title: Family size evolution in Drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods.
abstract: Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila-the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families-to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia's gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process.
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain Present address: CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto IEGEBA, Buenos Aires, Argentina.
authors.forename: Francisca C
authors.initials: FC
authors.lastname: Almeida
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Sánchez-Gracia
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain Present address: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Campos
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain jrozas@ub.edu.
authors.forename: Julio
authors.initials: J
authors.lastname: Rozas
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004330:Drosophila / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D005821:Genetic Techniques / Q000592:standards*; D006801:Humans; D018035:Receptors, Odorant / Q000235:genetics*
chemical_list: D018035:Receptors, Odorant
keywords: BadiRate; D. sechellia; chemosensory genes; gene birth-and-death; gene duplication; gene tree–species tree reconciliation