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Open Access Highly Accessed Research article

Reconciliation-based detection of co-evolving gene families

Yao-ban Chan1, Vincent Ranwez23 and Celine Scornavacca13*

Author Affiliations

1 ISEM, Université Montpellier 2, Montpellier, 34095, France

2 Montpellier SupAgro, UMR AGAP, F-34060 Montpellier, France

3 Institut de Biologie Computationnelle (IBC), 95 rue de la Galéra, 34095 Montpellier, France

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BMC Bioinformatics 2013, 14:332  doi:10.1186/1471-2105-14-332

Published: 20 November 2013



Genes located in the same chromosome region share common evolutionary events more often than other genes (e.g. a segmental duplication of this region). Their evolution may also be related if they are involved in the same protein complex or biological process. Identifying co-evolving genes can thus shed light on ancestral genome structures and functional gene interactions.


We devise a simple, fast and accurate probability method based on species tree-gene tree reconciliations to detect when two gene families have co-evolved. Our method observes the number and location of predicted macro-evolutionary events, and estimates the probability of having the observed number of common events by chance.


Simulation studies confirm that our method effectively identifies co-evolving families. This opens numerous perspectives on genome-scale analysis where this method could be used to pinpoint co-evolving gene families and thus help to unravel ancestral genome arrangements or undocumented gene interactions.