clock (MM) Mon. Apr 16 Tests of molecular clock Wed Apr 18 Analytical approaches Fri Apr 20 Lab: Identifying rate heterogeneity among lineages, BEAST and Multidivtime Week 14 Open: unfinished topics or suggestions for additional topics (MM) Mon Apr 23 To be determined. Wed. Apr 25 To be determined. Fri Apr 27 Open Lab: we will be in the laboratory to help you with any final issues with the analyses for your projects, presentation of results, etc.
Mon Apr 30
Prep Day, classes meet: Course Evaluations. Open discussion, critique of course, suggestions, problems encountered during course, etc.
Tues May 1
Redefined as Friday. No lab scheduled. Lab will be open for help in completing final project reports.
Wed May 2
Reading day; No class.
Fri May 4
Reading day; No class. Final Paper due.