Patterns of Positive Selection in Seven Ant Genomes

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

(2013) D. F. Simola et al.   GENOME RESEARCH

Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates

(2013) J Kulmuni et al.   HEREDITY

Accelerated Evolution of Innate Immunity Proteins in Social Insects: Adaptive Evolution or Relaxed Constraint?

(2013) Brock A. Harpur et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Polygenic Adaptation to Pathogens in the Human Genome

(2013) Josephine T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Selectome update: quality control and computational improvements to a database of positive selection

(2013) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

The Drosophila phenotype ontology

(2013) David Osumi-Sutherland et al.   Journal of Biomedical Semantics

Impaired fatty acid oxidation in a Drosophila model of mitochondrial trifunctional protein (MTP) deficiency

(2012) Yoshihito Kishita et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

(2012) Ari Löytynoja et al.   BIOINFORMATICS

The molecular basis of social behavior: models, methods and advances

(2012) Adria C LeBoeuf et al.   CURRENT OPINION IN NEUROBIOLOGY

THE EFFECTS OF KIN SELECTION ON RATES OF MOLECULAR EVOLUTION IN SOCIAL INSECTS

(2012) David W. Hall et al.   EVOLUTION

GENOMIC BASIS OF AGING AND LIFE-HISTORY EVOLUTION INDROSOPHILA MELANOGASTER

(2012) Silvia C. Remolina et al.   EVOLUTION

Juvenile hormone induces queen development in late-stage larvae of the ant Harpegnathos saltator

(2012) Clint A. Penick et al.   JOURNAL OF INSECT PHYSIOLOGY

A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities?

(2012) Ronald S. Burton et al.   MOLECULAR ECOLOGY

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparison of Pathway Analysis Approaches Using Lung Cancer GWAS Data Sets

(2012) Gordon Fehringer et al.   PLoS One

Major role of positive selection in the evolution of conservative segments of Drosophila proteins

(2012) G. A. Bazykin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

(2012) G. Zhang et al.   SCIENCE

Visualizing Long-Term Memory Formation in Two Neurons of the Drosophila Brain

(2012) C.-C. Chen et al.   SCIENCE

Ancestral Developmental Potential Facilitates Parallel Evolution in Ants

(2012) R. Rajakumar et al.   SCIENCE

Phylogenetic and Transcriptomic Analysis of Chemosensory Receptors in a Pair of Divergent Ant Species Reveals Sex-Specific Signatures of Odor Coding

(2012) Xiaofan Zhou et al.   PLoS Genetics

An Exploration of the Social Brain Hypothesis in Insects

(2012) Mathieu Lihoreau et al.   Frontiers in Physiology

DroPhEA: Drosophila phenotype enrichment analysis for insect functional genomics

(2011) Meng-Pin Weng et al.   BIOINFORMATICS

Genome-Wide Analysis of Self-Renewal in Drosophila Neural Stem Cells by Transgenic RNAi

(2011) Ralph A. Neumüller et al.   Cell Stem Cell

Stress and muscular dystrophy: A genetic screen for Dystroglycan and Dystrophin interactors in Drosophila identifies cellular stress response components

(2011) Mariya M. Kucherenko et al.   DEVELOPMENTAL BIOLOGY

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

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

The genome of the leaf-cutting antAcromyrmex echinatiorsuggests key adaptations to advanced social life and fungus farming

(2011) Sanne Nygaard et al.   GENOME RESEARCH

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

(2011) Eyal Privman et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu

(2011) Juan I. Montoya-Burgos   PLoS One

The Complete Mitochondrial Genome of the Asiatic Cavity-Nesting Honeybee Apis cerana (Hymenoptera: Apidae)

(2011) Hong-Wei Tan et al.   PLoS One

Molecular evolutionary analyses of insect societies

(2011) B. J. Fischman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

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

Relaxed selection is a precursor to the evolution of phenotypic plasticity

(2011) B. G. Hunt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of the fire ant Solenopsis invicta

(2011) Y. Wurm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the mitochondrial fusion-fission cycle and its role in aging

(2011) A. Kowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Draft genome of the red harvester ant Pogonomyrmex barbatus

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

Genes involved in convergent evolution of eusociality in bees

(2011) S. H. Woodard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

(2011) Garret Suen et al.   PLoS Genetics

Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae)

(2010) Dietrich Gotzek et al.   BMC EVOLUTIONARY BIOLOGY

Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

(2010) Robert M. Waterhouse et al.   Genome Biology and Evolution

Whole-Genome Positive Selection and Habitat-Driven Evolution in a Shallow and a Deep-Sea Urchin

(2010) Thomas A. Oliver et al.   Genome Biology and Evolution

Evolution of Gene Expression in Fire Ants: The Effects of Developmental Stage, Caste, and Species

(2010) L. Ometto et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Properties of the Branch-Site Test of Positive Selection

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

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera

(2010) M. C. Munoz-Torres et al.   NUCLEIC ACIDS RESEARCH

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

(2010) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Adaptive evolution of energy metabolism genes and the origin of flight in bats

(2010) Y.-Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

(2010) E. F. Kirkness et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parasitoidism, not sociality, is associated with the evolution of elaborate mushroom bodies in the brains of hymenopteran insects

(2010) S. M. Farris et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits

(2010) D. L. Kiss et al.   RNA

Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator

(2010) R. Bonasio et al.   SCIENCE

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

Nature versus nurture in social insect caste differentiation

(2010) Tanja Schwander et al.   TRENDS IN ECOLOGY & EVOLUTION

A doublecortin containing microtubule-associated protein is implicated in mechanotransduction in Drosophila sensory cilia

(2010) S. Bechstedt et al.   Nature Communications

Transcriptional Regulation by CHIP/LDB Complexes

(2010) Revital Bronstein et al.   PLoS Genetics

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

GENES WITH SOCIAL EFFECTS ARE EXPECTED TO HARBOR MORE SEQUENCE VARIATION WITHIN AND BETWEEN SPECIES

(2009) Timothy A. Linksvayer et al.   EVOLUTION

Gene expression profiling implicates OXPHOS complexes in lifespan extension of flies over-expressing a small mitochondrial chaperone, Hsp22

(2009) Hyun-Ju Kim et al.   EXPERIMENTAL GERONTOLOGY

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

Drosophila Suppressor of Sable Protein [Su(s)] Promotes Degradation of Aberrant and Transposon-Derived RNAs

(2009) Y.-S. Kuan et al.   MOLECULAR AND CELLULAR BIOLOGY

An Evolutionary Genome Scan for Longevity-Related Natural Selection in Mammals

(2009) R. W. Jobson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid Evolution of Immune Proteins in Social Insects

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

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum

(2009) Hee Shin Kim et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide RNAi Screen Identifies Genes Involved in Intestinal Pathogenic Bacterial Infection

(2009) S. J. F. Cronin et al.   SCIENCE

The role of positive selection in determining the molecular cause of species differences in disease

(2008) Jessica J Vamathevan et al.   BMC EVOLUTIONARY BIOLOGY

Incompatibility of Nuclear and Mitochondrial Genomes Causes Hybrid Sterility between Two Yeast Species

(2008) Hsin-Yi Lee et al.   CELL

Ageing in a eusocial insect: molecular and physiological characteristics of life span plasticity in the honey bee

(2008) D. Münch et al.   FUNCTIONAL ECOLOGY

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

(2008) R. A. Studer et al.   GENOME RESEARCH

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

(2008) D. C. S. G. Oliveira et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

Genetic and genomic analyses of the division of labour in insect societies

(2008) Chris R. Smith et al.   NATURE REVIEWS GENETICS

Selectome: a database of positive selection

(2008) E. Proux et al.   NUCLEIC ACIDS RESEARCH

VectorBase: a data resource for invertebrate vector genomics

(2008) D. Lawson et al.   NUCLEIC ACIDS RESEARCH

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

The Spectrum of Mitochondrial Mutation Differs across Species

(2008) Kristi L Montooth et al.   PLOS BIOLOGY

COPI Complex Is a Regulator of Lipid Homeostasis

(2008) Mathias Beller et al.   PLOS BIOLOGY

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics