Phylogeny and Evolution

The phylogenetic tree is a central concept in biology for students studying "Biodiversity, Ecology & Evolution," "Agricultural Biology," and "Eco-epidemiology." To address phylogeny, this course is divided into two successive parts, each lasting 22.5 hours: "Phylogeny and Evolution (Basics)" (HAB708B) and "Phylogeny and Evolution (Advanced)" (HAB714B).

The following subjects will be taught:

(i) History of the concept of evolution [Basics].

(ii) Phylogenetic systematics (characters, taxonomy rules, molecular barcodes, genomics, alignment, homology and homoplasy, orthology and paralogy) [half in Basics; half in Advanced].

(iii) Phylogenetic representation (networks, trees, root, dendrograms, topology, branch lengths) [Basics].

(iv) Phylogenetic inference methods based on distances [Advanced].

(v) The cladistic approach and the principle of maximum parsimony [Basics].

(vi) The probabilistic approach, the maximum likelihood principle, and sequence evolution models [Advanced].

(vii) Measures of phylogenetic robustness (bootstrap, topology comparison, multigenic corroboration, gene and species trees) [Advanced].

(viii) Applications to the phylogeny of some major taxonomic groups (mammals, eukaryotes) [Advanced].

Read phylogenetic trees and their parenthetical notation, and understand the information conveyed by their topologies and branch lengths. [Basics].

Reconstructing trees using distance methods. [Advanced].