Who is Who in Phylogenetic Networks

Publications of Eric Bapteste     Order by:   Type | Year

Associated keywords

abstract-network explicit-network from-rooted-trees lateral-gene-transfer phylogenetic-network phylogeny Program-HorizStory reconstruction software

Article (Journal)

1 Eric Bapteste, Leo van Iersel, Axel Janke, Scott Kelchner, Steven Kelk, James O. McInerney, David A. Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James B. Whitfield. Networks: expanding evolutionary thinking. In Trends in Genetics, Vol. 29(8):439-441, 2013. Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction. Note: http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf.         Toggle abstract "Networks allow the investigation of evolutionary relationships that do not fit a tree model. They are becoming a leading tool for describing the evolutionary relationships between organisms, given the comparative complexities among genomes. © 2013 Elsevier Ltd." 2 Dave MacLeod, Robert L. Charlebois, W. Ford Doolittle and Eric Bapteste. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. In BMCEB, Vol. 5(27), 2005. Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HorizStory, reconstruction, software. Note: http://dx.doi.org/10.1186/1471-2148-5-27.         Toggle 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. Conclusion: 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. © 2005 MacLeod et al; licensee BioMed Central Ltd."