Graduate Phylogenetics - Fall 2017

University of California, Merced – QSB/ES 244

A graduate course covering phylogenetic methods: theory, statistics and practice.
Syllabus

Instructor: Emily Jane McTavish

Time/Location: Lecture/Lab, Tuesday 3:00- 6:00 and Discussion Friday, 11:30-12:30 PM, SE1 198.
Lecture/Lab is registered students only, everyone is welcome at discussion.

Web View: https://mctavishlab.github.io/GradPhylo

Please complete setup instructions listed at https://mctavishlab.github.io/GradPhylo/installs

Intro slides
HW Week 1 (29 Aug)
Week 1 slides Tree terminology and applications
HW Week 2 (Sept 5)
Discussion paper Sept 1 Zhang et al. 2016 Genome-wide introgression among distantly related Heliconius butterfly species
Week 2 slides Inference
Discussion paper Sept 8
Merced Cluster slides
Week 3 slides Inference and likelihood
Discussion paper Sept 15 sent to list (unpublished)
Week 4 slides Likelihood and models
Week 5 slides Likelihood searching
Week 5 lab ML search lab
Week 6 slides Ascertainment Bias
Week 6 lab Model selection in PAUP demo (wasn’t enough time, optional)
Week 7 slides Intro to Bayesian inference
Monte Hall game link
Week 8 slides
MCMC tutorial in RevBayes
Week 9 slides
Optional Lab on diversification in RevBayes
Week 10 paper discussion and divergence time based on Tracy Heath’s slides
Week 11 Computer lab on BEAST 2: introduction
Week 11 Computer lab on BEAST 2: divergence time estimation
Week 12 Paper discussion; the coalescent and gene tree/species tree estimation
Week 13 Paper discussion; finish Gene Tree Spp Tree lecture; Optional SVD quartets lab
Week 14 Comparative methods and Ancestral state reconstruction images lab
Week 15 Topology testing

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