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
(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)
Detecting HGT from genomes: atypical nt composition
(Hacker & Carniel, 2001)
Detecting HGT from genomes: atypical nt composition
Detecting HGT from genomes: atypical nt composition
(Lawrence & Ochman, 1998)
Detecting HGT from genomes: atypical nt composition
(Lawrence & Ochman, 1998)
Detecting HGT from genomes: atypical nt composition
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