Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods
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 cond...
Guardado en:
| Autores principales: | , , , |
|---|---|
| Formato: | JOUR |
| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_17596653_v6_n7_p1669_Almeida |
| Aporte de: |
| id |
todo:paper_17596653_v6_n7_p1669_Almeida |
|---|---|
| record_format |
dspace |
| spelling |
todo:paper_17596653_v6_n7_p1669_Almeida2023-10-03T16:32:47Z Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods Almeida, F.C. Sánchez-Gracia, A. Campos, J.L. Rozas, J. 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 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_17596653_v6_n7_p1669_Almeida |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
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 |
| spellingShingle |
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 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 |
| topic_facet |
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 |
| description |
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. |
| format |
JOUR |
| author |
Almeida, F.C. Sánchez-Gracia, A. Campos, J.L. Rozas, J. |
| author_facet |
Almeida, F.C. Sánchez-Gracia, A. Campos, J.L. Rozas, J. |
| author_sort |
Almeida, F.C. |
| title |
Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods |
| title_short |
Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods |
| title_full |
Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods |
| title_fullStr |
Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods |
| title_full_unstemmed |
Family size evolution in drosophila chemosensory gene families: A comparative analysis with a critical appraisal of methods |
| title_sort |
family size evolution in drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods |
| url |
http://hdl.handle.net/20.500.12110/paper_17596653_v6_n7_p1669_Almeida |
| work_keys_str_mv |
AT almeidafc familysizeevolutionindrosophilachemosensorygenefamiliesacomparativeanalysiswithacriticalappraisalofmethods AT sanchezgraciaa familysizeevolutionindrosophilachemosensorygenefamiliesacomparativeanalysiswithacriticalappraisalofmethods AT camposjl familysizeevolutionindrosophilachemosensorygenefamiliesacomparativeanalysiswithacriticalappraisalofmethods AT rozasj familysizeevolutionindrosophilachemosensorygenefamiliesacomparativeanalysiswithacriticalappraisalofmethods |
| _version_ |
1807318842033045504 |