Molecular hyperdiversity and evolution in very large populations

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Global Population Genetic Structure of Caenorhabditis remanei Reveals Incipient Speciation

(2012) A. Dey et al.   GENETICS

Dynamics of Neutral and Selected Alleles When the Offspring Distribution Is Skewed

(2012) R. Der et al.   GENETICS

Dynamic Mutation-Selection Balance as an Evolutionary Attractor

(2012) S. Goyal et al.   GENETICS

Patterns of Neutral Diversity Under General Models of Selective Sweeps

(2012) G. Coop et al.   GENETICS

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

Genetic and Genomic Toolbox of the Chordate Ciona intestinalis

(2012) A. Stolfi 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

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity

(2012) ASHER D. CUTTER et al.   MOLECULAR ECOLOGY

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

(2012) Erik C Andersen et al.   NATURE GENETICS

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Adaptive evolution: evaluating empirical support for theoretical predictions

(2012) Carrie F. Olson-Manning et al.   NATURE REVIEWS GENETICS

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

Limits to the Rate of Adaptive Substitution in Sexual Populations

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

A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits

(2011) Karin C Kiontke et al.   BMC EVOLUTIONARY BIOLOGY

High Spontaneous Rate of Gene Duplication in Caenorhabditis elegans

(2011) Kendra J. Lipinski et al.   CURRENT BIOLOGY

Pervasive Multinucleotide Mutational Events in Eukaryotes

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

Evolutionary crossroads in developmental biology: the tunicates

(2011) P. Lemaire   DEVELOPMENT

POPULATION GENETICS AND OBJECTIVITY IN SPECIES DIAGNOSIS

(2011) Jody Hey et al.   EVOLUTION

Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single HaploidDrosophila melanogasterEmbryo

(2011) Charles H. Langley et al.   GENETICS

Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations

(2011) R. A. Neher et al.   GENETICS

The Role of the Effective Population Size in Compensatory Evolution

(2011) Robert Piskol et al.   Genome Biology and Evolution

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

(2011) D. R. Schrider et al.   GENOME RESEARCH

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination

(2011) R Frankham   HEREDITY

Polymorphism, Divergence, and the Role of Recombination in Saccharomyces cerevisiae Genome Evolution

(2011) A. D. Cutter et al.   MOLECULAR BIOLOGY AND EVOLUTION

Non-adaptive origins of interactome complexity

(2011) Ariel Fernández et al.   NATURE

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Nictation, a dispersal behavior of the nematode Caenorhabditis elegans, is regulated by IL2 neurons

(2011) Harksun Lee et al.   NATURE NEUROSCIENCE

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Extensive DNA-binding specificity divergence of a conserved transcription regulator

(2011) C. R. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterozygote advantage as a natural consequence of adaptation in diploids

(2011) D. Sellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele

(2011) Paul A. Jenkins et al.   THEORETICAL POPULATION BIOLOGY

Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

(2011) Michael J. McDonald et al.   PLOS BIOLOGY

Pervasive Adaptive Protein Evolution Apparent in Diversity Patterns around Amino Acid Substitutions in Drosophila simulans

(2011) Shmuel Sattath et al.   PLoS Genetics

Correlated Evolution of Nearby Residues in Drosophilid Proteins

(2011) Benjamin Callahan et al.   PLoS Genetics

Divergence with Gene Flow: Models and Data

(2010) Catarina Pinho et al.   Annual Review of Ecology Evolution and Systematics

An efficient method to find potentially universal population genetic markers, applied to metazoans

(2010) Anne Chenuil et al.   BMC EVOLUTIONARY BIOLOGY

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCI

(2010) Jay F. Storz et al.   EVOLUTION

The Evolutionary Dynamics of Operon Distributions in Eukaryote Genomes

(2010) A. D. Cutter et al.   GENETICS

Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?

(2010) P. Ralph et al.   GENETICS

Effective Population Size and the Efficacy of Selection on the X Chromosomes of Two Closely Related Drosophila Species

(2010) Peter Andolfatto et al.   Genome Biology and Evolution

Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans

(2010) D. R. Denver et al.   GENOME RESEARCH

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

(2010) W. Niu et al.   GENOME RESEARCH

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites

(2010) R J Haasl et al.   HEREDITY

A Simple Multiallele Model and Its Application to Identifying Preferred-Unpreferred Codons Using Polymorphism Data

(2010) K. Zeng   MOLECULAR BIOLOGY AND EVOLUTION

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

Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5

(2010) GUO-XIU WANG et al.   MOLECULAR ECOLOGY

Polymorphism and divergence within the ascidian genus Ciona

(2010) Marie L. Nydam et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The population genomics of plant adaptation

(2010) Mathieu Siol et al.   NEW PHYTOLOGIST

The population genetics of beneficial mutations

(2010) H. A. Orr   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic hitchhiking versus background selection: the controversy and its implications

(2010) W. Stephan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mutation rate is linked to diversification in birds

(2010) R. Lanfear et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fitness flux and ubiquity of adaptive evolution

(2010) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Limits to gene flow in a cosmopolitan marine planktonic diatom

(2010) G. Casteleyn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A time-invariant principle of genome evolution

(2010) S. De et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence?

(2010) W. Amos   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & 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

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

(2010) Daniel L. Halligan et al.   PLoS Genetics

Frail Hypotheses in Evolutionary Biology

(2010) Jacques Ninio   PLoS Genetics

Did Genetic Drift Drive Increases in Genome Complexity?

(2010) Kenneth D. Whitney et al.   PLoS Genetics

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

A SELECTION MODEL OF MOLECULAR EVOLUTION INCORPORATING THE EFFECTIVE POPULATION SIZE

(2009) Hans Ellegren   EVOLUTION

LEARNING ABOUT MODES OF SPECIATION BY COMPUTATIONAL APPROACHES

(2009) Céline Becquet et al.   EVOLUTION

EXTENSIVE VARIATION IN NATURAL COMPETENCE INHAEMOPHILUS INFLUENZAE

(2009) Heather Maughan et al.   EVOLUTION

Human Triallelic Sites: Evidence for a New Mutational Mechanism?

(2009) A. Hodgkinson et al.   GENETICS

Rate of Adaptation in Large Sexual Populations

(2009) R. A. Neher et al.   GENETICS

Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

(2009) A. Barriere et al.   GENOME RESEARCH

Studying Patterns of Recent Evolution at Synonymous Sites and Intronic Sites in Drosophila melanogaster

(2009) Kai Zeng et al.   JOURNAL OF MOLECULAR EVOLUTION

Indel-Associated Mutation Rate Varies with Mating System in Flowering Plants

(2009) J. D. Hollister et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomewide Association between Insertions/Deletions and the Nucleotide Diversity in Bacteria

(2009) L. Zhu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid Sequence Evolution of Transcription Factors Controlling Neuron Differentiation in Caenorhabditis

(2009) Richard Jovelin   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of the Caenorhabditis elegans Genome

(2009) A. D. Cutter et al.   MOLECULAR BIOLOGY AND EVOLUTION

How Robust Are "Isolation with Migration" Analyses to Violations of the IM Model? A Simulation Study

(2009) J. L. Strasburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targets of Balancing Selection in the Human Genome

(2009) A. M. Andres et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Coalescent under the evolution of coadaptation

(2009) K. RYO TAKAHASI   MOLECULAR ECOLOGY

The impact of epistatic selection on the genomic traces of selection

(2009) SARAH P. OTTO et al.   MOLECULAR ECOLOGY

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Validating, augmenting and refining genome-wide association signals

(2009) John P. A. Ioannidis et al.   NATURE REVIEWS GENETICS

Evolutionary selection between alternative modes of gene regulation

(2009) U. Gerland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive, Recent Intron Gains in Daphnia Populations

(2009) W. Li et al.   SCIENCE

Speciation as an active force in promoting genetic evolution

(2009) Chris Venditti et al.   TRENDS IN ECOLOGY & EVOLUTION

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

Pervasive Natural Selection in the Drosophila Genome?

(2009) Guy Sella et al.   PLoS Genetics

The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis

(2008) Stephen I. Wright et al.   Annual Review of Ecology Evolution and Systematics

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

Drift by drift: effective population size is limited by advection

(2008) John P Wares et al.   BMC EVOLUTIONARY BIOLOGY

Dissection of lin-11 enhancer regions in Caenorhabditis elegans and other nematodes

(2008) Sujatha Marri et al.   DEVELOPMENTAL BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

(2008) Luis-Miguel Chevin et al.   GENETICS

The Polymorphism Frequency Spectrum of Finitely Many Sites Under Selection

(2008) M. M. Desai et al.   GENETICS

Multilocus Patterns of Polymorphism and Selection Across the X Chromosome of Caenorhabditis remanei

(2008) A. D. Cutter   GENETICS

Gene Conversion and End-Joining-Repair Double-Strand Breaks in the Caenorhabditis elegans Germline

(2008) V. J. Robert et al.   GENETICS

High Nucleotide Divergence in Developmental Regulatory Genes Contrasts With the Structural Elements of Olfactory Pathways in Caenorhabditis

(2008) R. Jovelin et al.   GENETICS

Predicting the potential distribution of the vase tunicate Ciona intestinalis in Canadian waters: informing a risk assessment

(2008) T. W. Therriault et al.   ICES JOURNAL OF MARINE SCIENCE

Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: Problems and solutions

(2008) Andrey Zharkikh et al.   JOURNAL OF BIOTECHNOLOGY

Selection efficiency and effective population size inDrosophilaspecies

(2008) N. PETIT et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Synonymous and Nonsynonymous Polymorphisms versus Divergences in Bacterial Genomes

(2008) A. L. Hughes et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic Diversity in the Paramecium aurelia Species Complex

(2008) F. Catania et al.   MOLECULAR BIOLOGY AND EVOLUTION

Divergence Times in Caenorhabditis and Drosophila Inferred from Direct Estimates of the Neutral Mutation Rate

(2008) A. D. Cutter   MOLECULAR BIOLOGY AND EVOLUTION

Speciation with gene flow could be common

(2008) PATRIK NOSIL   MOLECULAR ECOLOGY

Genotype, haplotype and copy-number variation in worldwide human populations

(2008) Mattias Jakobsson et al.   NATURE

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

(2008) Dacheng Tian et al.   NATURE

Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata

(2008) Jeffrey Ross-Ibarra et al.   PLoS One

Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

(2008) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations

(2008) Yutaka Satou et al.   GENOME BIOLOGY

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources