More on neutral theory

OEB 192 – 10.09.15

Example: Neighbor Joining (NJ)

4. Choose Methods

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)]

4. Choose Methods

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

Discrete character methods

3. Choose Models

Ancestral Sequences

Observed Sequences

?Model

Choose “model”

5. Assess Reliability

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

5. Assess ReliabilityUtility of phylogeny: Molecular clock

(Korber et al., 2000)

5. Assess ReliabilityUtility of phylogeny: Molecular clock

(Korber et al., 2000)

5. Assess ReliabilityUtility of phylogeny: Molecular clock

(Hillis, 2000)

Utility of phylogeny: infer past environment?

(Gaucher et al., 2003)

Molecular signs of selection

(Sawyer & Malik, 2006)

Genetic exchange in bacteria/archaea

Monday (9/20): Horizontal gene transfer

Upcoming talks in microbial evolution…MSI Chalktalk Breakfast

Friday, Sept 17th 8:45-9:30 am

“Time series analyses of the flora during enteric infections”

Lynn BryHMS Host: Colleen Cavanaugh Please join us for coffee/tea/pastries at 8:30 am - Directions to 24 Oxford St: http://www.msi.harvard.edu/ov_dir.html- Join MSI-news listserv: Email: listserv@listserv.med.harvard.edu and in the body of your email, copy the text: subscribe msi-news