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Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Adaptive features of aquatic mammals' eye
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Spectral tuning in vertebrate short wavelength‐sensitive 1 (SWS1) visual pigments: Can wavelength sensitivity be inferred from sequence data?
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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution
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Spatial and temporal variability of light attenuation in large rivers of the Amazon
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Cetacean visual pigments
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Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal
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Molecular determinants of human red/green color discrimination
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Evolution of vertebrate visual pigments
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The hearing gene Prestin unites echolocating bats and whales
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Convergent sequence evolution between echolocating bats and dolphins
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Molecular Evolution: Gene Convergence in Echolocating Mammals
inferredcites →https://doi.org/10.1016/j.cub.2010.09.008openalex-snapshot
Cetaceans on a Molecular Fast Track to Ultrasonic Hearing
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Vision and the light environment
inferredcites →https://doi.org/10.1016/j.heares.2009.12.028openalex-snapshot
Prestin and the cholinergic receptor of hair cells: Positively-selected proteins in mammals
inferredcites →https://doi.org/10.1016/j.jmb.2004.07.044openalex-snapshot
The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2 Å Crystal Structure
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The p1D4-hrGFP II expression vector: A tool for expressing and purifying visual pigments and other G protein-coupled receptors
inferredcites →https://doi.org/10.1016/j.preteyeres.2004.03.001openalex-snapshot
Dark adaptation and the retinoid cycle of vision
inferredcites →https://doi.org/10.1016/j.tree.2014.04.001openalex-snapshot
Molecular evolution tracks macroevolutionary transitions in Cetacea
inferredcites →https://doi.org/10.1016/j.visres.2008.03.025openalex-snapshot
Evolution of vertebrate visual pigments
inferredcites →https://doi.org/10.1016/j.ympev.2009.10.007openalex-snapshot
High molecular diversity in the rhodopsin gene in closely related goby fishes: A role for visual pigments in adaptive speciation?
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Cone visual pigments of aquatic mammals
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Deep-sea and pelagic rod visual pigments identified in the mysticete whales
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Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal
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Eye evolution and its functional basis
inferredcites →https://doi.org/10.1017/s0952523898154056openalex-snapshot
The visual pigments of the bottlenose dolphin (Tursiops truncatus)
inferredcites →https://doi.org/10.1021/bi972500jopenalex-snapshot
Mechanism of Spectral Tuning in the Dolphin Visual Pigments
inferredcites →https://doi.org/10.1038/218955a0openalex-snapshot
Absorption Spectrum of Rhodopsin denatured with Acid
inferredcites →https://doi.org/10.1038/nature10530openalex-snapshot
A high-resolution map of human evolutionary constraint using 29 mammals
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Minke whale genome and aquatic adaptation in cetaceans
inferredcites →https://doi.org/10.1038/nrg3015openalex-snapshot
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Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi
inferredcites →https://doi.org/10.1073/pnas.051605998openalex-snapshot
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals
inferredcites →https://doi.org/10.1073/pnas.082666399openalex-snapshot
Functional role of internal water molecules in rhodopsin revealed by x-ray crystallography
inferredcites →https://doi.org/10.1073/pnas.86.21.8309openalex-snapshot
Glutamic acid-113 serves as the retinylidene Schiff base counterion in bovine rhodopsin.
inferredcites →https://doi.org/10.1073/pnas.97.21.11343openalex-snapshot
Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages
inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot
MRBAYES: Bayesian inference of phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
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Robust inference of positive selection from recombining coding sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btq429openalex-snapshot
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
inferredcites →https://doi.org/10.1093/gbe/evs123openalex-snapshot
Genome-Wide Scans for Candidate Genes Involved in the Aquatic Adaptation of Dolphins
inferredcites →https://doi.org/10.1093/molbev/msi097openalex-snapshot
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msi105openalex-snapshot
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
inferredcites →https://doi.org/10.1093/molbev/msi137openalex-snapshot
Adaptive Molecular Evolution in the Opsin Genes of Rapidly Speciating Cichlid Species
inferredcites →https://doi.org/10.1093/molbev/msi237openalex-snapshot
Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msn232openalex-snapshot
Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models
inferredcites →https://doi.org/10.1093/molbev/msp252openalex-snapshot
Vertebrate Rhodopsin Adaptation to Dim Light via Rapid Meta-II Intermediate Formation
inferredcites →https://doi.org/10.1093/molbev/msr311openalex-snapshot
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inferredcites →https://doi.org/10.1093/molbev/mss139openalex-snapshot
Correlation between Nuptial Colors and Visual Sensitivities Tuned by Opsins Leads to Species Richness in Sympatric Lake Victoria Cichlid Fishes
inferredcites →https://doi.org/10.1093/molbev/mst030openalex-snapshot
FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection
inferredcites →https://doi.org/10.1093/molbev/mst058openalex-snapshot
Nocturnal Light Environments Influence Color Vision and Signatures of Selection on the OPN1SW Opsin Gene in Nocturnal Lemurs
inferredcites →https://doi.org/10.1093/molbev/msu058openalex-snapshot
Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum
inferredcites →https://doi.org/10.1093/molbev/msu064openalex-snapshot
Divergent Positive Selection in Rhodopsin from Lake and Riverine Cichlid Fishes
inferredcites →https://doi.org/10.1093/nar/gkm290openalex-snapshot
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1098/rsbl.2015.0349openalex-snapshot
Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion
inferredcites →https://doi.org/10.1098/rspb.1997.0023openalex-snapshot
Mechanisms of wavelength tuning in the rod opsins of deep-sea fishes
inferredcites →https://doi.org/10.1098/rstb.2009.0039openalex-snapshot
Evolution of colour vision in mammals
inferredcites →https://doi.org/10.1098/rstb.2009.0044openalex-snapshot
Evolution and spectral tuning of visual pigments in birds and mammals
inferredcites →https://doi.org/10.1107/s0021889892009944openalex-snapshot
PROCHECK: a program to check the stereochemical quality of protein structures
inferredcites →https://doi.org/10.1110/ps.062416606openalex-snapshot
Statistical potential for assessment and prediction of protein structures
inferredcites →https://doi.org/10.1111/j.1365-2656.2006.01101.xopenalex-snapshot
Deep‐diving foraging behaviour of sperm whales ( Physeter macrocephalus )
inferredcites →https://doi.org/10.1111/j.1420-9101.2011.02290.xopenalex-snapshot
Signature of selection on the rhodopsin gene in the marine radiation of American seven‐spined gobies (Gobiidae, Gobiosomatini)
inferredcites →https://doi.org/10.1111/j.1748-7692.2011.00467.xopenalex-snapshot
Estimated absorbance spectra of the visual pigments of the North Atlantic right whale (Eubalaena glacialis)
inferredcites →https://doi.org/10.1126/science.162.3850.230openalex-snapshot
Molecular Basis of Visual Excitation
inferredcites →https://doi.org/10.1126/science.289.5480.739openalex-snapshot
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
inferredcites →https://doi.org/10.1146/annurev-earth-040809-152453openalex-snapshot
The Origin(s) of Whales
inferredcites →https://doi.org/10.1186/1471-2105-11-579openalex-snapshot
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
inferredcites →https://doi.org/10.1186/1471-2148-14-96openalex-snapshot
Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes
inferredcites →https://doi.org/10.1242/jeb.204.19.3333openalex-snapshot
The molecular basis for spectral tuning of rod visual pigments in deep-sea fish
inferredcites →https://doi.org/10.1371/journal.pbio.0040433openalex-snapshot
Divergent Selection on Opsins Drives Incipient Speciation in Lake Victoria Cichlids
inferredcites →https://doi.org/10.1371/journal.pgen.1003432openalex-snapshot
Rod Monochromacy and the Coevolution of Cetacean Retinal Opsins
inferredcites →https://doi.org/10.1371/journal.pone.0008326openalex-snapshot
Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments
inferredcites →https://doi.org/10.1371/journal.pone.0008838openalex-snapshot
Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)
inferredcites →https://doi.org/10.1371/journal.pone.0068200openalex-snapshot
Transcriptome Characterisation of the Ant Formica exsecta with New Insights into the Evolution of Desaturase Genes in Social Hymenoptera
inferredcites →https://doi.org/10.1578/016754203101024040openalex-snapshot
Colour vision in aquatic mammals—facts and open questions
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1111/jfb.15828zenodo-depositor-declared
Evolution of rhodopsin in flatfishes (Pleuronectiformes) is associated with depth and migratory behavior
inferred← citeshttps://doi.org/10.1002/1873-3468.12637openalex-snapshot
An experimental comparison of human and bovine rhodopsin provides insight into the molecular basis of retinal disease
inferred← citeshttps://doi.org/10.1002/ece3.11186openalex-snapshot
Short‐wavelength‐sensitive 1 (SWS1) opsin gene duplications and parallel visual pigment tuning support ultraviolet communication in damselfishes (Pomacentridae)
inferred← citeshttps://doi.org/10.1002/ece3.8595openalex-snapshot
Evolutionary analyses of visual opsin genes in frogs and toads: Diversity, duplication, and positive selection
inferred← citeshttps://doi.org/10.1002/pro.2902openalex-snapshot
A comparative study of rhodopsin function in the great bowerbird ( P tilonorhynchus nuchalis): Spectral tuning and light‐activated kinetics
inferred← citeshttps://doi.org/10.1007/s00239-026-10333-4openalex-snapshot
Evolutionary Transitions Drive Molecular Adaptation in Sculpin Rhodopsin
inferred← citeshttps://doi.org/10.1016/j.conb.2021.08.005openalex-snapshot
Evolution of sensory systems
inferred← citeshttps://doi.org/10.1016/j.gde.2017.09.005openalex-snapshot
Insights into visual pigment adaptation and diversity from model ecological and evolutionary systems
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2020.10.151openalex-snapshot
Accelerated evolution and positive selection of rhodopsin in Tibetan loaches living in high altitude
inferred← citeshttps://doi.org/10.1016/j.yhbeh.2020.104771openalex-snapshot
Functional evolution of vertebrate sensory receptors
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106737openalex-snapshot
Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing
inferred← citeshttps://doi.org/10.1073/pnas.1705765114openalex-snapshot
Evolution of nonspectral rhodopsin function at high altitudes
inferred← citeshttps://doi.org/10.1073/pnas.2118145119openalex-snapshot
Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behavior
inferred← citeshttps://doi.org/10.1093/gbe/evae223openalex-snapshot
Parallel Spectral Tuning of a Cone Visual Pigment Provides Evidence for Ancient Deep-Sea Adaptations in Cetaceans
inferred← citeshttps://doi.org/10.1093/gbe/evag068openalex-snapshot
Pressure-tolerant Evolution in Rhodopsin of Deep-diving Whales
inferred← citeshttps://doi.org/10.1093/molbev/msaa070openalex-snapshot
Positive Selection and Inactivation in the Vision and Hearing Genes of Cetaceans
inferred← citeshttps://doi.org/10.1093/molbev/msad030openalex-snapshot
Adaptation of Antarctic Icefish Vision to Extreme Environments
inferred← citeshttps://doi.org/10.1093/molbev/msad063openalex-snapshot
Diversified Mammalian Visual Adaptations to Bright- or Dim-Light Environments
inferred← citeshttps://doi.org/10.1093/molbev/msae049openalex-snapshot
Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments
inferred← citeshttps://doi.org/10.1093/molbev/msx192openalex-snapshot
Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America
inferred← citeshttps://doi.org/10.1093/molbev/msy025openalex-snapshot
Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry
inferred← citeshttps://doi.org/10.1093/molbev/msy140openalex-snapshot
Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments
inferred← citeshttps://doi.org/10.1098/rspb.2016.2743openalex-snapshot
Epistatic interactions influence terrestrial–marine functional shifts in cetacean rhodopsin
inferred← citeshttps://doi.org/10.1098/rspb.2017.2835openalex-snapshot
The role of ecological factors in shaping bat cone opsin evolution
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Molecular palaeontology illuminates the evolution of ecdysozoan vision
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Adaptive evolution and loss of a putative magnetoreceptor in passerines
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Convergent patterns of evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes in electric fishes
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Insect opsins and evo-devo: what have we learned in 25 years?
inferred← citeshttps://doi.org/10.1101/2021.08.27.457945openalex-snapshot
Evolutionary analyses of visual opsin genes in anurans reveals diversity and positive selection suggestive of functional adaptation to distinct light environments
inferred← citeshttps://doi.org/10.1101/2023.03.25.534197openalex-snapshot
Evidence for adaptive evolution towards high magnetic sensitivity of potential magnetoreceptor in songbirds
inferred← citeshttps://doi.org/10.1101/503516openalex-snapshot
Opsin gene evolution in amphibious and terrestrial combtooth blennies (Blenniidae)
inferred← citeshttps://doi.org/10.1111/evo.13396openalex-snapshot
Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms
inferred← citeshttps://doi.org/10.1111/evo.13810openalex-snapshot
Evolutionary signatures of photoreceptor transmutation in geckos reveal potential adaptation and convergence with snakes
inferred← citeshttps://doi.org/10.1111/mec.14149openalex-snapshot
Molecular adaptation in the world's deepest‐living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas
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Expression plasticity and evolutionary changes extensively shape the sugar‐mimic alkaloid adaptation of nondigestive glucosidase in lepidopteran mulberry‐specialist insects
inferred← citeshttps://doi.org/10.1111/mec.15102openalex-snapshot
Cardinalfishes (Apogonidae) show visual system adaptations typical of nocturnally and diurnally active fish
inferred← citeshttps://doi.org/10.1126/science.aav4632openalex-snapshot
Vision using multiple distinct rod opsins in deep-sea fishes
inferred← citeshttps://doi.org/10.1146/annurev-cellbio-120219-024915openalex-snapshot
The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function
inferred← citeshttps://doi.org/10.1186/s12859-016-1204-5openalex-snapshot
LMAP: Lightweight Multigene Analyses in PAML
inferred← citeshttps://doi.org/10.1186/s13227-023-00218-8openalex-snapshot
Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia
inferred← citeshttps://doi.org/10.1242/bio.062593openalex-snapshot
Opsin gene evolution in aquatic, amphibious and terrestrial blennies (Blenniidae)
inferred← citeshttps://doi.org/10.1242/jeb.156430openalex-snapshot
Cone-like rhodopsin expressed in the all cone retina of the colubrid pine snake as a potential adaptation to diurnality
inferred← citeshttps://doi.org/10.1242/jeb.175281openalex-snapshot
Short term colour vision plasticity on the reef: Changes in opsin expression under varying light conditions differ between ecologically distinct reef fish species
inferred← citeshttps://doi.org/10.1242/jeb.243907openalex-snapshot
Seeing Picasso: an investigation into the visual system of the triggerfish Rhinecanthus aculeatus
inferred← citeshttps://doi.org/10.1360/n052018-00211openalex-snapshot
Molecular adaptation mechanism of secondary aquatic life in cetaceans
inferred← citeshttps://doi.org/10.3389/feduc.2023.1278279openalex-snapshot
Incorporating evolution into neuroscience teaching
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New Insight Into Visual Adaptation in the Mudskipper Cornea: From Morphology to the Cornea-Related COL8A2 Gene
inferred← citeshttps://doi.org/10.3389/fmars.2019.00761openalex-snapshot
A Case Study of a Near Vessel Strike of a Blue Whale: Perceptual Cues and Fine-Scale Aspects of Behavioral Avoidance
inferred← citeshttps://doi.org/10.3389/fmars.2021.743663openalex-snapshot
The Adaptive Evolution and Gigantism Mechanisms of the Hadal “Supergiant” Amphipod Alicella gigantea
inferred← citeshttps://doi.org/10.3390/ani14010066openalex-snapshot
Neuroanatomy of the Cetacean Sensory Systems
inferred← citeshttps://doi.org/10.3390/genes14020416openalex-snapshot
Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review
inferred← citeshttps://doi.org/10.3390/vision6040059openalex-snapshot
The Colours of Octopus: Using Spectral Data to Measure Octopus Camouflage
inferred← citeshttps://doi.org/10.6084/m9.figshare.26618713openalex-snapshot
Additional file 1 of Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia
inferred← citeshttps://doi.org/10.6084/m9.figshare.26618716openalex-snapshot
Additional file 2 of Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia
inferred← citeshttps://doi.org/10.6084/m9.figshare.26618719openalex-snapshot
Additional file 3 of Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia
inferred← citeshttps://doi.org/10.6084/m9.figshare.26618722openalex-snapshot
Additional file 4 of Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia
inferred← citeshttps://doi.org/10.7554/elife.35957openalex-snapshot
Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision
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