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OEB 192 – 10.09.13
“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
multi-C C1(& all use methanol)
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
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
A1B1
A2B2 A4
B4A3
B3
1. Collect Sequence DataOrtholog vs. paralog?
2. Sequence Alignment
CGGATAAACCGGATAGACCGCTGATAAACCGGATAC
taxa1taxa2taxa3taxa4
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 HallBioLabs Building
OEB Weekly Seminar Series
Gunter WagnerYale University
Transcription factor protein evolution and the origin of evolutionary novelties
Host: Abzhanov Lab