First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )
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Transcript of First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )
![Page 1: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/1.jpg)
First Phylogenetics Assignment:
Due Oct 27th (not Oct. 20th)
![Page 2: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/2.jpg)
Horizontal Gene transfer
1. Atypical nucleotide compositionLawrence and Ochman paper
2. Presence/absence of genesWelch et al 2002
3. Incongruent Phlyogenies
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Genetic exchange in bacteria/archaea
Transformation
Transduction
Conjugation
Often detected by atypical nucleotide composition
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Detecting HGT from genomes: atypical nt composition
(Lawrence & Ochman, 1997)
![Page 5: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/5.jpg)
Detecting HGT from genomes: atypical nt composition
![Page 6: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/6.jpg)
Detecting HGT from genomes: atypical nt composition
![Page 7: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/7.jpg)
Detecting HGT from genomes: atypical nt composition
(Lawrence & Ochman, 1998)
![Page 8: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/8.jpg)
Molecular archaeology of the Escherichia coli genome
(Lawrence & Ochman, 1998)
![Page 9: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/9.jpg)
Horizontal Gene transfer
1. Atypical nucleotide compositionLawrence and Ochman paper
2. Presence/absence of genesWelch et al 2002
3. Incongruent Phlyogenies
![Page 10: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/10.jpg)
Detecting HGT from genomes: atypical nt composition
![Page 11: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/11.jpg)
Detecting HGT: differential gene content
(Welch et al., 2002)
(Pál et al., 2005)
![Page 12: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/12.jpg)
Horizontal Gene transfer
1. Atypical nucleotide compositionLawrence and Ochman paper
2. Presence/absence of genesWelch et al 2002
3. Incongruent Phlyogenies
![Page 13: First Phylogenetics Assignment: Due Oct 27 th (not Oct. 20 th )](https://reader031.fdocuments.us/reader031/viewer/2022032704/56649d5e5503460f94a3eb1a/html5/thumbnails/13.jpg)
Detecting HGT: incongruent phylogeny/synteny
HGT only Loss only
(Koonin, 2003)
Ex: glycerol-3-P DH
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Detecting HGT: plants!?!
Rafflesia (Malpighiales)Rafflesia (Malpighiales)
(Davis & Wurdack, 2004)
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Detecting HGT: bacteria to insects!?!
(Hottop et al., 2007)
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Can gene histories be retraced?
(Xie et al., 2004)
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Can gene histories be retraced?
(Kunin et al., 2005)
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Is there still an organismal tree?
(Daubin et al., 2003)
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Is there still an organismal tree?
(Daubin et al., 2003)
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Limitations to HGT
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Decrease in recombination w/ sequence divergence
(Fraser et al., 2007)
Bacillus subtilis
Bacillus mojavensis
Streptococcus pneumoniae
E. coli
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Next week….Are there species? Or is it just a
continuum?