Lecture 1 - Introduction to Systematics and Phylogenetics. Notes Slides.
Costello et al. (2013). An estimate of current diversity (that focuses on macrobial species).
Locey and Lennon (2016). An estimate of the number of extant microbial species.
Li and Wiens (2023). An estimate of current diversity derived by extrapolating the rate of cryptic species in insects.
Lecture 2 - The History of Phylogenetic Inference. Notes Slides.
Quinn (2017). An interesting take on the evolution of the term "cladist."
Lecture 3 - Characters: Homology and Morphology. Notes Slides.
Lecture 4 - Characters: Molecular. Notes Slides.
Edwards et al. (2002). An early example of alignment-free genomic distances used for phylogeny.
Steenwyk & King (2024). A recent discussion on the use of conserved syntenic groups in phylogenomics.
Lecture 5 - Alignment. Notes Slides.
Lecture 6A - Introduction to Trees and Optimality Criteria: Parsimony. Notes Slides.
Lecture 6B - Optimality Criteria: Maximum Likelihod & Minimum Evolution. Notes Slides.
Lecture 7 - "Algorithmic Approaches" to Tree Building. Notes Slides.
Lecture 8 - Searching Tree Space. Notes Slides.
Lecture 9 - The Importance of Models of Sequence Evolution. Notes Slides.