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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-artmethods may produce very different rate estimates, whichmay 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 hadnegligible 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 themost 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 thesemethods in amore 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. © The Author(s) 2014.

Registro:

Documento: Artículo
Título:Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods
Autor:Almeida, F.C.; Sánchez-Gracia, A.; Campos, J.L.; Rozas, J.
Filiación:Departament de Genètica, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
CONICET, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Buenos Aires, Argentina
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
Palabras clave:BadiRate; Chemosensory genes; D. sechellia; Gene birth-and-death; Gene duplication; Gene tree-species tree reconciliation; olfactory receptor; animal; comparative study; computer simulation; Drosophila; gene duplication; genetic procedures; genetics; human; molecular evolution; olfactory receptor; standards; Animals; Computer Simulation; Drosophila; Evolution, Molecular; Gene Duplication; Genetic Techniques; Humans; Receptors, Odorant
Año:2014
Volumen:6
Número:7
Página de inicio:1669
Página de fin:1682
DOI: http://dx.doi.org/10.1093/gbe/evu130
Título revista:Genome Biology and Evolution
Título revista abreviado:Genome Biolog. Evol.
ISSN:17596653
CAS:Receptors, Odorant
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17596653_v6_n7_p1669_Almeida

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Citas:

---------- APA ----------
Almeida, F.C., Sánchez-Gracia, A., Campos, J.L. & Rozas, J. (2014) . Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods. Genome Biology and Evolution, 6(7), 1669-1682.
http://dx.doi.org/10.1093/gbe/evu130
---------- CHICAGO ----------
Almeida, F.C., Sánchez-Gracia, A., Campos, J.L., Rozas, J. "Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods" . Genome Biology and Evolution 6, no. 7 (2014) : 1669-1682.
http://dx.doi.org/10.1093/gbe/evu130
---------- MLA ----------
Almeida, F.C., Sánchez-Gracia, A., Campos, J.L., Rozas, J. "Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods" . Genome Biology and Evolution, vol. 6, no. 7, 2014, pp. 1669-1682.
http://dx.doi.org/10.1093/gbe/evu130
---------- VANCOUVER ----------
Almeida, F.C., Sánchez-Gracia, A., Campos, J.L., Rozas, J. Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods. Genome Biolog. Evol. 2014;6(7):1669-1682.
http://dx.doi.org/10.1093/gbe/evu130