Reconciliation-based detection of co-evolving gene families
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
BMC Bioinformatics 2013, 14:332 doi:10.1186/1471-2105-14-332Published: 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.