Multinucleotide mutations cause false inferences of lineage-specific positive selection

Deep sequencing of natural and experimental populations ofDrosophila melanogasterreveals biases in the spectrum of new mutations

(2017) Zoe June Assaf et al.   GENOME RESEARCH

Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster

(2017) Mohammad A. Siddiq et al.   Nature Ecology & Evolution

Evolutionary switches between two serine codon sets are driven by selection

(2016) Igor B. Rogozin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multi-nucleotide de novo Mutations in Humans

(2016) Søren Besenbacher et al.   PLoS Genetics

Concurrent Nucleotide Substitution Mutations in the Human Genome Are Characterized by a Significantly Decreased Transition/Transversion Ratio

(2015) Wenjuan Zhu et al.   HUMAN MUTATION

Complex Multiple-Nucleotide Substitution Mutations Causing Human Inherited Disease Reveal Novel Insights into the Action of Translesion Synthesis DNA Polymerases

(2015) Jian-Min Chen et al.   HUMAN MUTATION

Positive Selection in CD8+T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages

(2015) Heather M. Machkovech et al.   JOURNAL OF VIROLOGY

Gene-Wide Identification of Episodic Selection

(2015) Ben Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide patterns and properties of de novo mutations in humans

(2015) Laurent C Francioli et al.   NATURE GENETICS

Convergent evolution of the genomes of marine mammals

(2015) Andrew D Foote et al.   NATURE GENETICS

Evolutionary insights into host–pathogen interactions from mammalian sequence data

(2015) Manuela Sironi et al.   NATURE REVIEWS GENETICS

Error-prone polymerase activity causes multinucleotide mutations in humans

(2014) Kelley Harris et al.   GENOME RESEARCH

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Patterns of Positive Selection in Seven Ant Genomes

(2014) Julien Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Escape from bacterial iron piracy through rapid evolution of transferrin

(2014) M. F. Barber et al.   SCIENCE

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

(2013) Jian-Min Chen et al.   HUMAN MUTATION

The Branch-Site Test of Positive Selection Is Surprisingly Robust but Lacks Power under Synonymous Substitution Saturation and Variation in GC

(2013) Walid H. Gharib et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dual Host-Virus Arms Races Shape an Essential Housekeeping Protein

(2013) Ann Demogines et al.   PLOS BIOLOGY

DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions inSaccharomyces cerevisiae

(2012) Jana E. Stone et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

DNA polymerase ζ generates tandem mutations in immunoglobulin variable regions

(2012) Huseyin Saribasak et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods

(2012) Weiwei Zhai et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating Empirical Codon Hidden Markov Models

(2012) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent Evolution of Escape from Hepaciviral Antagonism in Primates

(2012) Maulik R. Patel et al.   PLOS BIOLOGY

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Pervasive Multinucleotide Mutational Events in Eukaryotes

(2011) Daniel R. Schrider et al.   CURRENT BIOLOGY

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive evolution of young gene duplicates in mammals

(2009) M. V. Han et al.   GENOME RESEARCH

Gene Conversion Among Paralogs Results in Moderate False Detection of Positive Selection Using Likelihood Methods

(2009) Claudio Casola et al.   JOURNAL OF MOLECULAR EVOLUTION

Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates

(2009) Hanyi Zhuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

(2009) M. Nozawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

False-positive results obtained from the branch-site test of positive selection

(2008) Yoshiyuki Suzuki   GENES & GENETIC SYSTEMS

Protein kinase R reveals an evolutionary model for defeating viral mimicry

(2008) Nels C. Elde et al.   NATURE

DNA polymerases and human disease

(2008) Lawrence A. Loeb et al.   NATURE REVIEWS GENETICS

Low-fidelity DNA synthesis by human DNA polymerase theta

(2008) M. E. Arana et al.   NUCLEIC ACIDS RESEARCH

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

(2008) S. Yokoyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of protein-coding genes in Drosophila

(2008) Amanda M. Larracuente et al.   TRENDS IN GENETICS

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics