Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments

The gene cortex controls mimicry and crypsis in butterflies and moths

(2016) Nicola J. Nadeau et al.   NATURE

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Rapid adaptive evolution of colour vision in the threespine stickleback radiation

(2016) Diana J. Rennison et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback

(2016) David A. Marques et al.   PLoS Genetics

Multiple Genetic Mechanisms Contribute to Visual Sensitivity Variation in the Labridae

(2015) Genevieve A.C. Phillips et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing

(2015) Andrew M. Glazer et al.   G3-Genes Genomes Genetics

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

(2014) Z. A. Szpiech et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes

(2014) Fabio Cortesi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species

(2014) Kohta Yoshida et al.   PLoS Genetics

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Role of the iridescent eye in stickleback female mate choice

(2013) I. N. Flamarique et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping

(2013) Bruce E. Deagle et al.   MOLECULAR ECOLOGY

Diurnal lighting patterns and habitat alter opsin expression and colour preferences in a killifish

(2013) A. M. Johnson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Losses of functional opsin genes, short-wavelength cone photopigments, and color vision—A significant trend in the evolution of mammalian vision

(2013) GERALD H. JACOBS   VISUAL NEUROSCIENCE

Abrupt changes in defence and trophic morphology of the giant threespine stickleback (Gasterosteussp.) following colonization of a vacant habitat

(2012) Stephen D. Leaver et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Pronounced heritable variation and limited phenotypic plasticity in visual pigments and opsin expression of threespine stickleback photoreceptors

(2012) I. N. Flamarique et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Opsin Evolution in Damselfish: Convergence, Reversal, and Parallel Evolution Across Tuning Sites

(2012) Christopher M. Hofmann et al.   JOURNAL OF MOLECULAR EVOLUTION

Visual Pigment Molecular Evolution in the Trinidadian Pike Cichlid (Crenicichla frenata): A Less Colorful World for Neotropical Cichlids?

(2012) Cameron J. Weadick et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Opsin gene duplication and divergence in ray-finned fish

(2011) Diana J. Rennison et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Female mating preferences, lighting environment, and a test of the sensory bias hypothesis in the bluefin killifish

(2010) Rebecca C. Fuller et al.   ANIMAL BEHAVIOUR

Structure and Activation of the Visual Pigment Rhodopsin

(2010) Steven O. Smith   Annual Review of Biophysics

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Plasticity of opsin gene expression in cichlids from Lake Malawi

(2010) CHRISTOPHER M. HOFMANN et al.   MOLECULAR ECOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) P. Librado et al.   BIOINFORMATICS

Gene duplication and differential gene expression play an important role in the diversification of visual pigments in fish

(2009) C. M. Hofmann et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

S14-03 From trait to base pairs: Parallel evolution of pelvic reduction in three-spined sticklebacks occurs by repeated deletion of a tissue-specific pelvic enhancer at Pitx1

(2009) Yingguang Frank Chan et al.   MECHANISMS OF DEVELOPMENT

To see in different seas: spatial variation in the rhodopsin gene of the sand goby (Pomatoschistus minutus)

(2009) MAARTEN H. D. LARMUSEAU et al.   MOLECULAR ECOLOGY

Evolution of opsins and phototransduction

(2009) Y. Shichida et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Fish Eye Out of Water: Ten Visual Opsins in the Four-Eyed Fish, Anableps anableps

(2009) Gregory L. Owens et al.   PLoS One

Is Genetic Evolution Predictable?

(2009) D. L. Stern et al.   SCIENCE

Adaptation of visual spectra and opsin genes in seabreams

(2009) Feng Yu Wang et al.   VISION RESEARCH

The molecular basis of color vision in colorful fish: Four Long Wave-Sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites

(2008) Matthew N Ward et al.   BMC EVOLUTIONARY BIOLOGY

Ontogenetic changes in photoreceptor opsin gene expression in coho salmon (Oncorhynchus kisutch, Walbaum)

(2008) S. E. Temple et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The influence of ontogeny and light environment on the expression of visual pigment opsins in the retina of the black bream, Acanthopagrus butcheri

(2008) J. Shand et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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 vertebrate visual pigments

(2008) James K. Bowmaker   VISION RESEARCH

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics

Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?

(2007) J ARENDT et al.   TRENDS IN ECOLOGY & EVOLUTION