This document contains notes from a presentation on inferring phylogenetic trees and lateral gene transfer. It discusses challenges with accurately reconstructing the tree of life due to early ancestral signal being lost, biases in models, and lateral gene transfer. Methods for detecting lateral gene transfer like using k-mers or codon usage and phylogenetic discordance are presented. The document also discusses hypotheses for lateral gene transfer involving gene complexity, selfish operons, and public goods. Examples of lateral gene transfer studies in bacteria are provided.

1. http://www.nimr.mrc.ac.uk/images/multimedia/news/large/cake-large.jpg

3. Robert Beiko
Faculty of Computer Science*
Dalhousie University
Halifax, 2 feet of snow last week, Canada
April 5, 2014

4. The dream of a Tree of Life

5. Can a ToL be
[correctly]
[reliably]
[accurately]
inferred?
Woese

6. “All happy phylogenies are alike;
each unhappy phylogeny is
unhappy in its own way.”
- Evolution Leo
Tolstoy

7. Creevey et al. Proc. R. Soc. Lond. B (2004)
Early ancestral signal
is probably gone

8. It gets
worse
W. Ford Doolittle, Sci Am (1999)

9. OMFG it gets even worse
Kunin et al. (2005) Genome Res

10. make it stop make it stop
Dagan et al. (2008) PNAS

11. Do not adjust your model

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

13. Finding LGT
en.wikipedia.org

14. K-mersorcodonusage
Wang et al. (2001) MBE

15. Phylogeneticdiscordance
Concordance weighted Discordance weighted

16. Euchlamydispirokaryotes
Extremarchalsobacteriae

17. Phylogenetics!
MAFs, SPRs, LGTs
Chris Whidden
+ Norbert Zeh

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

20. Hypotheses about LGT
Hypotheses about LGT

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

25. LGT stories

26. P. aeruginosa
P. fluorescens
P. lePewtida
P. syringae
P. entomophila
P. stutzeri
P. mendocina
(Catherine) Holloway and Beiko, 2010
“Plume”

27. Proteobacteria
Planar is plainer, could be pain-er
Beiko, 2011

28. 244 taxa
40,631 trees
= Bacterial SPR supertree
LGT patterns for Clostridium
Whidden et al., 2014

29. Cold case – Aquifex aeolicus & friends
(Rob) Eveleigh et al., 2013

30. LGT in the Wild

31. Hehemann et al. (2010) Nature

32. Smillie et al. (2011) Science

33. Lachnospiraceae – Gut / mouth enthusiasts
(Conor) Meehan and Beiko (2014) GBE
“Good” strains ..?
“Not so good” strains ..?

34. Butyrate production – a crucial
function, subject to LGT

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