Abstract
BackgroundGenes 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.ResultsWe 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.ConclusionsSimulation 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.
Highlights
Genes located in the same chromosome region share common evolutionary events more often than other genes
The problem of detecting co-evolution at the amino acid level has been extensively studied recently ([4,5]; among others)
Reconciliation methods construct a mapping between a gene tree and a species tree to explain their incongruence by macro-evolutionary events such as speciations, gene duplications, horizontal gene transfers etc
Summary
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
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