Phylogeny: A short introduction to the core concepts of trees, homologs, orthologs, and paralogs
Channel: Lars Juhl Jensen
Date: 01/11/2021

A short introduction to the core concepts of phylogeny. The presentation provides a minimal introduction to the basic ideas and terminology related to taxonomy and phylogeny, such as taxa, species trees, clades, gene trees, homologs, orthologs, and paralogs.

0:00 Introduction: classification of organisms, evolution of species and genes, terminology, tree construction, tree comparison, and subdivision of homologs
0:31 Terminology: taxonomy, taxa, taxonomic levels, phylogeny, phylogenetic species trees, and monophyletic groups / clades
1:41 Gene and species trees: multiple sequence alignment, gene tree construction, maximum parsimony, maximum likelihood, species tree construction, marker genes, concatenated alignments, and consensus gene trees
2:53 Orthologs and paralogs: tree comparison, speciation and gene duplication events, two types of homologs, and definitions of orthologs and paralogs
4:37: Why care: fundamental questions about evolution and direct applications to function prediction and interaction transfer