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Multinucleotide mutations cause false inferences of lineage-specific positive selection
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/em.21728openalex-snapshot
DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1002/humu.22501openalex-snapshot
A New and More Accurate Estimate of the Rate of Concurrent Tandem-Base Substitution Mutations in the Human Germline: ∼0.4% of the Single-Nucleotide Substitution Mutation Rate
inferredcites →https://doi.org/10.1002/humu.22749openalex-snapshot
Concurrent Nucleotide Substitution Mutations in the Human Genome Are Characterized by a Significantly Decreased Transition/Transversion Ratio
inferredcites →https://doi.org/10.1002/humu.22831openalex-snapshot
Complex Multiple-Nucleotide Substitution Mutations Causing Human Inherited Disease Reveal Novel Insights into the Action of Translesion Synthesis DNA Polymerases
inferredcites →https://doi.org/10.1007/s00239-005-0129-9openalex-snapshot
Adaptive Evolution of Multicolored Fluorescent Proteins in Reef-Building Corals
inferredcites →https://doi.org/10.1007/s00239-009-9241-6openalex-snapshot
Gene Conversion Among Paralogs Results in Moderate False Detection of Positive Selection Using Likelihood Methods
inferredcites →https://doi.org/10.1016/j.cub.2011.05.013openalex-snapshot
Pervasive Multinucleotide Mutational Events in Eukaryotes
inferredcites →https://doi.org/10.1016/j.tig.2007.12.001openalex-snapshot
Evolution of protein-coding genes in Drosophila
inferredcites →https://doi.org/10.1038/35010014openalex-snapshot
Low fidelity DNA synthesis by human DNA polymerase-η
inferredcites →https://doi.org/10.1038/nature02601openalex-snapshot
Positive selection at sites of multiple amino acid replacements since rat–mouse divergence
inferredcites →https://doi.org/10.1038/nature06341openalex-snapshot
Evolution of genes and genomes on the Drosophila phylogeny
inferredcites →https://doi.org/10.1038/ng.3198openalex-snapshot
Convergent evolution of the genomes of marine mammals
inferredcites →https://doi.org/10.1038/ng.3292openalex-snapshot
Genome-wide patterns and properties of de novo mutations in humans
inferredcites →https://doi.org/10.1038/nrg3015openalex-snapshot
Molecular spandrels: tests of adaptation at the genetic level
inferredcites →https://doi.org/10.1038/nrg3098openalex-snapshot
Variation in the mutation rate across mammalian genomes
inferredcites →https://doi.org/10.1038/nrg3905openalex-snapshot
Evolutionary insights into host–pathogen interactions from mammalian sequence data
inferredcites →https://doi.org/10.1073/pnas.0901855106openalex-snapshot
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods
inferredcites →https://doi.org/10.1073/pnas.1615832113openalex-snapshot
Evolutionary switches between two serine codon sets are driven by selection
inferredcites →https://doi.org/10.1084/jem.20112234openalex-snapshot
DNA polymerase ζ generates tandem mutations in immunoglobulin variable regions
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
inferredcites →https://doi.org/10.1093/molbev/msh117openalex-snapshot
Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models
inferredcites →https://doi.org/10.1093/molbev/msi232openalex-snapshot
Site-to-Site Variation of Synonymous Substitution Rates
inferredcites →https://doi.org/10.1093/molbev/msi237openalex-snapshot
Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
inferredcites →https://doi.org/10.1093/molbev/msm042openalex-snapshot
Multiple Hypothesis Testing to Detect Lineages under Positive Selection that Affects Only a Few Sites
inferredcites →https://doi.org/10.1093/molbev/msm064openalex-snapshot
An Empirical Codon Model for Protein Sequence Evolution
inferredcites →https://doi.org/10.1093/molbev/msq303openalex-snapshot
Statistical Properties of the Branch-Site Test of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msr125openalex-snapshot
A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection
inferredcites →https://doi.org/10.1093/molbev/mss104openalex-snapshot
Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods
inferredcites →https://doi.org/10.1093/molbev/mss266openalex-snapshot
Estimating Empirical Codon Hidden Markov Models
inferredcites →https://doi.org/10.1093/molbev/mst062openalex-snapshot
The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC
inferredcites →https://doi.org/10.1093/molbev/msu141openalex-snapshot
Patterns of Positive Selection in Seven Ant Genomes
inferredcites →https://doi.org/10.1093/molbev/msu173openalex-snapshot
An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit
inferredcites →https://doi.org/10.1093/molbev/msv022openalex-snapshot
Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
inferredcites →https://doi.org/10.1093/molbev/msv035openalex-snapshot
Gene-Wide Identification of Episodic Selection
inferredcites →https://doi.org/10.1093/molbev/msv184openalex-snapshot
Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures
inferredcites →https://doi.org/10.1093/nar/gkn310openalex-snapshot
Low-fidelity DNA synthesis by human DNA polymerase theta
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003973openalex-snapshot
Heterotachy, an Important Process of Protein Evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004148openalex-snapshot
Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026171openalex-snapshot
Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040152openalex-snapshot
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040153openalex-snapshot
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
inferredcites →https://doi.org/10.1101/gr.085951.108openalex-snapshot
Adaptive evolution of young gene duplicates in mammals
inferredcites →https://doi.org/10.1101/gr.170696.113openalex-snapshot
Error-prone polymerase activity causes multinucleotide mutations in humans
inferredcites →https://doi.org/10.1101/gr.219956.116openalex-snapshot
Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
inferredcites →https://doi.org/10.1126/science.1182213openalex-snapshot
Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer
inferredcites →https://doi.org/10.1126/science.1259329openalex-snapshot
Escape from bacterial iron piracy through rapid evolution of transferrin
inferredcites →https://doi.org/10.1126/science.287.5456.1283openalex-snapshot
Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions
inferredcites →https://doi.org/10.1266/ggs.83.331openalex-snapshot
False-positive results obtained from the branch-site test of positive selection
inferredcites →https://doi.org/10.1371/journal.pgen.1000144openalex-snapshot
Patterns of Positive Selection in Six Mammalian Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1002764openalex-snapshot
Detecting Individual Sites Subject to Episodic Diversifying Selection
inferredcites →https://doi.org/10.1371/journal.pgen.1006315openalex-snapshot
Multi-nucleotide de novo Mutations in Humans
inferredcites →https://doi.org/10.1534/genetics.103.023226openalex-snapshot
Estimating the Frequency of Events That Cause Multiple-Nucleotide Changes
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.ympev.2018.04.030openalex-snapshot
Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)
inferred← citeshttps://doi.org/10.1093/gbe/evy274openalex-snapshot
Genome Sequence of Jaltomata Addresses Rapid Reproductive Trait Evolution and Enhances Comparative Genomics in the Hyper-Diverse Solanaceae
inferred← citeshttps://doi.org/10.1111/jeb.13597openalex-snapshot
Molecular evolution of the sex peptide network in Drosophila
inferred← citeshttps://doi.org/10.1111/mec.14780openalex-snapshot
Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance
inferred← citeshttps://doi.org/10.7554/elife.35957openalex-snapshot
Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision
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