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

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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)

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)

Detecting HGT: differential gene content

(Welch et al., 2002)

(Pál et al., 2005)

Measurements of natural horizontal gene transfer (HGT)

(Sørensen 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

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