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This article is part of the supplement: Proceedings of the Tenth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

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Gene trees and species trees: irreconcilable differences

Krister M Swenson12 and Nadia El-Mabrouk1

Author Affiliations

1 Département d'Informatique (DIRO), Université de Montréal, H3C 3J7, Canada

2 McGill Centre for Bioinformatics, McGill University, H3C 2B4, Canada

BMC Bioinformatics 2012, 13(Suppl 19):S15  doi:10.1186/1471-2105-13-S19-S15

Published: 19 December 2012



Reconciliation is the classical method for inferring a duplication and loss history from a set of extant genes. It is based upon the notion of embedding the gene tree into the species tree, the incongruence between the two indicating evidence for duplication and loss. However, results obtained by this method are highly dependent upon the considered species and gene trees. Thus, painstaking attention has been given to the development of methods for reconstructing accurate gene trees.


This paper highlights the fact that errors in gene trees are not the only reasons for the inference of an erroneous duplication-loss history. More precisely, we prove that, under certain reasonable hypotheses based on the widely accepted link between function and sequence constraints, even a well-supported gene tree yield a reconciliation that does not correspond to the true history. We then provide the theoretical underpinnings for a conservative approach to infer histories given such gene trees. We apply our method to the mammalian interleukin-1 (IL) gene tree, that has been used as a model example to illustrate the role of reconciliation.