ArticleGenetics2006
Estimating the genomewide rate of adaptive protein evolution in Drosophila.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
74 citing papers in PubMed, 133 citations in OpenAlex.
- Article
- Estimating the proportion of beneficial mutations that are not adaptive in mammals.PLoS genetics · 2024Article
- Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes.Genomics, proteomics & bioinformatics · 2022Article
- Two decades of suspect evidence for adaptive molecular evolution-negative selection confounding positive-selection signals.National science review · 2022Article
- Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna.Molecular biology and evolution · 2022Article
- Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations.Genome biology and evolution · 2022Article
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species.Molecular biology and evolution · 2020Article
- Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group.BMC evolutionary biology · 2019Article
- Transcriptomic basis and evolution of the ant nurse-larval social interactome.PLoS genetics · 2019Article
- Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development.PLoS biology · 2018Article
- RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates.Genetics · 2018Article
- Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data.Genetics · 2017Article
- Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry.Genome biology and evolution · 2017Article
- Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers.Molecular biology and evolution · 2017Article
- Recurrent Innovation at Genes Required for Telomere Integrity in Drosophila.Molecular biology and evolution · 2017Article
- Article
- Article
- Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis.PLoS genetics · 2016Article
- Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements.Genome biology and evolution · 2015Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
When polymorphism and divergence data are available for multiple loci, extended forms of the McDonald-Kreitman test can be used to estimate the average proportion of the amino acid divergence due to adaptive evolution--a statistic denoted alpha. But such tests are subject to many biases. Most serious is the possibility that high estimates of alpha reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in alpha is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of alpha from the same model organisms have also varied widely. This study clarifies the reasons for these discrepancies, identifying several method-specific biases in widely used estimators and assessing the power of the methods. As part of this process, a new maximum-likelihood estimator is introduced. This estimator is applied to a newly compiled data set of 115 genes from Drosophila simulans, each with each orthologs from D. melanogaster and D. yakuba. In this way, it is estimated that alpha approximately 0.4+/-0.1, a value that does not vary substantially between different loci or over different periods of divergence. The implications of these results are discussed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.