BIOS E-127 – 08.09.29
Phenetics vs. cladistics
Lysozyme amino acid changes in unrelated ruminants
Phenetics vs. cladistics
Maximum Parsimony
Microbial systematics
• Formerly Pseudomonas (partial list): Ralstonia, Burkholderia, Hydrogenophaga, Sphingomonas, Methylobacterium, Cellvibrio, Xanthomonas, Acidovorax, Hydrogenophillus, Brevundimonas, Pandoraea
multi-C C1(& all use methanol)
Molecular phylogenetics• Zuckerkandl & Pauling. 1965. Molecules as documents of
evolutionary history. J Theor Biol. 8:357-366.
• Neutral theory (Motoo Kimura, 1968)
16S rRNA as phylogenetic marker• Why a good molecule?
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
Ortholog vs. paralog?
CGGATAAACCGGATAGACCGCGATAAACCGGATAAC
taxa1taxa2taxa3taxa4
Alignment
Example: Neighbor Joining (NJ)
Taxa CharactersSpecies A ATGGCTATTCTTATAGTACGSpecies B ATCGCTAGTCTTATATTACASpecies C TTCACTAGACCTGTGGTCCASpecies D TTGACCAGACCTGTGGTCCGSpecies E TTGACCAGTTCTCTAGTTCG
A
B
C
DE
Choose methods: distance-based
A B C D E Species A ---- 4 10 9 8Species B ---- 8 11 10Species C ---- 3 8Species D ---- 5Species E ----
A B C D E Species A ---- 4 10 9 8Species B -19.3 ---- 8 11 10Species C -10 -14.7 ---- 3 8Species D -10.7 -11.3 -16 ---- 5Species E -12.7 -13.3 -12 -14.7 ----
M(AB)=d(AB) -[(r(A) + r(B))/(N-2)]
Ancestral Sequences
Observed Sequences
?Model
Choose “model”
Maximum Parsimony (MP): Model: Evolution goes through the least number of changes
Maximum Likelihood (ML): L (data| model)
Bayesian Inference
Pr(data)
Pr(model)model)|Pr(datadata)|Pr(model
Markov chain Monte Carlo (MCMC) method for sampling from posterior probability distribution
Discrete character methods
I. Bootstrap
Re-sampling to produce pseudo-dataset (random weighting)
II. Jacknife
Sampling with replacement
III. Permutation test
Random deletion of sub-dataset
Randomize dataset to build null likelihood distribution
CGATCGTTA
CAATGATAG
CGCTGATAA
CGCTGATCG
taxa1
taxa2
taxa3
taxa4
123456789
Dataset1: 729338554Dataset2: 631981282
…
Dataset1: 1-3-56789Dataset2: 12-45678-
…
10073
Assess reliability
Reconstructed ancestral sequences to infer paleoenvironment
(Gaucher et al., 2003)
Signs of selection
(Sawyer & Malik, 2006)
5. Assess ReliabilityMolecular clock: HIV-1 origin
(Korber et al., 2000)
Genetic exchange in bacteria/archaea
Detecting HGT from genomes: atypical nt composition
(Hacker & Carniel, 2001)
Monday (10/6): Microbial species, biogeography & population genetics II.
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