First Phylogenetics Assignment:

Due Oct 27th (not Oct. 20th)

Horizontal Gene transfer

1. Atypical nucleotide compositionLawrence and Ochman paper

2. Presence/absence of genesWelch et al 2002

3. Incongruent Phlyogenies

Genetic exchange in bacteria/archaea

Transformation

Transduction

Conjugation

Often detected by atypical nucleotide composition

Detecting HGT from genomes: atypical nt composition

(Lawrence & Ochman, 1997)

Detecting HGT from genomes: atypical nt composition

Detecting HGT from genomes: atypical nt composition

Detecting HGT from genomes: atypical nt composition

(Lawrence & Ochman, 1998)

Molecular archaeology of the Escherichia coli genome

(Lawrence & Ochman, 1998)

Horizontal Gene transfer

1. Atypical nucleotide compositionLawrence and Ochman paper

2. Presence/absence of genesWelch et al 2002

3. Incongruent Phlyogenies

Detecting HGT from genomes: atypical nt composition

Detecting HGT: differential gene content

(Welch et al., 2002)

(Pál et al., 2005)

Horizontal Gene transfer

1. Atypical nucleotide compositionLawrence and Ochman paper

2. Presence/absence of genesWelch et al 2002

3. Incongruent Phlyogenies

Detecting HGT: incongruent phylogeny/synteny

HGT only Loss only

(Koonin, 2003)

Ex: glycerol-3-P DH

Detecting HGT: plants!?!

Rafflesia (Malpighiales)Rafflesia (Malpighiales)

(Davis & Wurdack, 2004)

Detecting HGT: bacteria to insects!?!

(Hottop et al., 2007)

Can gene histories be retraced?

(Xie et al., 2004)

Can gene histories be retraced?

(Kunin et al., 2005)

Is there still an organismal tree?

(Daubin et al., 2003)

Is there still an organismal tree?

(Daubin et al., 2003)

Limitations to HGT

Decrease in recombination w/ sequence divergence

(Fraser et al., 2007)

Bacillus subtilis

Bacillus mojavensis

Streptococcus pneumoniae

E. coli

Next week….Are there species? Or is it just a

continuum?