Divergent Positive Selection in Rhodopsin from Lake and Riverine Cichlid Fishes

Asymmetry of the rhodopsin dimer in complex with transducin

(2013) Beata Jastrzebska et al.   FASEB JOURNAL

Nocturnal Light Environments Influence Color Vision and Signatures of Selection on the OPN1SW Opsin Gene in Nocturnal Lemurs

(2013) Carrie C. Veilleux 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

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptome Characterisation of the Ant Formica exsecta with New Insights into the Evolution of Desaturase Genes in Social Hymenoptera

(2013) Hélène Badouin 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

Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution

(2013) J. H. Arbour et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rapid Release of Retinal from a Cone Visual Pigment following Photoactivation

(2012) Min-Hsuan Chen et al.   BIOCHEMISTRY

Rhodopsin Forms a Dimer with Cytoplasmic Helix 8 Contacts in Native Membranes

(2012) Adam M. Knepp et al.   BIOCHEMISTRY

Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses

(2012) Cameron J Weadick et al.   BMC EVOLUTIONARY BIOLOGY

Adaptive evolution of Toll-like receptor 5 in domesticated mammals

(2012) Sarah A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Convergent Evolution within an Adaptive Radiation of Cichlid Fishes

(2012) Moritz Muschick et al.   CURRENT BIOLOGY

Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods

(2012) Weiwei Zhai et al.   MOLECULAR BIOLOGY AND EVOLUTION

Correlation between Nuptial Colors and Visual Sensitivities Tuned by Opsins Leads to Species Richness in Sympatric Lake Victoria Cichlid Fishes

(2012) Ryutaro Miyagi et al.   MOLECULAR BIOLOGY AND 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

Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fishTriportheus albus

(2012) GEORGINA M. COOKE et al.   MOLECULAR ECOLOGY

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Diet-Morphology Correlations in the Radiation of South American Geophagine Cichlids (Perciformes: Cichlidae: Cichlinae)

(2012) Hernán López-Fernández et al.   PLoS One

Effect of channel mutations on the uptake and release of the retinal ligand in opsin

(2012) R. Piechnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Mechanism of Thermal Noise in Rod Photoreceptors

(2012) S. Gozem et al.   SCIENCE

Deep-sea and pelagic rod visual pigments identified in the mysticete whales

(2012) NICOLE BISCHOFF et al.   VISUAL NEUROSCIENCE

Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal

(2012) CONSTANZE BICKELMANN et al.   VISUAL NEUROSCIENCE

Maximum likelihood analysis of mammalian p53 indicates the presence of positively selected sites and higher tumorigenic mutations in purifying sites

(2011) Maola M.G. Khan et al.   GENE

Speciation within genomic networks: a case study based on Steatocranus cichlids of the lower Congo rapids

(2011) J. SCHWARZER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

An Improved Likelihood Ratio Test for Detecting Site-Specific Functional Divergence among Clades of Protein-Coding Genes

(2011) Cameron J. Weadick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient Hybridization and Phenotypic Novelty within Lake Malawi's Cichlid Fish Radiation

(2011) M. J. Genner et al.   MOLECULAR BIOLOGY AND EVOLUTION

dN/dS-Based Methods Detect Positive Selection Linked to Trade-Offs between Different Fitness Traits in the Coat Protein of Potato virus Y

(2011) B. Moury et al.   MOLECULAR BIOLOGY AND EVOLUTION

Opsin gene duplication and divergence in ray-finned fish

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

Multilocus phylogeny of Crenicichla (Teleostei: Cichlidae), with biogeography of the C. lacustris group: Species flocks as a model for sympatric speciation in rivers

(2011) Lubomír Piálek et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Crystal structure of metarhodopsin II

(2011) Hui-Woog Choe et al.   NATURE

Change of Positive Selection Pressure on HIV-1 Envelope Gene Inferred by Early and Recent Samples

(2011) Izumi Yoshida et al.   PLoS One

Time and Origin of Cichlid Colonization of the Lower Congo Rapids

(2011) Julia Schwarzer et al.   PLoS One

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Parallel amino acid replacements in the rhodopsins of the rockfishes (Sebastes spp.) associated with shifts in habitat depth

(2010) A. SIVASUNDAR et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Retinal release from opsin in molecular dynamics simulations

(2010) Ting Wang et al.   JOURNAL OF MOLECULAR RECOGNITION

Reverse Evolution in RH1 for Adaptation of Cichlids to Water Depth in Lake Tanganyika

(2010) H. Nagai 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

Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby, Pomatoschistus minutus

(2010) MAARTEN H. D. LARMUSEAU et al.   MOLECULAR ECOLOGY

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

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

Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

(2010) Yong-Yi Shen et al.   PLoS One

Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies

(2010) Adriana D. Briscoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The root of the East African cichlid radiations

(2009) Julia Schwarzer et al.   BMC EVOLUTIONARY BIOLOGY

Dimerization in GPCR mobility and signaling

(2009) Martin J Lohse   CURRENT OPINION IN PHARMACOLOGY

Cichlid fish visual systems: mechanisms of spectral tuning

(2009) Karen CARLETON   Integrative Zoology

Vertebrate Rhodopsin Adaptation to Dim Light via Rapid Meta-II Intermediate Formation

(2009) T. Sugawara et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and spectral tuning of visual pigments in birds and mammals

(2009) D. M. Hunt et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Ligand Channel through the G Protein Coupled Receptor Opsin

(2009) Peter W. Hildebrand et al.   PLoS One

Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

(2009) Huabin Zhao et al.   PLoS One

In defense of statistical methods for detecting positive selection

(2009) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response to Yang et al.: Problems with Bayesian methods of detecting positive selection at the DNA sequence level

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

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

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

A G protein-coupled receptor at work: the rhodopsin model

(2009) Klaus Peter Hofmann et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2008) Wm. Leo Smith et al.   CLADISTICS

False-positive results obtained from the branch-site test of positive selection

(2008) Yoshiyuki Suzuki   GENES & GENETIC SYSTEMS

Rhodopsin: Structure, signal transduction and oligomerisation

(2008) Michael B. Morris et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Crystal structure of opsin in its G-protein-interacting conformation

(2008) Patrick Scheerer et al.   NATURE

Speciation through sensory drive in cichlid fish

(2008) Ole Seehausen et al.   NATURE

Crystal structure of the ligand-free G-protein-coupled receptor opsin

(2008) Jung Hee Park et al.   NATURE

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