Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals

Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes

(2019) David Castellano et al.   GENETICS

Overestimation of the adaptive substitution rate in fluctuating populations

(2018) Marjolaine Rousselle et al.   Biology Letters

A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data

(2018) Paul Simion et al.   BMC BIOLOGY

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

(2018) Nicolas Galtier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biased inference of selection due to GC-biased gene conversion and the rate of protein evolution in flycatchers when accounting for it

(2018) Paulina Bolívar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Influence of recombination and GC-biased gene conversion on the adaptive and non-adaptive substitution rate in mammals vs. birds

(2018) M Rousselle et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantifying how constraints limit the diversity of viable routes to adaptation

(2018) Sam Yeaman et al.   PLoS Genetics

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

OUP accepted manuscript

(2017)   Genome Biology and Evolution

Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species

(2017) Jun Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence that the rate of strong selective sweeps increases with population size in the great apes

(2017) Kiwoong Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determining the factors driving selective effects of new nonsynonymous mutations

(2017) Christian D. Huber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data

(2017) Paula Tataru et al.   GENETICS

Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster

(2016) Peter D. Keightley et al.   GENETICS

Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies

(2016) Marjolaine Rousselle et al.   Genome Biology and Evolution

Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations

(2016) Tomotaka Matsumoto et al.   MOLECULAR BIOLOGY AND EVOLUTION

SLiM 2: Flexible, Interactive Forward Genetic Simulations

(2016) Benjamin C. Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Protein Evolution in Animals and the Effective Population Size Hypothesis

(2016) Nicolas Galtier   PLoS Genetics

Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster

(2016) Peter D. Keightley et al.   GENETICS

The rate of adaptive evolution in animal mitochondria

(2015) Jennifer E. James et al.   MOLECULAR ECOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

(2014) E. J. P. Douzery et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

A cost-effective straightforward protocol for shotgun Illumina libraries designed to assemble complete mitogenomes from non-model species

(2014) Marie-Ka Tilak et al.   Conservation Genetics Resources

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Rate of Molecular Adaptation in a Changing Environment

(2013) João M. Lourenço et al.   MOLECULAR BIOLOGY AND EVOLUTION

Frequent adaptation and the McDonald-Kreitman test

(2013) P. W. Messer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population size and the rate of evolution

(2013) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

Strong Purifying Selection at Synonymous Sites in D. melanogaster

(2013) David S. Lawrie et al.   PLoS Genetics

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

(2013) Philippe Gayral et al.   PLoS Genetics

The Nearly Neutral and Selection Theories of Molecular Evolution Under the Fisher Geometrical Framework: Substitution Rate, Population Size, and Complexity

(2012) P. Razeto-Barry et al.   GENETICS

The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis

(2012) Georgia Tsagkogeorga et al.   Genome Biology and Evolution

The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes

(2012) Toni I. Gossmann et al.   Genome Biology and Evolution

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

(2012) V. CAHAIS et al.   Molecular Ecology Resources

Evolutionary rescue and the limits of adaptation

(2012) G. Bell   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Limits to the Rate of Adaptive Substitution in Sexual Populations

(2012) Daniel B. Weissman et al.   PLoS Genetics

Characterizing the Influence of Effective Population Size on the Rate of Adaptation: Gillespie’s Darwin Domain

(2011) Jeffrey D. Jensen et al.   Genome Biology and Evolution

Non-adaptive origins of interactome complexity

(2011) Ariel Fernández et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Effective Population Size Is Positively Correlated with Levels of Adaptive Divergence among Annual Sunflowers

(2010) J. L. Strasburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

(2010) T. I. Gossmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Understanding Adaptation in Large Populations

(2010) Nick Barton   PLoS Genetics

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

(2010) Talia Karasov et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Genetic Basis of Phenotypic Adaptation II: The Distribution of Adaptive Substitutions in the Moving Optimum Model

(2009) Michael Kopp et al.   GENETICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome

(2008) Adam R. Boyko et al.   PLoS Genetics