{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T13:24:48Z","timestamp":1777296288662,"version":"3.51.4"},"reference-count":70,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T00:00:00Z","timestamp":1775779200000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32270462"],"award-info":[{"award-number":["32270462"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32270453"],"award-info":[{"award-number":["32270453"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070409"],"award-info":[{"award-number":["32070409"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fundamental Research Funds"},{"name":"Central Universities","award":["GK202401001"],"award-info":[{"award-number":["GK202401001"]}]},{"name":"Excellent Graduate Training Program of Shaanxi Normal University","award":["LHRCTS23088"],"award-info":[{"award-number":["LHRCTS23088"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The origin of dim-light vision in vertebrates has been attributed to an early duplication event in an ancestral form of pigment called RH, which led to the formation of the RH1 (rhodopsin) and RH2 (rhodopsin-like) opsins. Two sites (122 and 189) are known to critically underlie rhodopsin's sensitivity in low light; however, the evolutionary trajectory leading to dim-light vision remains unclear. We built a large comparative dataset of vertebrate RH1 and RH2 sequences and inferred their respective ancestral protein sequences alongside their common ancestor. Sequence comparisons revealed that known critical sites underpinning RH1 kinetics did not evolve at the origin of this molecule, and instead first evolved in RH (M122E) as well as later in the RH1 of ancestor of jawed vertebrates (P189I). To assess the phenotypic impacts of these changes, we conducted in vitro protein expression and found that the retinal release rate of RH1 became significantly slower following its divergence from RH2, with further deceleration at the origin of jawed vertebrates. We also constructed single RH1 mutants and found that the replacement S295A accounted for the observed difference in retinal release between RH and RH1. Finally, to validate these phenotypic consequences in vivo, we compared zebrafish overexpressing RH, RH1, or the mutant RH-S295A, and recorded increased locomotor rebound following light-intensity reduction in the latter two treatments. We conclude that highly sensitive dim-light vision in vertebrates evolved via three main stages of molecular adaptation, at the origins of RH and RH1, and subsequently in the ancestral RH1 of jawed vertebrates.<\/jats:p>","DOI":"10.1093\/molbev\/msag096","type":"journal-article","created":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T11:57:05Z","timestamp":1775649425000},"source":"Crossref","is-referenced-by-count":0,"title":["Comparative phenotypic analysis of rhodopsin supports stepwise evolution of dim-light vision in early vertebrates"],"prefix":"10.1093","volume":"43","author":[{"given":"Yimeng","family":"Cui","sequence":"first","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University , Xi\u2019an ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyang","family":"Lu","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for the Biodiversity Conservation and Sustainable Utilization in the Middle and Lower Reaches of Yangtze River Basin, College of Life Sciences, Nanjing Normal University , Nanjing ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine , Beijing ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengqi","family":"Shuai","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for the Biodiversity Conservation and Sustainable Utilization in the Middle and Lower Reaches of Yangtze River Basin, College of Life Sciences, Nanjing Normal University , Nanjing ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Sun","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for the Biodiversity Conservation and Sustainable Utilization in the Middle and Lower Reaches of Yangtze River Basin, College of Life Sciences, Nanjing Normal University , Nanjing ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaoqi","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University , Xi\u2019an ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanfang","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University , Xi\u2019an ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruijuan","family":"Dong","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine , Beijing ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leilei","family":"Shi","sequence":"additional","affiliation":[{"name":"Nutshell Therapeutics , Shanghai ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen J","family":"Rossiter","sequence":"additional","affiliation":[{"name":"School of Biological and Behavioural Sciences, Queen Mary, University of London , London ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6496-3744","authenticated-orcid":false,"given":"Shixia","family":"Xu","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for the Biodiversity Conservation and Sustainable Utilization in the Middle and Lower Reaches of Yangtze River Basin, College of Life Sciences, Nanjing Normal University , Nanjing ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9258-7237","authenticated-orcid":false,"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Shaanxi Normal University , Xi\u2019an ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,4,9]]},"reference":[{"key":"2026042708285566800_msag096-B1","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1-2","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2026042708285566800_msag096-B2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.07166","article-title":"A Cambrian origin for vertebrate rods","volume":"4","author":"Asteriti","year":"2015","journal-title":"eLife"},{"key":"2026042708285566800_msag096-B3","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1016\/j.ydbio.2004.04.006","article-title":"An artificial promoter construct for heat-inducible misexpression during fish embryogenesis","volume":"271","author":"Bajoghli","year":"2004","journal-title":"Dev Biol"},{"key":"2026042708285566800_msag096-B4","doi-asserted-by":"publisher","first-page":"2995","DOI":"10.1111\/evo.12794","article-title":"The molecular origin and evolution of dim-light vision in mammals","volume":"69","author":"Bickelmann","year":"2015","journal-title":"Evolution"},{"key":"2026042708285566800_msag096-B5","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1093\/bfgp\/eln039","article-title":"The neurogenetic frontier\u2014lessons from misbehaving zebrafish","volume":"7","author":"Burgess","year":"2008","journal-title":"Brief Funct Genomic Proteomic"},{"key":"2026042708285566800_msag096-B6","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.35957","article-title":"Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision","volume":"7","author":"Castiglione","year":"2018","journal-title":"eLife"},{"key":"2026042708285566800_msag096-B7","doi-asserted-by":"publisher","first-page":"4117","DOI":"10.1021\/bi201522h","article-title":"Rapid release of retinal from a cone visual pigment following photoactivation","volume":"51","author":"Chen","year":"2012","journal-title":"Biochemistry"},{"key":"2026042708285566800_msag096-B8","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/nature09789","article-title":"Crystal structure of metarhodopsin II","volume":"471","author":"Choe","year":"2011","journal-title":"Nature"},{"key":"2026042708285566800_msag096-B9","doi-asserted-by":"publisher","first-page":"2925","DOI":"10.1098\/rstb.2009.0099","article-title":"The evolution of early vertebrate photoreceptors","volume":"364","author":"Collin","year":"2009","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"2026042708285566800_msag096-B10","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1016\/0042-6989(91)90086-K","article-title":"The scotopic photoreceptors and their visual pigments of fishes: functions and adaptations","volume":"31","author":"Crescitelli","year":"1991","journal-title":"Vision Res"},{"key":"2026042708285566800_msag096-B11","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1093\/bioinformatics\/btr088","article-title":"ProtTest 3: fast selection of best-fit models of protein evolution","volume":"27","author":"Darriba","year":"2011","journal-title":"Bioinformatics"},{"key":"2026042708285566800_msag096-B12","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"Darriba","year":"2012","journal-title":"Nat Methods"},{"key":"2026042708285566800_msag096-B13","doi-asserted-by":"publisher","first-page":"2713","DOI":"10.1096\/fj.06-8057com","article-title":"Functional characterization, tuning, and regulation of visual pigment gene expression in an anadromous lamprey","volume":"21","author":"Davies","year":"2007","journal-title":"FASEB J"},{"key":"2026042708285566800_msag096-B14","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1101\/gr.084509.108","article-title":"Into the blue: gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii","volume":"19","author":"Davies","year":"2009","journal-title":"Genome Res"},{"key":"2026042708285566800_msag096-B15","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2016.2743","article-title":"Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin","volume":"284","author":"Dungan","year":"2017","journal-title":"Proc Biol Sci."},{"key":"2026042708285566800_msag096-B16","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2118145119","article-title":"Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: implications for ancestral diving behavior","volume":"119","author":"Dungan","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026042708285566800_msag096-B17","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/S1350-9462(00)00014-8","article-title":"Vertebrate photoreceptors","volume":"20","author":"Ebrey","year":"2001","journal-title":"Prog Retin Eye Res"},{"key":"2026042708285566800_msag096-B18","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1093\/molbev\/msw223","article-title":"Robustness of reconstructed ancestral protein functions to statistical uncertainty","volume":"34","author":"Eick","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B19","doi-asserted-by":"publisher","DOI":"10.1242\/jcs.254995","article-title":"Identification of additional outer segment targeting signals in zebrafish rod opsin","volume":"134","author":"Fang","year":"2021","journal-title":"J Cell Sci"},{"key":"2026042708285566800_msag096-B20","doi-asserted-by":"publisher","first-page":"5073","DOI":"10.1074\/jbc.270.10.5073","article-title":"Structure and function in rhodopsin. Measurement of the rate of metarhodopsin II decay by fluorescence spectroscopy","volume":"270","author":"Farrens","year":"1995","journal-title":"J Biol Chem"},{"key":"2026042708285566800_msag096-B21","doi-asserted-by":"publisher","first-page":"17375","DOI":"10.1074\/jbc.M117.784017","article-title":"The cytoplasmic tail of rhodopsin triggers rapid rod degeneration in kinesin-2 mutants","volume":"292","author":"Feng","year":"2017","journal-title":"J Biol Chem"},{"key":"2026042708285566800_msag096-B22","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2023.0530","article-title":"Convergent evolutionary shifts in rhodopsin retinal release explain shared opsin repertoires in monotremes and crocodilians","volume":"290","author":"Guo","year":"2023","journal-title":"Proc Biol Sci."},{"key":"2026042708285566800_msag096-B23","doi-asserted-by":"publisher","first-page":"2422","DOI":"10.1093\/molbev\/msy140","article-title":"Functional shifts in bat dim-light visual pigment are associated with differing echolocation abilities and reveal molecular adaptation to photic-limited environments","volume":"35","author":"Gutierrez","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B24","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.ydbio.2022.10.014","article-title":"The evolutionary history and spectral tuning of vertebrate visual opsins","volume":"493","author":"Hagen","year":"2023","journal-title":"Dev Biol"},{"key":"2026042708285566800_msag096-B25","doi-asserted-by":"publisher","DOI":"10.1016\/j.preteyeres.2022.101116","article-title":"Rhodopsin, light-sensor of vision","volume":"93","author":"Hofmann","year":"2023","journal-title":"Prog Retin Eye Res"},{"key":"2026042708285566800_msag096-B26","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.aquatox.2010.02.003","article-title":"Toxicity, uptake kinetics and behavior assessment in zebrafish embryos following exposure to perfluorooctanesulphonicacid (PFOS)","volume":"98","author":"Huang","year":"2010","journal-title":"Aquat Toxicol"},{"key":"2026042708285566800_msag096-B27","doi-asserted-by":"publisher","first-page":"2322","DOI":"10.1073\/pnas.94.6.2322","article-title":"Single amino acid residue as a functional determinant of rod and cone visual pigments","volume":"94","author":"Imai","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026042708285566800_msag096-B28","doi-asserted-by":"publisher","first-page":"7219","DOI":"10.1021\/bi002937i","article-title":"Engineering a functional blue-wavelength-shifted rhodopsin mutant","volume":"40","author":"Janz","year":"2001","journal-title":"Biochemistry"},{"key":"2026042708285566800_msag096-B29","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B30","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac174","article-title":"TimeTree 5: an expanded resource for species divergence times","volume":"39","author":"Kumar","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B31","doi-asserted-by":"publisher","first-page":"15245","DOI":"10.1021\/bi026444k","article-title":"Conserved proline residue at position 189 in cone visual pigments as a determinant of molecular properties different from rhodopsins","volume":"41","author":"Kuwayama","year":"2002","journal-title":"Biochemistry"},{"key":"2026042708285566800_msag096-B32","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaf231","article-title":"Tandem gene clusters as phylogenetic anchors reveal the hidden history of vertebrate visual opsins","volume":"42","author":"Lagman","year":"2025","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B33","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1038\/nrn2283","article-title":"Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup","volume":"8","author":"Lamb","year":"2007","journal-title":"Nat Rev Neurosci"},{"key":"2026042708285566800_msag096-B34","doi-asserted-by":"publisher","first-page":"2064","DOI":"10.1093\/molbev\/msw095","article-title":"Evolution of vertebrate phototransduction: cascade activation","volume":"33","author":"Lamb","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B35","doi-asserted-by":"publisher","first-page":"15568","DOI":"10.1038\/s41598-017-15868-7","article-title":"The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation","volume":"7","author":"Lin","year":"2017","journal-title":"Sci Rep"},{"key":"2026042708285566800_msag096-B36","doi-asserted-by":"publisher","first-page":"24583","DOI":"10.1074\/jbc.273.38.24583","article-title":"Mechanisms of spectral tuning in blue cone visual pigments: visible and Raman spectroscopy of blue-shifted rhodopsin mutants","volume":"273","author":"Lin","year":"1998","journal-title":"J Biol Chem"},{"key":"2026042708285566800_msag096-B37","doi-asserted-by":"publisher","first-page":"12627","DOI":"10.1073\/pnas.1900481116","article-title":"Scotopic rod vision in tetrapods arose from multiple early adaptive shifts in the rate of retinal release","volume":"116","author":"Liu","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026042708285566800_msag096-B38","doi-asserted-by":"publisher","first-page":"4104","DOI":"10.1021\/ct500487h","article-title":"Coarse-graining of TIP4P\/2005, TIP4P-Ew, SPC\/E, and TIP3P to monatomic anisotropic water models using relative entropy minimization","volume":"10","author":"Lu","year":"2014","journal-title":"J Chem Theory Comput"},{"key":"2026042708285566800_msag096-B39","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1111\/jfb.15828","article-title":"Evolution of rhodopsin in flatfishes (Pleuronectiformes) is associated with depth and migratory behavior","volume":"105","author":"Macpherson","year":"2024","journal-title":"J Fish Biol"},{"key":"2026042708285566800_msag096-B40","author":"Maddison"},{"key":"2026042708285566800_msag096-B41","author":"Midford"},{"key":"2026042708285566800_msag096-B42","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1021\/ja510553f","article-title":"Kinetics of thermal activation of an ultraviolet cone pigment","volume":"137","author":"Mooney","year":"2015","journal-title":"J Am Chem Soc"},{"key":"2026042708285566800_msag096-B43","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1016\/j.cub.2014.12.031","article-title":"Single-photon sensitivity of lamprey rods with cone-like outer segments","volume":"25","author":"Morshedian","year":"2015","journal-title":"Curr Biol"},{"key":"2026042708285566800_msag096-B44","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1126\/science.aav4632","article-title":"Vision using multiple distinct rod opsins in deep-sea fishes","volume":"364","author":"Musilova","year":"2019","journal-title":"Science"},{"key":"2026042708285566800_msag096-B45","doi-asserted-by":"publisher","DOI":"10.1016\/j.visres.2023.108204","article-title":"The evolution of the green-light-sensitive visual opsin genes (RH2) in teleost fishes","volume":"206","author":"Musilova","year":"2023","journal-title":"Vision Res"},{"key":"2026042708285566800_msag096-B46","doi-asserted-by":"publisher","first-page":"5932","DOI":"10.1073\/pnas.89.13.5932","article-title":"Primary structures of chicken cone visual pigments: vertebrate rhodopsins have evolved out of cone visual pigments","volume":"89","author":"Okano","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026042708285566800_msag096-B47","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1126\/science.289.5480.739","article-title":"Crystal structure of rhodopsin: a G protein-coupled receptor","volume":"289","author":"Palczewski","year":"2000","journal-title":"Science"},{"key":"2026042708285566800_msag096-B48","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1146\/annurev.biochem.75.103004.142743","article-title":"G protein-coupled receptor rhodopsin","volume":"75","author":"Palczewski","year":"2006","journal-title":"Annu Rev Biochem"},{"key":"2026042708285566800_msag096-B49","doi-asserted-by":"publisher","first-page":"R318","DOI":"10.1016\/j.cub.2006.03.090","article-title":"Molecular evidence for dim-light vision in the last common ancestor of the vertebrates","volume":"16","author":"Pisani","year":"2006","journal-title":"Curr Biol"},{"key":"2026042708285566800_msag096-B50","doi-asserted-by":"publisher","first-page":"4","DOI":"10.3390\/biology13010004","article-title":"Zebrafish optokinetic reflex: minimal reporting guidelines and recommendations","volume":"13","author":"Rodwell","year":"2023","journal-title":"Biology (Basel)"},{"key":"2026042708285566800_msag096-B51","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"Mrbayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst Biol"},{"key":"2026042708285566800_msag096-B52","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1038\/s42003-018-0164-x","article-title":"Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates","volume":"1","author":"Sato","year":"2018","journal-title":"Commun Biol"},{"key":"2026042708285566800_msag096-B53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3003164","article-title":"Cadherin-16 regulates acoustic sensory gating in zebrafish through endocrine signaling","volume":"23","author":"Schloss","year":"2025","journal-title":"PLoS Biol"},{"key":"2026042708285566800_msag096-B54","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.jes.2021.11.008","article-title":"Mepanipyrim induces visual developmental toxicity and vision-guided behavioral alteration in zebrafish larvae","volume":"124","author":"Shen","year":"2023","journal-title":"J Environ Sci (China)"},{"key":"2026042708285566800_msag096-B55","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.aquatox.2019.02.024","article-title":"Optical toxicity of triphenyl phosphate in zebrafish larvae","volume":"210","author":"Shi","year":"2019","journal-title":"Aquat Toxicol"},{"key":"2026042708285566800_msag096-B56","doi-asserted-by":"publisher","first-page":"1970","DOI":"10.1080\/15548627.2019.1596487","article-title":"Autophagy in Xenopus laevis rod photoreceptors is independently regulated by phototransduction and misfolded RHOP23H","volume":"15","author":"Wen","year":"2019","journal-title":"Autophagy"},{"key":"2026042708285566800_msag096-B57","doi-asserted-by":"publisher","first-page":"5726","DOI":"10.1093\/molbev\/msab262","article-title":"Convergent phenotypic evolution of rhodopsin for dim-light sensing across deep-diving vertebrates","volume":"38","author":"Xia","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B58","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1016\/j.cell.2025.01.002","article-title":"Evolution and genetic adaptation of fishes to the deep sea","volume":"188","author":"Xu","year":"2025","journal-title":"Cell"},{"key":"2026042708285566800_msag096-B59","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1111\/jeb.13730","article-title":"Visual and nonvisual opsin genes of sharks and other nonosteichthyan vertebrates: genomic exploration of underwater photoreception","volume":"34","author":"Yamaguchi","year":"2021","journal-title":"J Evol Biol"},{"key":"2026042708285566800_msag096-B60","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2220728120","article-title":"Whale shark rhodopsin adapted to deep-sea lifestyle by a substitution associated with human disease","volume":"120","author":"Yamaguchi","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026042708285566800_msag096-B61","doi-asserted-by":"publisher","first-page":"11081","DOI":"10.1038\/srep11081","article-title":"Origin of the low thermal isomerization rate of rhodopsin chromophore","volume":"5","author":"Yanagawa","year":"2015","journal-title":"Sci Rep"},{"key":"2026042708285566800_msag096-B62","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1093\/oxfordjournals.molbev.a025957","article-title":"Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution","volume":"15","author":"Yang","year":"1998","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B63","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B64","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae257","article-title":"Circadian rhythm mechanisms underlying convergent adaptation of unihemispheric slow-wave sleep in marine mammals","volume":"41","author":"Yin","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026042708285566800_msag096-B65","doi-asserted-by":"publisher","DOI":"10.1093\/sleep\/zsae018","article-title":"Adaptive changes in BMAL2 with increased locomotion associated with the evolution of unihemispheric slow-wave sleep in mammals","volume":"47","author":"Yin","year":"2024","journal-title":"Sleep"},{"key":"2026042708285566800_msag096-B66","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1002\/2211-5463.12843","article-title":"Origin and adaptation of green-sensitive (RH2) pigments in vertebrates","volume":"10","author":"Yokoyama","year":"2020","journal-title":"FEBS Open Bio"},{"key":"2026042708285566800_msag096-B67","doi-asserted-by":"publisher","first-page":"13480","DOI":"10.1073\/pnas.0802426105","article-title":"Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates","volume":"105","author":"Yokoyama","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026042708285566800_msag096-B68","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/S1350-9462(00)00002-1","article-title":"Molecular evolution of vertebrate visual pigments","volume":"19","author":"Yokoyama","year":"2000","journal-title":"Prog Retin Eye Res"},{"key":"2026042708285566800_msag096-B69","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1146\/annurev.genom.9.081307.164228","article-title":"Evolution of dim-light and color vision pigments","volume":"9","author":"Yokoyama","year":"2008","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"2026042708285566800_msag096-B70","doi-asserted-by":"publisher","first-page":"1495","DOI":"10.1093\/molbev\/mst075","article-title":"Synthetic biology of phenotypic adaptation in vertebrates: the next frontier","volume":"30","author":"Yokoyama","year":"2013","journal-title":"Mol Biol Evol"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msag096\/68021446\/msag096.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/4\/msag096\/68021446\/msag096.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/4\/msag096\/68021446\/msag096.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T12:29:06Z","timestamp":1777292946000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msag096\/8650812"}},"subtitle":[],"editor":[{"given":"Keith","family":"Crandall","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,1]]},"references-count":70,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msag096","relation":{},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,4]]},"published":{"date-parts":[[2026,4,1]]},"article-number":"msag096"}}