title: Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement.
abstract: BACKGROUND
  When organismal phylogenies based on sequences of single marker genes are poorly resolved, a logical approach is to add more markers, on the assumption that weak but congruent phylogenetic signal will be reinforced in such multigene trees. Such approaches are valid only when the several markers indeed have identical phylogenies, an issue which many multigene methods (such as the use of concatenated gene sequences or the assembly of supertrees) do not directly address. Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies.
  
  
  RESULTS
  We have developed software that aims to extract evidence for vertical and lateral inheritance from a set of gene trees compared against an arbitrary reference tree. This evidence is then displayed as a synthesis showing support over the tree for vertical inheritance, overlaid with explicit lateral gene transfer (LGT) events inferred to have occurred over the history of the tree. Like splits-tree methods, one can thus identify nodes at which conflict occurs. Additionally one can make reasonable inferences about vertical and lateral signal, assigning putative donors and recipients.
  
  
  CONCLUSIONS
  A tool such as ours can serve to explore the reticulated dimensionality of molecular evolution, by dissecting vertical and lateral inheritance at high resolution. By this, we mean that individual nodes can be examined not only for congruence, but also for coherence in light of LGT. We assert that our tools will facilitate the comparison of phylogenetic trees, and the interpretation of conflicting data.
authors.affiliation: GenomeAtlantic, 1721 Lower Water Street, Suite 401, Halifax, NS, B3J 1S5, Canada. djmacleo@dal.ca
authors.forename: Dave
authors.initials: D
authors.lastname: MacLeod
authors.forename: Robert L
authors.initials: RL
authors.lastname: Charlebois
authors.forename: Ford
authors.initials: F
authors.lastname: Doolittle
authors.forename: Eric
authors.initials: E
authors.lastname: Bapteste
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D022761:Gene Transfer, Horizontal; D005819:Genetic Markers; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D011381:Programming Languages; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D005819:Genetic Markers