BIOS E-127 – 08.09.29. Phenetics vs. cladistics Lysozyme amino acid changes in unrelated ruminants Phenetics vs. cladistics.

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.