Schedule
All sessions are in Loeb G70 (basement of Loeb building)
Friday, May 26, 2023
| 18:00 - 21:00 | Swope Terrace (overlooking Eel Pond) | Opening Reception |
Saturday, May 27, 2023
| 09:00 - 10:30 | Beerli | Welcome, Introductions, and Workshop introduction |
| 10:30 - 12:00 | Lewis | Introduction to Phylogenetics |
| 14:00 - 15:30 | Huelsenbeck | Introduction to Likelihood |
| 15:30 - 17:00 | Huelsenbeck | Simulating Molecular Evolution |
| 19:00 - 20:30 | TAs | Intro computer lab |
| 20:30 - 22:00 | TAs | Alignment lab |
Sunday, May 28, 2023
| 08:00 - 09:00 | Huelsenbeck | C++ Programming Workshop (optional) (Programming Book) |
| 09:00 - 10:30 | Lewis | Maximum likelihood (cont.) |
| 10:30 - 12:00 | Swofford | Model Selection |
| 14:00 - 15:30 | Swofford | Introduction to PAUP* |
| 15:30 - 17:00 | Swofford | PAUP* lab |
| 19:00 - 20:30 | Minh | IQ-TREE Introduction |
| 20:30 - 22:00 | Minh | IQ-TREE lab IQ-TREE quiz |
| Minh | IQ-TREE Solutions | |
| 22:00 - 23:59 | Loeb Quad | Evening social gathering |
Monday, May 29, 2023
| 08:00 - 09:00 | Huelsenbeck | C++ Programming Workshop (optional) |
| 09:00 - 10:30 | Lewis | Bayesian phylogenetics (part 1) |
| 10:30 - 12:00 | Lewis | Bayesian phylogenetics (part 2) |
| 14:00 - 15:30 | Brown | Introduction to graphical models and RevBayes |
| 15:30 - 17:00 | Brown | Gene tree estimation with RevBayes |
| 19:00 - 20:30 | Heath | Divergence time estimation |
| 20:30 - 22:00 | Heath | Divergence time estimation Lab |
Tuesday, May 30, 2023
| 08:00 - 09:00 | Huelsenbeck | C++ Programming Workshop (optional) |
| 09:00 - 10:30 | Beerli | Introduction to The Coalescent |
| 10:30 - 12:00 | Beerli | Extending the coalescent |
| 14:00 - 15:30 | Kubatko | Species Tree Estimation |
| 15:30 - 17:00 | Kubatko, Swofford | Species Tree Lab Slides, Species Tree Lab Tutorial |
| 19:00 - 20:30 | Solís-Lemus | Network models lecture (2023 version) |
| 20:30 - 22:00 | Solís-Lemus | Network models tutorial |
Wednesday, May 31, 2023
| 08:00 - 09:00 | Huelsenbeck | C++ Programming Workshop (optional) |
| 09:00 - 10:30 | Edwards | Multilocus phylogeography and phylogenetics |
| 10:30 - 12:00 | Edwards | Pangenomes and evolution |
| 12:00 - 12:15 | group photo (don’t miss it!) | (we still need to decide where: Lillie steps? Swope terrace?) |
| 14:00 - 15:30 | Yoder | What are we even talking about when we say “species tree”? |
| 15:30 - 17:00 | Yoder | What are we even talking about when we say “species tree”? (cont.) |
| 19:00 - 20:30 | Swope Terrace | Course Dinner Party |
| 20:30 - 22:00 | Swope Terrace | Course Dinner Party |
| 22:00 - 23:59 | Loeb Quad | Post-dinner social gathering |
Thursday, June 1, 2023
Free Day (sleep in, catch up on email, visit Martha’s Vineyard, go whale watching in Hyannis, etc.)
Friday, June 2, 2023
| 08:00 - 09:00 | Huelsenbeck | C++ Programming Workshop (optional) |
| 09:00 - 10:30 | Bielawski | Theories of molecular evolution: Lecture slides |
| 10:30 - 12:00 | Bielawski | Intro to codon models: Lecture slides |
| 14:00 - 15:30 | Chang | Protein evolution & ancestral reconstruction |
| 15:30 - 17:00 | Chang | Adaptive protein evolution |
| 19:00 - 20:30 | Bielawski | PAML lab, lab slides |
| 20:30 - 22:00 | Bielawski | Additional resources, advanced lab |
| 22:00 - 23:59 | Loeb Quad | Social |
Saturday, June 3, 2023
| 08:00 - 09:00 | Huelsenbeck | C++ Programming Workshop (optional) |
| 09:00 - 10:30 | Smith | Machine learning and Molecular Evolution |
| 10:30 - 12:00 | Smith | Machine learning and Molecular Evolution |
| 14:00 - 15:30 | Susko | Bootstrap and tree topology tests |
| 15:30 - 17:00 | Susko | Bootstrap and tree topology tests |
| 19:00 - 20:30 | Beerli | Model comparison in biogeography/population genetics using MIGRATE |
| 20:30 - 22:00 | Beerli | Model comparison in biogeography/population genetics using MIGRATE |
| 22:00 - 23:59 | Loeb Quad | Social |
Sunday, June 4, 2023
| 09:00 - 10:30 | Eme | Amino acid models and deep time phylogenetics |
| 10:30 - 12:00 | Eme | Amino acid models and deep time phylogenetics |
| 14:00 - 15:30 | McTavish | Phylogenomics slides, Tree updating lab |
| 15:30 - 17:00 | McTavish | Open Tree slides, Tree comparison lab |
| 19:00 - 20:30 | Knowles | Evolutionary applications of genomic data |
| 20:30 - 22:00 | Knowles | Evolutionary applications of genomic data (cont.) |
| 22:00 - 23:59 | Loeb Quad | Almost-the-end party |
Monday, June 5, 2023
| 09:00 - 10:30 | Swofford/Bielawski | Scientific ethics panel discussion (Holder 2019 lecture) |
| 10:30 - 12:00 | Open lab |