12. What is the meaning of this??
• Signal saturation + tiny branches that happened a
long, long, long time ago
• Other unpleasant biases (G+C, rates, etc)
• Lateral gene transfer
18. Building a MAF by
edge cutting
Example case: a & c are sisters in the species tree, but not in the gene tree.
What can we do to the gene tree?
19. • Naïve case: O(3kn)
• Fancy refinements: O(2.42kn)
• Even fancier refinements: O(2kn) (conjectured)
FIXED PARAMETER TRACTABLE –
Exponential in the distance between trees, not the
number of leaves
21. The Complexity Hypothesis
(Jain et al., 1999)
• “Informational” proteins have more interactions
with other proteins in the cell, and are therefore
less likely to be successfully transferred than, say,
metabolic stuff
• Cohen et al. (2011): forget about function, it’s all
about the connections with other proteins in the
cell
22. The Selfish Operon Hypothesis:
Lawrence and Roth (1996)
• Genes associate in operons because it facilitates
transfer of all constituents of a pathway at once
• If the genes were dispersed throughout the
genome, then the selective advantage of a pathway
could not be propagated via transfer
23. The Public Goods Hypothesis:
McInerney et al. (2011)
• Genes are public goods that can be freely shared
and cannot be excluded from being available
• These genes are constantly acquired and integrated
into genomes, invalidating the idea of a unifying
Tree of Life
24. Highways of gene sharing:
Beiko et al. (2005)
• Gene sharing occurs preferentially between
lineages, and successful gene acquisitions often
reflect shared ecology
35. Finding LGT in the
microbiome?
• Illumina sequencing - aaaaargh!
• Mixed samples! [imagine what happens
when you try to assemble!]
• Strain-level differentiation!
• etc
36. What does it all mean?
LGT seriously undermines the recovery (and validity?) of
the Tree of Life
Even so, aggregation methods (supertrees, etc.) can
provide a useful scaffold for inferring LGT events
LGT serves as a useful starting point for hypotheses of
habitat adaptation / invasion
Metagenomic data offer new context to LGT events (and
genomic data show we should be looking at
communities), but present huge challenges to inference
