ArticleMolecular biology and evolution2010
Estimates of the effect of natural selection on protein-coding content.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 46 citations in OpenAlex.
- piqtree: a python package for seamless phylogenetic inference with IQ-TREE.Molecular biology and evolution · 2026Article
- The performance of genetic-constraint metrics varies significantly across the human noncoding genome.bioRxiv : the preprint server for biology · 2026Article
- The effects of repeated whole genome duplication events on the evolution of cytokinin signaling pathway.BMC evolutionary biology · 2018Article
- Did aculeate silk evolve as an antifouling material?PloS one · 2018Article
- Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data.Genome biology and evolution · 2017Article
- Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.The Plant cell · 2016Article
- The relationship between dN/dS and scaled selection coefficients.Molecular biology and evolution · 2015Article
- The "naked coral" hypothesis revisited--evidence for and against scleractinian monophyly.PloS one · 2014Article
- Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery.G3 (Bethesda, Md.) · 2013Article
- CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models.Molecular biology and evolution · 2013Article
- Article
- Dynamic evolution of venom proteins in squamate reptiles.Nature communications · 2012Article
- Differential evolution of MAGE genes based on expression pattern and selection pressure.PloS one · 2012Article
- Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples.PloS one · 2011Article
- Exploiting CpG hypermutability to identify phenotypically significant variation within human protein-coding genes.Genome biology and evolution · 2011Article
- Positive selection differs between protein secondary structure elements in Drosophila.Genome biology and evolution · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of natural selection is key to understanding many core biological processes, including the emergence of competition, cooperation, and complexity, and has important applications in the targeted development of vaccines. Selection is hard to observe directly but can be inferred from molecular sequence variation. For protein-coding nucleotide sequences, the ratio of nonsynonymous to synonymous substitutions (omega) distinguishes neutrally evolving sequences (omega = 1) from those subjected to purifying (omega < 1) or positive Darwinian (omega > 1) selection. We show that current models used to estimate omega are substantially biased by naturally occurring sequence compositions. We present a novel model that weights substitutions by conditional nucleotide frequencies and which escapes these artifacts. Applying it to the genomes of pathogens causing malaria, leprosy, tuberculosis, and Lyme disease gave significant discrepancies in estimates with approximately 10-30% of genes affected. Our work has substantial implications for how vaccine targets are chosen and for studying the molecular basis of adaptive evolution.
Indexed as
Identifiers
What OpenQuestion holds
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.