Identifying and reconstructing lateral transfers from distance matrices by combing the minimum contradiction method and neighbor-net

Marc Thuillard, Vincent Moulton

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5 Citations (Scopus)

Abstract

Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota.
Original languageEnglish
Pages (from-to)453-470
Number of pages18
JournalJournal of Bioinformatics and Computational Biology
Volume9
Issue number4
DOIs
Publication statusPublished - 2011

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