ArticleGenome biology and evolution2014
Family size evolution in Drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids.Molecular biology and evolution · 2025Article
- Review
- Rapid expansion and specialization of the TAS2R bitter taste receptor family in amphibians.PLoS genetics · 2025Article
- Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae.G3 (Bethesda, Md.) · 2023Article
- Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae.bioRxiv : the preprint server for biology · 2023Article
- Comparative analysis of detoxification-related gene superfamilies across five hemipteran species.BMC genomics · 2022Article
- Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae.G3 (Bethesda, Md.) · 2022Article
- Reconstructing Gene Gains and Losses with BadiRate.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Evolution of the Insect PPK Gene Family.Genome biology and evolution · 2021Article
- DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics.Genome biology and evolution · 2021Article
- Article
- How interactions with plant chemicals shape insect genomes.Current opinion in insect science · 2019Review
- Positive selection at sites of chemosensory genes is associated with the recent divergence and local ecological adaptation in cactophilic Drosophila.BMC evolutionary biology · 2018Article
- Evolution of Gustatory Receptor Gene Family Provides Insights into Adaptation to Diverse Host Plants in Nymphalid Butterflies.Genome biology and evolution · 2018Article
- Comparative Genomics Reveals Thousands of Novel Chemosensory Genes and Massive Changes in Chemoreceptor Repertories across Chelicerates.Genome biology and evolution · 2018Article
- The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees.Genome biology and evolution · 2017Article
- Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics' and structural biology's lenses.Scientific reports · 2017Article
- Evolutionary Insights into Taste Perception of the Invasive Pest Drosophila suzukii.G3 (Bethesda, Md.) · 2016Article
- Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families.Genome biology and evolution · 2016Article
- The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii.BMC genomics · 2016Article
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4 authors.
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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-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.
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