title: Reconciliation-based detection of co-evolving gene families.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Yao-ban
authors.initials: YB
authors.lastname: Chan
authors.forename: Vincent
authors.initials: V
authors.lastname: Ranwez
authors.affiliation: ISEM, Université Montpellier 2, Montpellier, 34095, France. celine.scornavacca@univ-montp2.fr.
authors.forename: Celine
authors.initials: C
authors.lastname: Scornavacca
mesh_terms: D003198:Computer Simulation; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D011336:Probability; D020560:Proteobacteria / Q000235:genetics; D011897:Random Allocation; D056916:Segmental Duplications, Genomic