ArticleGenetics2007
Rapid detection of positive selection in genes and genomes through variation clusters.
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 65 citations in OpenAlex.
- Genetic and genomic insights of the Comcáac people.Journal of community genetics · 2025Review
- Deciphering the role of FOXP4 in long COVID: exploring genetic associations, evolutionary conservation, and drug identification through bioinformatics analysis.Functional & integrative genomics · 2024Article
- RlmQ: a newly discovered rRNA modification enzyme bridging RNA modification and virulence traits inRNA (New York, N.Y.) · 2024Article
- A chromosome-level genome assembly of the Rhus gall aphid Schlechtendalia chinensis provides insight into the endogenization of Parvovirus-like DNA sequences.BMC genomics · 2024Article
- Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.Nature communications · 2023Article
- Genome-wide scans for selective sweeps using convolutional neural networks.Bioinformatics (Oxford, England) · 2023Article
- Nonadaptive molecular evolution of seminal fluid proteins in Drosophila.Evolution; international journal of organic evolution · 2021Article
- Divergent evolution and purifying selection of the Type 2 diabetes gene sequences in Drosophila: a phylogenomic study.Genetica · 2020Article
- Evolutionary Diversity in the Intracellular Microsporidian Parasite Nosema sp. Infecting Wild Silkworm Revealed by IGS Nucleotide Sequence Diversity.Journal of molecular evolution · 2020Article
- Evolution of the Plasmodium vivax multidrug resistance 1 gene in the Greater Mekong Subregion during malaria elimination.Parasites & vectors · 2020Article
- Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes.Evolutionary bioinformatics online · 2020Article
- Natural selection and repeated patterns of molecular evolution following allopatric divergence.eLife · 2019Article
- Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.Cell systems · 2019Article
- Article
- Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies.The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2018Review
- Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.Molecular biology and evolution · 2017Article
- A familial study of azoospermic men identifies three novel causative mutations in three new human azoospermia genes.Genetics in medicine : official journal of the American College of Medical Genetics · 2017Article
- Virulence evolution of a sterilizing plant virus: Tuning multiplication and resource exploitation.Virus evolution · 2017Article
- Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.Cancer research · 2016Article
- mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome.Human mutation · 2016Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Positive selection in genes and genomes can point to the evolutionary basis for differences among species and among races within a species. The detection of positive selection can also help identify functionally important protein regions and thus guide protein engineering. Many existing tests for positive selection are excessively conservative, vulnerable to artifacts caused by demographic population history, or computationally very intensive. I here propose a simple and rapid test that is complementary to existing tests and that overcomes some of these problems. It relies on the null hypothesis that neutrally evolving DNA regions should show a Poisson distribution of nucleotide substitutions. The test detects significant deviations from this expectation in the form of variation clusters, highly localized groups of amino acid changes in a coding region. In applying this test to several thousand human-chimpanzee gene orthologs, I show that such variation clusters are not generally caused by relaxed selection. They occur in well-defined domains of a protein's tertiary structure and show a large excess of amino acid replacement over silent substitutions. I also identify multiple new human-chimpanzee orthologs subject to positive selection, among them genes that are involved in reproductive functions, immune defense, and the nervous system.
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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.