What can sequences tell us? BIOL E-127– 10/15/07.

What can sequences tell us?

BIOL E-127– 10/15/07

Reconstructed ancestral sequences to infer paleoenvironment

(Gaucher et al., 2003)

Signs of selection

(Sawyer & Malik, 2006)

Genetic exchange in bacteria/archaea

Detecting HGT: incongruent phylogeny/synteny

HGT only Loss only

(Koonin, 2003)

Ex: glycerol-3-P DH

Detecting HGT: formaldehyde metabolism in methylotrophs

(Kalyuzhnaya et al., 2005)

Detecting HGT: formaldehyde metabolism in methylotrophs

E

LUCA

D

LUCA

E

LUCA

D

LUCA

A

LUCA

LUCA

B

C

LUCA

A

LUCA

LUCA

B

C

LUCA

Scenarios for pathway evolution

(Chistoserdova et al., 2004)

Detecting HGT: plants!?!

Rafflesia (Malpighiales)Rafflesia (Malpighiales)

(Davis & Wurdack, 2004)

Detecting HGT: bacteria to insects!?!

(Hottop et al., 2007)

HGT genes often clustered

(Price et al., 2005)

Detecting HGT from genomes: atypical nt composition

(Lawrence & Ochman, 1997)


(Hacker & Carniel, 2001)


(Lawrence & Ochman, 1998)

Detecting HGT: differential gene content

(Welch et al., 2002)

(Pál et al., 2005)

Measurements of natural horizontal gene transfer (HGT)

(Sørensen et al., 2005)

Limitations to HGT

Decrease in recombination w/ sequence divergence

(Fraser et al., 2007)

Bacillus subtilis

Bacillus mojavensis

Streptococcus pneumoniae

E. coli

What can sequences tell us? BIOL E-127– 10/15/07.

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