MIT CompBio Lecture 20 - Phylogenomics (Fall 2019)

MIT Computational Biology: Genomes, Networks, Evolution, Health http://compbio.mit.edu/6.047/ Prof. Manolis Kellis Full playlist with all videos in order is here: https://www.youtube.com/playlist?list=PLypiXJdtIca6U5uQOCHjP9Op3gpa177fK All slides from Fall 2019 are here: https://stellar.mit.edu/S/course/6/fa19/6.047/materials.html Outline for this lecture: 1. Reconciliation: Mapping gene trees to species trees - Inferring orthologs/paralogs, gene duplication and loss - Reconciliation: problem, examples, MPR (max parsimony) 2. Phylogenomics: Gene/species tree reconstruction - Species tree: supermatrix, supertree, min MPR cost - Gene tree: tree scaling and learning, generative model 3. Evolution in populations: Models and algorithms - Wright-Fischer (Fw), Coalescent (Bw), Multi-Species Coal. - Coalescent times distribution, coalescent simulations 4. Incomplete lineage sorting: blend pop/species models - Using ILS: species tree, divergence times, population sizes - Dealing with ILS: Unified model: allele-locus-species tree - Deal w/ recombination: Ancestral recombination graphs (ARGs) 5. Evolution of Evolutionary Theory: Modern Synthesis