Graduate Phylogenetics - Fall 2026

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 and Thursday 12 AM - 1:15 PM, SE 1 298

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

August 27, 2026
Class intro

September 1, 2026
HPC intro

September 3, 2026
Tree thinking exercises
The Ancestors are not among us

September 8, 2026, Tree Terms and Formats

September 10, 2026,
HPC hands on demo slurm
HPC hands on demo - salloc

September 14, 2026,
Models and Data

September 22, 2026,
Scarpetta et al. Iguanas rafted more than 8,000 km from North America to Fiji

September 22, 2026,
Data and Inference

September 24, 2026,
Chen et al. A genome-based phylogeny for Mollusca is concordant with fossils and morphology

September 29, 2026,
Likelihood
Phylo site pattern and likelihod demos

October 1, 2026,
Shultz et al. Ancient gene linkages support ctenophores as sister to other animals

October 6, 2026,
ML_search
IQ-Tree tutorial

October 8, 2026,
Steenwyk and King, Integrative phylogenomics positions sponges at the root of the animal tree.
Dunn et al. 2025
Keep calm and be transparent: advice from scientists who retracted their papers

October 13, 2026,
Data for phylogenetic analysis
Assembly and alignment lab

October 15 2026,
Lescroat et al. Phylogenomics and museomics reveal five distinct species of tiger cats in South America

October 20, 2026,
Discordance

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