OEB 192 – “Evolutionary speculation constitutes a kind of metascience, which has the same intellectual fascination for some biologists that metaphysical speculation possessed for some mediaeval scholastics. It can be considered a relatively harmless habit, like eating peanuts, unless it assumes the form of an obsession; then it becomes a vice” (Stanier, 1970)

Tree of Life: primary divisions

Microbial systematics Formerly Pseudomonas (partial list): Ralstonia, Burkholderia, Hydrogenophaga, Sphingomonas, Methylobacterium, Cellvibrio, Xanthomonas, Acidovorax, Hydrogenophillus, Brevundimonas, Pandoraea

16S rRNA as phylogenetic marker Why a good molecule? 70S 30S 50S

Tree of Life: three “domains” Based on 16S rRNA (Woese, 1987):

Tree of Life: three “domains” Based on 16S rRNA (Pace, 1997):

Bacteria & Archaeal: all genomes as of 12 Feb., 2010 (Lee, Robinson & Marx, in prep)

Tree basics: meaning

Tree basics: rotation

Tree basics: shape

Tree basics: character change

Key phylogenetic terms

Phenetics vs. cladistics

Lysozyme amino acid changes in unrelated ruminants Phenetics vs. cladistics

Maximum Parsimony Parsimony – shortest tree (fewest homoplasies)

Neutral theory Developed by Motoo Kimura, 1968

Good Dataset [A1, A2, A3, A4] [A1, B2, A3, A4] Bad Dataset A B species 1 species 2 species 3 species 4 A1 B1 A2 B2 A4 B4 A3 B3 1. Collect Sequence Data Ortholog vs. paralog?

2. Sequence Alignment CGGATAAAC CGGATAGAC CGCTGATAAAC CGGATAC taxa1 taxa2 taxa3 taxa4 Alignment

Wednesday (9/15): Molecular evolution & phylogenetic inference: case of HIV & comment…

Upcoming talks in (microbial) evolution… Wednesday, 9/15 11:00 AM Main Lecture Hall BioLabs Building OEB Weekly Seminar Series Gunter Wagner Yale University Transcription factor protein evolution and the origin of evolutionary novelties Host: Abzhanov Lab