BIOSCI 700: Phylogenetics

Semester 1, 2026

The University of Auckland

Course Information

Lectures: Tuesdays, 1–3pm
Labs: Even-week Thursdays, 9am–12pm
Location: MAC1 (Building 106, Room 112)
Textbook: Decoding Genomes (Stadler et al, 2024)

Instructors

  • Weeks 1–5, 7, 10–12: Alexei Drummond (a.drummond@auckland.ac.nz)
  • Week 6: David Welch (Guest)
  • Week 8: Caroline Puente-Lelievre (Guest)
  • Week 9: Simon Greenhill (Guest)
Week 1 Begins 2 March
Required Reading: Decoding Genomes — Chapter 1
Recommended additional reading: Six impossible things before breakfast
Week 2 Begins 9 March
Required Reading: Decoding Genomes — Chapter 3: Sequence Alignments
Tuesday 1–3pm
Thursday 10am–12pm
  • Lab (available for catch-up)
Week 3 Begins 16 March
Required Reading: Decoding Genomes — Chapter 6: Phylogenetic Trees
Tuesday 1–3pm
Thursday 9am–12pm
  • Lab 1 Alignment and Phylogenetic Reconstruction
Week 4 Begins 23 March
Required Reading: Decoding Genomes — Chapter 5: Molecular Evolution
Tuesday 1–3pm
Week 5 Begins 30 March
Required Reading: Decoding Genomes — Chapter 10: Bayesian Inference
Tuesday 1–3pm
Thursday 9am–12pm
  • Lab 2 Phylogenetic inference with BEAST2
Break 3 April – 17 April
Mid-Semester Break
Week 6 Begins 20 April
Guest Lecture
"Phylodynamics with application to epidemics in NZ"
David Welch
Week 7 Begins 27 April
Required Reading: Decoding Genomes — Chapter 9: Phylodynamics
Tuesday 1–3pm
Week 8 Begins 4 May
Guest Lecture
"Protein structure and the beginning of a third era in phylogenetics"
Caroline Puente-Lelievre
Week 9 Begins 11 May
Guest Lecture
"Cultural Phylogenies"
Simon Greenhill
Week 10 Begins 18 May
Required Reading: Decoding Genomes — Chapter 8: Traits and Comparative Methods
Tuesday 1–3pm
Week 11 Begins 25 May
Required Reading: Uyeda et al. (2018) — Rethinking phylogenetic comparative methods
Tuesday 1–3pm
Week 12 Begins 1 June
Tuesday 1–3pm
Study Begins 9 June
Study Week
Exam Begins 16 June
Examination Week