Advanced Phylogeny and Evolution

"The phylogenetic tree is a central concept in biology for students in the "Biodiversity, Ecology & Evolution", "Biology Agrosciences" and "Eco-epidemiology" majors. To tackle phylogeny, this UE is divided into two successive parts of 22.5h each: "Phylogeny and Evolution (Basics)" (HAB708B) and "Phylogeny and Evolution (Advanced)" (HAB714B).

The following skills will be taught:

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

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

(iii) Phylogenetic representation (networks, trees, roots, dendrograms, topology, branch lengths) [Bases].

(iv) Distance-based phylogenetic inference methods [Advanced].

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

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

(vii) Measures of phylogeny robustness (bootstrap, topology comparison, multigene 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].