Vision using multiple distinct rod opsins in deep-sea fishes

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations

(2018) Jagdish Suresh Patel et al.   PLoS Computational Biology

The dual rod system of amphibians supports colour discrimination at the absolute visual threshold

(2017) Carola A. M. Yovanovich et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

(2017) Martin Malmstrøm et al.   Scientific Data

Pushing the limits of photoreception in twilight conditions: The rod-like cone retina of the deep-sea pearlsides

(2017) Fanny de Busserolles et al.   Science Advances

From crypsis to mimicry: changes in colour and the configuration of the visual system during ontogenetic habitat transitions in a coral reef fish

(2016) Fabio Cortesi et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

A second visual rhodopsin gene,rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes

(2016) James M. Morrow et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Evolution of the immune system influences speciation rates in teleost fishes

(2016) Martin Malmstrøm et al.   NATURE GENETICS

Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes

(2016) Michael Matschiner et al.   SYSTEMATIC BIOLOGY

Rphylopars: fast multivariate phylogenetic comparative methods for missing data and within-species variation

(2016) Eric W. Goolsby et al.   Methods in Ecology and Evolution

Colour thresholds in a coral reef fish

(2016) C. M. Champ et al.   Royal Society Open Science

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Spectral Tuning in the Eyes of Deep-Sea Lanternfishes (Myctophidae): A Novel Sexually Dimorphic Intra-Ocular Filter

(2015) Fanny de Busserolles et al.   BRAIN BEHAVIOR AND EVOLUTION

Cyp27c1 Red-Shifts the Spectral Sensitivity of Photoreceptors by Converting Vitamin A1 into A2

(2015) Jennifer M. Enright et al.   CURRENT BIOLOGY

Colour vision in marine organisms

(2015) Justin Marshall et al.   CURRENT OPINION IN NEUROBIOLOGY

An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function

(2015) Wayne I.L. Davies et al.   GENOME RESEARCH

Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment

(2015) Sarah Z. Dungan et al.   MOLECULAR BIOLOGY AND EVOLUTION

An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

(2015) Dahiana Arcila et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Constraints on the timescale of animal evolutionary history

(2015) MJ Benton et al.   PALAEONTOLOGIA ELECTRONICA

Extraordinary diversity of visual opsin genes in dragonflies

(2015) Ryo Futahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

(2015) J. Cracraft et al.   SCIENCE

Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

(2015) K. J. Mitchell et al.   SCIENCE

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud

(2015) Enis Afgan et al.   PLoS One

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

(2014) Matthew W. Pennell et al.   BIOINFORMATICS

Early Eocene mammals from the Driftwood Creek beds, Driftwood Canyon Provincial Park, northern British Columbia

(2014) Jaelyn J. Eberle et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

The visual ecology of a deep-sea fish, the escolar Lepidocybium flavobrunneum (Smith, 1843)

(2014) E. Landgren et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Epistatic Adaptive Evolution of Human Color Vision

(2014) Shozo Yokoyama et al.   PLoS Genetics

Hide and Seek in the Open Sea: Pelagic Camouflage and Visual Countermeasures

(2013) Sönke Johnsen   Annual Review of Marine Science

Evolutionary rates and HBV: issues of rate estimation with Bayesian molecular methods

(2013) Remco Bouckaert et al.   ANTIVIRAL THERAPY

The Evolution of Complexity in the Visual Systems of Stomatopods: Insights from Transcriptomics

(2013) Megan L. Porter et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Morphology, taxonomy, and phylogeny of Triassic pholidophorid fishes (Actinopterygii, Teleostei)

(2013) Gloria Arratia   JOURNAL OF VERTEBRATE PALEONTOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Temporal Patterns of Diversification across Global Cichlid Biodiversity (Acanthomorpha: Cichlidae)

(2013) Caleb D. McMahan et al.   PLoS One

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

(2013) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

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

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

(2013) Daniel L. Rabosky et al.   Nature Communications

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

A Unique Advantage for Giant Eyes in Giant Squid

(2012) Dan-Eric Nilsson et al.   CURRENT BIOLOGY

Molecular ecology and adaptation of visual photopigments in craniates

(2012) WAYNE I. L. DAVIES et al.   MOLECULAR ECOLOGY

Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 years of taxonomic confusion

(2012) Alex Dornburg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A multilocus molecular phylogeny of boxfishes (Aracanidae, Ostraciidae; Tetraodontiformes)

(2012) Francesco Santini et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparable Ages for the Independent Origins of Electrogenesis in African and South American Weakly Electric Fishes

(2012) Sébastien Lavoué et al.   PLoS One

Phylogenetic Interrelationships of Ginglymodian Fishes (Actinopterygii: Neopterygii)

(2012) Adriana López-Arbarello   PLoS One

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Evolution of Pharyngognathy: A Phylogenetic and Functional Appraisal of the Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond

(2012) P. C. Wainwright et al.   SYSTEMATIC BIOLOGY

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

(2011) Masanori Nakatani et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A novel rhodopsin-like gene expressed in zebrafish retina

(2011) JAMES M. MORROW et al.   VISUAL NEUROSCIENCE

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

A new species of Enchodus (Aulopiformes: Enchodontidae) from the Cretaceous (Albian to Cenomanian) of Zimapán, Hidalgo, México

(2010) CHRISTOPHER FIELITZ et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Gymnogeophagus eocenicus, n. sp. (Perciformes: Cichlidae), an Eocene cichlid from the Lumbrera Formation in Argentina

(2010) Maria C. Malabarba et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleostean fishes

(2010) Jun Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae)

(2010) Hernán López-Fernández et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Estimating divergence times of lizardfishes and their allies (Euteleostei: Aulopiformes) and the timing of deep-sea adaptations

(2010) Matthew P. Davis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diversity of Mesozoic semionotiform fishes and the origin of gars (Lepisosteidae)

(2010) Lionel Cavin   NATURWISSENSCHAFTEN

A new genus and species of Heroini (Perciformes: Cichlidae) from the early Eocene of southern South America

(2010) Patricia Alano Perez et al.   Neotropical Ichthyology

Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity

(2010) E. A. Widder   SCIENCE

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

(2009) Francesco Santini et al.   BMC EVOLUTIONARY BIOLOGY

Santanasalmo elegans gen. et sp. nov., a basal euteleostean fish from the Lower Cretaceous of the Araripe Basin, northeastern Brazil

(2009) Valéria Gallo et al.   CRETACEOUS RESEARCH

Sedimentological, geochemical and paleontological insights applied to continental omission surfaces: A new approach for reconstructing an eocene foreland basin in NW Argentina

(2009) C. del Papa et al.   JOURNAL OF SOUTH AMERICAN EARTH SCIENCES

Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data

(2009) Adela Roa-Varón et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

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

Ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction

(2009) M. Friedman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A new Eocene catostomid (Teleostei: Cypriniformes) from northeastern China and early divergence of Catostomidae

(2009) Juan Liu et al.   Science in China. Series D, Earth sciences / Chinese Academy of Sciences

Evolution of Dim-Light and Color Vision Pigments

(2008) Shozo Yokoyama   Annual Review of Genomics and Human Genetics

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Phylogeny, taxonomy, and evolution of Neotropical cichlids (Teleostei: Cichlidae: Cichlinae)

(2008) Wm. Leo Smith et al.   CLADISTICS

Morphology and phylogenetic relationships of certain neoteleostean fishes from the Upper Cretaceous of Sendenhorst, Germany

(2008) Kathrin Dietze   CRETACEOUS RESEARCH

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

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

A review of early gadiform evolution and diversification: first record of a rattail fish skull (Gadiformes, Macrouridae) from the Eocene of Antarctica, with otoliths preserved in situ

(2008) Jürgen Kriwet et al.   NATURWISSENSCHAFTEN

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

Chronostratigraphy of Campanian–Maastrichtian platform carbonates and rudist associations of Salento (Apulia, Italy)

(2007) Malte Schlüter et al.   CRETACEOUS RESEARCH