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Adaptation and convergence in circadian-related genes in Iberian freshwater fish

https://doi.org/10.1101/706713
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Unraveling the mechanisms of the vertebrate circadian clock: zebrafish may light the way
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The HMMER Web Server for Protein Sequence Similarity Search
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Non‐canonical expression patterns and evolutionary rates of sex‐biased genes in a seasonal fish
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Phylogenetic Relationships within GenusLeuciscus(Pisces, Cyprinidae) in Portuguese Fresh Waters, Based on Mitochondrial DNA CytochromebSequences
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Comparative Analysis of Period Genes in Teleost Fish Genomes
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The Circadian Clock of Teleost Fish: A Comparative Analysis Reveals Distinct Fates for Duplicated Genes
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Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa
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Analysis of DNA-damage response to ionizing radiation in serum-shock synchronized human fibroblasts
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Migration patterns counteract seasonal isolation of Squalius torgalensis, a critically endangered freshwater fish inhabiting a typical Circum-Mediterranean small drainage
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Comparative genomic analysis of teleost fish bmal genes
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Multi-locus species tree of the chub genus Squalius (Leuciscinae: Cyprinidae) from western Iberia: new insights into its evolutionary history
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Habitat patchiness affects distribution and microhabitat use of endangered Mira chub Squalius torgalensis (Actinopterygii, Cypriniformes)
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Helix geometry in proteins
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Studying the Evolution of the Vertebrate Circadian Clock
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Different ecophysiological responses of freshwater fish to warming and acidification
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Molecular chaperones as regulatory elements of cellular networks
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An insight into the molecular basis for convergent evolution in fish antifreeze Proteins
inferredcites →https://doi.org/10.1016/j.cub.2011.04.024openalex-snapshot
Circadian Rhythms: Lost in Post-Translation
inferredcites →https://doi.org/10.1016/j.cub.2012.10.048openalex-snapshot
Convergent Evolution within an Adaptive Radiation of Cichlid Fishes
inferredcites →https://doi.org/10.1016/j.febslet.2011.04.007openalex-snapshot
It's time to swim! Zebrafish and the circadian clock
inferredcites →https://doi.org/10.1016/j.gene.2015.07.086openalex-snapshot
Molecular evolution of cryptochromes in fishes
inferredcites →https://doi.org/10.1016/j.gene.2015.07.088openalex-snapshot
Identification and expression of lypc, a novel dark-inducible member of Ly6 superfamily in zebrafish Danio rerio
inferredcites →https://doi.org/10.1016/j.jhydrol.2017.03.024openalex-snapshot
The role of riparian vegetation density, channel orientation and water velocity in determining river temperature dynamics
inferredcites →https://doi.org/10.1016/j.jmb.2016.03.014openalex-snapshot
Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability
inferredcites →https://doi.org/10.1016/j.jtherbio.2015.11.009openalex-snapshot
Transcriptome profiling of two Iberian freshwater fish exposed to thermal stress
inferredcites →https://doi.org/10.1016/j.jtherbio.2017.02.009openalex-snapshot
Thermal stress in Danio rerio : a link between temperature, light, thermo-TRP channels, and clock genes
inferredcites →https://doi.org/10.1016/j.margen.2008.06.003openalex-snapshot
Comparative analysis of teleost fish genomes reveals preservation of different ancient clock duplicates in different fishes
inferredcites →https://doi.org/10.1016/j.molmet.2013.05.002openalex-snapshot
Role of the circadian clock gene Per2 in adaptation to cold temperature
inferredcites →https://doi.org/10.1016/j.str.2009.08.011openalex-snapshot
Structure and Signaling Mechanism of Per-ARNT-Sim Domains
inferredcites →https://doi.org/10.1016/j.ympev.2018.12.020openalex-snapshot
Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data
inferredcites →https://doi.org/10.1016/s0092-8674(00)80566-8openalex-snapshot
Molecular Bases for Circadian Clocks
inferredcites →https://doi.org/10.1016/s0169-5347(03)00033-8openalex-snapshot
Evolution by gene duplication: an update
inferredcites →https://doi.org/10.1016/s0960-9822(06)00352-6openalex-snapshot
PAS: a multifunctional domain family comes to light
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Prediction of protein conformation
inferredcites →https://doi.org/10.1038/3703openalex-snapshot
Zebrafish Clock rhythmic expression reveals independent peripheral circadian oscillators
inferredcites →https://doi.org/10.1038/ng1700openalex-snapshot
Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism
inferredcites →https://doi.org/10.1038/nm1334openalex-snapshot
TFE3 transcriptionally activates hepatic IRS-2, participates in insulin signaling and ameliorates diabetes
inferredcites →https://doi.org/10.1038/nn.3543openalex-snapshot
Emerging roles for post-transcriptional regulation in circadian clocks
inferredcites →https://doi.org/10.1038/nrg3540openalex-snapshot
Evolutionary biochemistry: revealing the historical and physical causes of protein properties
inferredcites →https://doi.org/10.1038/s41437-018-0173-zopenalex-snapshot
Convergent evolution on the hypoxia-inducible factor (HIF) pathway genes EGLN1 and EPAS1 in high-altitude ducks
inferredcites →https://doi.org/10.1038/s41598-018-27080-2openalex-snapshot
Mutations in blind cavefish target the light-regulated circadian clock gene, period 2
inferredcites →https://doi.org/10.1038/srep08113openalex-snapshot
Molecular evolution and functional divergence of zebrafish (Danio rerio) cryptochrome genes
inferredcites →https://doi.org/10.1046/j.1365-2427.2002.00941.xopenalex-snapshot
Functional heterogeneity of dry‐season fish refugia across a Mediterranean catchment: the role of habitat and predation
inferredcites →https://doi.org/10.1046/j.1365-2443.2002.00579.xopenalex-snapshot
Zebrafish CRY represses transcription mediated by CLOCK‐BMAL heterodimer without inhibiting its binding to DNA
inferredcites →https://doi.org/10.1046/j.1365-2443.2003.00669.xopenalex-snapshot
Temperature compensation and temperature resetting of circadian rhythms in mammalian cultured fibroblasts
inferredcites →https://doi.org/10.1073/pnas.0305436101openalex-snapshot
E-box function in a period gene repressed by light
inferredcites →https://doi.org/10.1073/pnas.0607993103openalex-snapshot
A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity
inferredcites →https://doi.org/10.1073/pnas.0704588104openalex-snapshot
Light signaling to the zebrafish circadian clock by Cryptochrome 1a
inferredcites →https://doi.org/10.1073/pnas.0705614104openalex-snapshot
Circadian control by the reduction/oxidation pathway: Catalase represses light-dependent clock gene expression in the zebrafish
inferredcites →https://doi.org/10.1073/pnas.0802426105openalex-snapshot
Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
inferredcites →https://doi.org/10.1073/pnas.1720487115openalex-snapshot
Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau
inferredcites →https://doi.org/10.1073/pnas.181228598openalex-snapshot
A cell-based system that recapitulates the dynamic light-dependent regulation of the vertebrate clock
inferredcites →https://doi.org/10.1074/jbc.m117.794289openalex-snapshot
Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo
inferredcites →https://doi.org/10.1089/dna.1983.2.329openalex-snapshot
A Method for Isolation of Intact, Translationally Active Ribonucleic Acid
inferredcites →https://doi.org/10.1093/bioinformatics/14.9.755openalex-snapshot
Profile hidden Markov models.
inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot
MRBAYES: Bayesian inference of phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/8.3.275openalex-snapshot
The rapid generation of mutation data matrices from protein sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bth254openalex-snapshot
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot
HyPhy: hypothesis testing using phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/bti263openalex-snapshot
ProtTest: selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/bioinformatics/bti320openalex-snapshot
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
inferredcites →https://doi.org/10.1093/bioinformatics/btr088openalex-snapshot
ProtTest 3: fast selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv362openalex-snapshot
IBS: an illustrator for the presentation and visualization of biological sequences
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/msn067openalex-snapshot
An Improved General Amino Acid Replacement Matrix
inferredcites →https://doi.org/10.1093/molbev/msr125openalex-snapshot
A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection
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Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
inferredcites →https://doi.org/10.1093/molbev/msv035openalex-snapshot
Gene-Wide Identification of Episodic Selection
inferredcites →https://doi.org/10.1093/molbev/msx335openalex-snapshot
Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes
inferredcites →https://doi.org/10.1093/molbev/msy096openalex-snapshot
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
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STRING: a database of predicted functional associations between proteins
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M-Coffee: combining multiple sequence alignment methods with T-Coffee
inferredcites →https://doi.org/10.1093/nar/gkr245openalex-snapshot
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
inferredcites →https://doi.org/10.1093/nar/gkr367openalex-snapshot
HMMER web server: interactive sequence similarity searching
inferredcites →https://doi.org/10.1093/nar/gkt1359openalex-snapshot
The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light
inferredcites →https://doi.org/10.1093/nar/gku1003openalex-snapshot
STRING v10: protein–protein interaction networks, integrated over the tree of life
inferredcites →https://doi.org/10.1093/nar/gku989openalex-snapshot
UniProt: a hub for protein information
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The Pfam protein families database: towards a more sustainable future
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HMMER web server: 2018 update
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Thermostability and Aliphatic Index of Globular Proteins
inferredcites →https://doi.org/10.1093/protein/13.3.179openalex-snapshot
Factors enhancing protein thermostability
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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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Plasticity in thermal tolerance has limited potential to buffer ectotherms from global warming
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Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms
inferredcites →https://doi.org/10.1111/gcb.12240openalex-snapshot
Temperature variation makes ectotherms more sensitive to climate change
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Seasonal changes in fish community structure of intermittent streams in the middle reaches of the Guadiana basin, Portugal
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Comparative phylogeography of endemic cyprinids in the south‐west Iberian Peninsula: evidence for a new ichthyogeographic area
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Identification of cryptochrome DASH from vertebrates
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Biogeography of Iberian freshwater fishes revisited: the roles of historical versus contemporary constraints
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Phylogeography of the cyprinid Squalius aradensis and implications for conservation of the endemic freshwater fauna of southern Portugal
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Understanding phylogenetic incongruence: lessons from phyllostomid bats
inferredcites →https://doi.org/10.1126/science.281.5378.825openalex-snapshot
How Temperature Changes Reset a Circadian Oscillator
inferredcites →https://doi.org/10.1126/science.aaf9070openalex-snapshot
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inferredcites →https://doi.org/10.1128/mcb.15.11.6055openalex-snapshot
Molecular Cloning and Characterization of NF-IL3A, a Transcriptional Activator of the Human Interleukin-3 Promoter
inferredcites →https://doi.org/10.1186/1471-2164-14-682openalex-snapshot
Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake
inferredcites →https://doi.org/10.1186/1471-2164-8-163openalex-snapshot
The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms
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A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes
inferredcites →https://doi.org/10.1186/1740-3391-3-7openalex-snapshot
Evolution of temporal order in living organisms
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Molecular biogeography of Europe: Pleistocene cycles and postglacial trends
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Molecular phylogenetics reveals convergent evolution in lower Congo River spiny eels
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MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae
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Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish
inferredcites →https://doi.org/10.1371/journal.pbio.0030351openalex-snapshot
Temperature Regulates Transcription in the Zebrafish Circadian Clock
inferredcites →https://doi.org/10.1371/journal.pbio.0050034openalex-snapshot
System-Driven and Oscillator-Dependent Circadian Transcription in Mice with a Conditionally Active Liver Clock
inferredcites →https://doi.org/10.1371/journal.pbio.1000223openalex-snapshot
Light Directs Zebrafish period2 Expression via Conserved D and E Boxes
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.1371/journal.pcbi.1002940openalex-snapshot
Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish
inferredcites →https://doi.org/10.1371/journal.pgen.1002764openalex-snapshot
Detecting Individual Sites Subject to Episodic Diversifying Selection
inferredcites →https://doi.org/10.1371/journal.pone.0017080openalex-snapshot
The Light Responsive Transcriptome of the Zebrafish: Function and Regulation
inferredcites →https://doi.org/10.1371/journal.pone.0024521openalex-snapshot
Synchronization of Circadian Per2 Rhythms and HSF1-BMAL1:CLOCK Interaction in Mouse Fibroblasts after Short-Term Heat Shock Pulse
inferredcites →https://doi.org/10.1371/journal.pone.0099172openalex-snapshot
Daily Rhythmicity of Clock Gene Transcripts in Atlantic Cod Fast Skeletal Muscle
inferredcites →https://doi.org/10.1371/journal.pone.0181325openalex-snapshot
Protein analysis and gene expression indicate differential vulnerability of Iberian fish species under a climate change scenario
inferredcites →https://doi.org/10.1371/journal.pone.0186935openalex-snapshot
Convergent evolution of reduced energy demands in extremophile fish
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Protein Identification and Analysis Tools in the ExPASy Server
inferredcites →https://doi.org/10.1385/1-59259-890-0:571openalex-snapshot
Protein Identification and Analysis Tools on the ExPASy Server
inferredcites →https://doi.org/10.1534/genetics.104.037051openalex-snapshot
Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution
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On the Adaptive Significance of Circadian Clocks for Their Owners
inferredcites →https://doi.org/10.3390/genes10080622openalex-snapshot
The Molecular Evolution of Circadian Clock Genes in Spotted Gar (Lepisosteus oculatus)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/g3journal/jkae162openalex-snapshot
Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates
inferred← citeshttps://doi.org/10.1111/mec.15217openalex-snapshot
Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon
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