Cichlid visual systems can evolve rapidly during adaptive radiations. The Bermin crater lake species flock in Cameroon, comprising 13 (nine valid and four undescribed) Coptodon species, offers an ideal model to investigate visual adaptation to the deep-water light environments. Here, we examine visual opsin genes sequences and expression using 109 retina transcriptomes, focusing on interspecific variation with habitat depth, as well as on seasonal changes in the migratory species between depths. All species possess a multichromatic system with at least five cone opsins. While opsin coding sequences show limited divergence-consistent with the flock's recent origin-opsin expression profiles vary substantially. Deep-water species showed reduced sws1 and sws2b expression, in line with lower UV and violet light availability in deeper waters. Unexpectedly, proportional expression of the red-sensitive lws opsin gene increases with depth, contrasting with patterns in other lacustrine cichlids. In the seasonally migrating species Coptodon imbrifernus, opsin expression is plastic, with decreased sws2b levels in deeper-dwelling dry-season individuals. To contextualize our findings, we compared Bermin cichlids to the older Barombi Mbo crater lake radiation. While single cone adaptations to the depth were convergent (loss of UV/violet sensitivity, enhanced blue sensitivity), double cone response diverged: lws expression was lost in Barombi Mbo while increased in Bermin deep-water species. Our findings suggest that plasticity in opsin expression plays a crucial role at the onset of sensory evolution, potentially paving the way for future genetic change. This study underscores the power of young systems like Bermin for uncovering the mechanisms driving early visual system diversification.

Department of Aquatic Ecosystems Management Institute of Fisheries and Aquatic Sciences University of Douala Douala Cameroon

Department of Biological Sciences University of Ngaoundéré Ngaoundéré Cameroon

Department of Zoology Faculty of Science Charles University Prague Czech Republic

Military Health Institute Military Medical Agency Prague Czech Republic

Zoological Institute University of Basel Basel 4051 Switzerland

Zobrazit více v PubMed

Alonso  F  et al.  Fibrillin-1 regulates endothelial sprouting during angiogenesis. Proc Natl Acad Sci U S A. 2023:120:e2221742120. 10.1073/pnas.2221742120. PubMed DOI PMC

Andrews  S. 2010. FastQC: a quality control tool for high throughput sequence data. [accessed 2022 Jul]. http://www.bioinformatics.babraham.ac.uk/projects/fastqc

Asenjo  AB, Rim  J, Oprian  DD. Molecular determinants of human red/green color discrimination. Neuron. 1994:12:1131–1138. 10.1016/0896-6273(94)90320-4. PubMed DOI

Astudillo-Clavijo  V  et al.  Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol. 2023:72:134–149. 10.1093/sysbio/syac051. PubMed DOI PMC

Baden  T  et al.  The functional diversity of retinal ganglion cells in the mouse. Nature. 2016:529:345–350. 10.1038/nature16468. PubMed DOI PMC

Baden  T. Ancestral photoreceptor diversity as the basis of visual behaviour. Nat Ecol Evol. 2024:8:374–386. 10.1038/s41559-023-02291-7. PubMed DOI

Baden  T  et al.  A standardized nomenclature for the rods and cones of the vertebrate retina. PLoS Biol. 2025:23:e3003157. 10.1371/journal.pbio.3003157. PubMed DOI PMC

Bandelt  HJ, Forster  P, Röhl  A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999:16:37–48. 10.1093/oxfordjournals.molbev.a026036. PubMed DOI

Barlow  G. The cichlid fishes: nature's Grand experiment in evolution. Basic Books; 2008.

Barlow  HB, Hill  RM. Selective sensitivity to direction of movement in ganglion cells of the rabbit retina. Science. 1963:139:412–414. 10.1126/science.139.3553.412. PubMed DOI

Bertinetti  C, Torres-Dowdall  J. Phenotypic plasticity in visual opsin gene expression: a meta-analysis in teleost fish. J Exp Biol. 2025:228:jeb250332. 10.1242/jeb.250332. PubMed DOI PMC

Bezault  E  et al.  Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa. BMC Genet. 2011:12:102. 10.1186/1471-2156-12-102. PubMed DOI PMC

Bolton  CM, Bekaert  M, Eilertsen  M, Helvik  JV, Migaud  H. Rhythmic clock gene expression in Atlantic salmon parr brain. Front Physiol. 2021:12:761109. 10.3389/fphys.2021.761109. PubMed DOI PMC

Bowmaker  JK. Evolution of vertebrate visual pigments. Vision Res.  2008:48:2022–2041. 10.1016/j.visres.2008.03.025. PubMed DOI

Bowmaker  JK, Hunt  DM. Molecular biology of photoreceptor spectral sensitivity. In: Archer  SN, Djamgoz  MBA, Loew  ER, Partridge  JC, Vallerga  S, editors. Adaptive mechanisms in the ecology of vision. Springer; 1999. p. 439–462.

Bringmann  A  et al.  Müller cells in the healthy and diseased retina. Prog Retin Eye Res. 2006:25:397–424. 10.1016/j.preteyeres.2006.05.003. PubMed DOI

Bringmann  A  et al.  Role of retinal glial cells in neurotransmitter uptake and metabolism. Neurochem Int. 2009:54:143–160. 10.1016/j.neuint.2008.10.014. PubMed DOI

Burress  ED, Tan  M. Ecological opportunity alters the timing and shape of adaptive radiation. Evolution. 2017:71:2650–2660. 10.1111/evo.13362. PubMed DOI

Bushnell  B. BBMap: a fast, accurate, splice-aware aligner. Lawrence Berkeley National Laboratory; 2014. https://sourceforge.net/projects/bbmap/, last accessed July 27, 2025.

Carleton  KL  et al.  Visual sensitivities tuned by heterochronic shifts in opsin gene expression. BMC Biol. 2008:6:22. 10.1186/1741-7007-6-22. PubMed DOI PMC

Carleton  KL. Cichlid fish visual systems: mechanisms of spectral tuning. Integr Zool. 2009:4:75–86. 10.1111/j.1749-4877.2008.00137.x. PubMed DOI

Carleton  KL  et al.  Genetic basis of differential opsin gene expression in cichlid fishes. J Evol Biol. 2010:23:840–853. 10.1111/j.1420-9101.2010.01954.x. PubMed DOI PMC

Carleton  KL, Dalton  BE, Escobar-Camacho  D, Nandamuri  SP. Proximate and ultimate causes of variable visual sensitivities: insights from cichlid fish radiations. Genesis. 2016:54:299–325. 10.1002/dvg.22940. PubMed DOI PMC

Carleton  KL, Kocher  TD. Cone opsin genes of African cichlid fishes: tuning spectral sensitivity by differential gene expression. Mol Biol Evol. 2001:18:1540–1550. 10.1093/oxfordjournals.molbev.a003940. PubMed DOI

Carleton  KL, Parry  JW, Bowmaker  JK, Hunt  DM, Seehausen  O. Colour vision and speciation in lake Victoria cichlids of the genus PubMed DOI

Carleton  KL, Yourick  MR. Axes of visual adaptation in the ecologically diverse family Cichlidae. Semin Cell Dev Biol. 2020:106:43–52. 10.1016/j.semcdb.2020.04.015. PubMed DOI PMC

Carruthers  M  et al.  Rapid divergence of visual systems and signaling traits to contrasting light regimes during early speciation of African crater lake cichlid fish. Mol Biol Evol. 2025:42:msaf204. 10.1093/molbev/msaf204. PubMed DOI PMC

Chang  BS, Crandall  KA, Carulli  JP, Hartl  DL. Opsin phylogeny and evolution: a model for blue shifts in wavelength regulation. Mol Phylogenet Evol. 1995:4:31–43. 10.1006/mpev.1995.1004. PubMed DOI

Constance  CM, Fan  JY, Preuss  F, Green  CB, Price  JL. The circadian clock-containing photoreceptor cells in PubMed DOI

Corbo  JC. Vitamin A1/A2 chromophore exchange: its role in spectral tuning and visual plasticity. Dev Biol. 2021:475:145–155. 10.1016/j.ydbio.2021.03.002. PubMed DOI PMC

Cortesi  F  et al.  Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes. Proc Natl Acad Sci U S A. 2015:112:1493–1498. 10.1073/pnas.1417803112. PubMed DOI PMC

Cortesi  F, Camacho  DE, Luehrmann  M, Sommer  GM, Musilova  Z. 2021 May 9. Multiple ancestral duplications of the red-sensitive opsin gene (LWS) in teleost fishes and convergent spectral shifts to green vision in gobies [preprint]. bioRxiv 443214. 10.1101/2021.05.08.443214 DOI

Cribari-Neto  F, Zeileis  A. Beta regression in R. J Stat Softw. 2010:34:1–24. 10.18637/jss.v034.i02. DOI

Dalton  BE, Loew  ER, Cronin  TW, Carleton  KL. Spectral tuning by opsin coexpression in retinal regions that view different parts of the visual field. Proc Biol Sci. 2014:281:20141980. 10.1098/rspb.2014.1980. PubMed DOI PMC

Dalton  BE, Lu  J, Leips  J, Cronin  TW, Carleton  KL. Variable light environments induce plastic spectral tuning by regional opsin coexpression in the African cichlid fish, PubMed DOI PMC

De Lange  H. The attenuation of ultraviolet and visible radiation in Dutch inland waters. Aquat Ecol. 2000:34:215–226. 10.1023/A:1009943211779. DOI

Douglas  RH, Mullineaux  CW, Partridge  JC. Long-wave sensitivity in deep-sea stomiid dragonfish with far-red bioluminescence: evidence for a dietary origin of the chlorophyll-derived retinal photosensitizer of PubMed DOI PMC

Dunz  AR, Schliewen  UK. Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”. Mol Phylogenet Evol. 2013:68:64–80. 10.1016/j.ympev.2013.03.015. PubMed DOI

Enright  JM  et al.  Cyp27c1 red-shifts the spectral sensitivity of photoreceptors by converting vitamin A1 into A2. Curr Biol. 2015:25:3048–3057. 10.1016/j.cub.2015.10.018. PubMed DOI PMC

Escobar-Camacho  D, Ramos  E, Martins  C, Carleton  KL. The opsin genes of Amazonian cichlids. Mol Ecol. 2017:26:1343–1356. 10.1111/mec.13957. PubMed DOI PMC

Fernald  RD, Liebman  PA. Visual receptor pigments in the African cichlid fish, PubMed DOI

Fogg  LG  et al.  Development of dim-light vision in the nocturnal reef fish family Holocentridae. I: retinal gene expression. J Exp Biol. 2022:225:jeb244513. 10.1242/jeb.244513. PubMed DOI PMC

Fogg  LG  et al.  Developing and adult reef fish show rapid light-induced plasticity in their visual system. Mol Ecol. 2023:32:167–181. 10.1111/mec.16744. PubMed DOI PMC

Foster  TN, Williamson  AG, Foster  BR, Toomey  MB. Light environment and seasonal variation in the visual system of the red shiner (Cyprinella lutrensis). J Exp Biol. 2025:228:jeb249878. 10.1242/jeb.249878. PubMed DOI

Freeman  BD, Machado  FS, Tanowitz  HB, Desruisseaux  MS. Endothelin-1 and its role in the pathogenesis of infectious diseases. Life Sci. 2014:118:110–119. 10.1016/j.lfs.2014.04.021. PubMed DOI PMC

Genner  MJ, Turner  GF. The mbuna cichlids of Lake Malawi: a model for rapid speciation and adaptive radiation. Fish Fish. 2005:6:1–34. 10.1111/j.1467-2679.2005.00173.x. DOI

Halstenberg  S  et al.  Diurnal rhythm of cone opsin expression in the teleost fish PubMed DOI

Härer  A, Karagic  N, Meyer  A, Torres-Dowdall  J. Reverting ontogeny: rapid phenotypic plasticity of colour vision in cichlid fish. R Soc Open Sci.  2019:6:190841. 10.1098/rsos.190841. PubMed DOI PMC

Hauser  FE  et al.  Evolution, inactivation and loss of short wavelength-sensitive opsin genes during the diversification of Neotropical cichlids. Mol Ecol.  2021:30:1688–1703. 10.1111/mec.15838. PubMed DOI

Hofmann  CM  et al.  The eyes have it: regulatory and structural changes both underlie cichlid visual pigment diversity. PLoS Biol.  2009:7:e1000266. 10.1371/journal.pbio.1000266. PubMed DOI PMC

Hofmann  CM, Carleton  KL. Gene duplication and differential gene expression play an important role in the diversification of visual pigments in fish. Integr Comp Biol.  2009:49:630–643. 10.1093/icb/icp079. PubMed DOI

Hubmacher  D, Reinhardt  DP, Plesec  T, Schenke-Layland  K, Apte  SS. Human eye development is characterized by coordinated expression of fibrillin isoforms. Invest Ophthalmol Vis Sci. 2014:55:7934–7944. 10.1167/iovs.14-15453. PubMed DOI PMC

Hunt  DM, Fitzgibbon  J, Slobodyanyuk  SJ, Bowmaker  JK. Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal. Vision Res.  1996:36:1217–1224. 10.1016/0042-6989(95)00228-6. PubMed DOI

Jiang  Q  et al.  Functional convergence of on-off direction-selective ganglion cells in the visual thalamus. Curr Biol. 2022:32:3110–3120.e6. 10.1016/j.cub.2022.06.023. PubMed DOI PMC

Jordan  R  et al.  Photopigment spectral absorbance of Lake Malawi cichlids. J Fish Biol. 2006:68:1291–1299. 10.1111/j.0022-1112.2006.00992.x. DOI

Kearse  M  et al.  Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012:28:1647–1649. 10.1093/bioinformatics/bts199. PubMed DOI PMC

Kling  GW. Comparative transparency, depth of mixing, and stability of stratification in lakes of Cameroon, West Africa. Limnol Oceanogr. 1988:33:27–40. 10.4319/lo.1988.33.1.0027. DOI

Kochendoerfer  GG, Lin  SW, Sakmar  TP, Mathies  RA. How color visual pigments are tuned. Trends Biochem Sci. 1999:24:300–305. 10.1016/S0968-0004(99)01432-2. PubMed DOI

Leigh  JW, Bryant  D. PopART: full-feature software for haplotype network construction. Methods Ecol Evol. 2015:6:1110–1116. 10.1111/2041-210X.12410. DOI

Levine  JS, MacNichol  EF  Jr, Kraft  T, Collins  BA. Intraretinal distribution of cone pigments in certain teleost fishes. Science. 1979:204:523–526. 10.1126/science.432658. PubMed DOI

Li  H, Durbin  R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009:25:1754–1760. 10.1093/bioinformatics/btp324. PubMed DOI PMC

Lin  JJ, Wang  FY, Li  WH, Wang  TY. The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation. Sci Rep. 2017:7:15568. 10.1038/s41598-017-15868-7. PubMed DOI PMC

Love  MI, Huber  W, Anders  S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014:15:550. 10.1186/s13059-014-0550-8. PubMed DOI PMC

Luehrmann  M  et al.  Short-term colour vision plasticity on the reef: changes in opsin expression under varying light conditions differ between ecologically distinct fish species. J Exp Biol. 2018:221:jeb175281. 10.1242/jeb.175281. PubMed DOI

Lupše  N  et al.  Visual gene expression reveals a cone-to-rod developmental progression in deep-sea fishes. Mol Biol Evol. 2021:38:5664–5677. 10.1093/molbev/msab281. PubMed DOI PMC

Lupše  N  et al.  Developmental changes of opsin gene expression in ray-finned fishes (Actinopterygii). Proc Biol Sci.  2022:289:1986. 10.1098/rspb.2022.1855. PubMed DOI PMC

Maier  MM, Gessler  M. Comparative analysis of the human and mouse Hey1 promoter: hey genes are new Notch target genes. Biochem Biophys Res Commun. 2000:275:652–660. 10.1006/bbrc.2000.3354. PubMed DOI

Martin  CH  et al.  Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation. Evolution. 2015:69:1406–1422. 10.1111/evo.12674. PubMed DOI

Michiels  NK  et al.  Red fluorescence in reef fish: a novel signalling mechanism?  BMC Ecol. 2008:8:16. 10.1186/1472-6785-8-16. PubMed DOI PMC

Musilová  Z  et al.  Vision using multiple distinct rod opsins in deep-sea fishes. Science. 2019a:364:588–592. 10.1126/science.aav4632. PubMed DOI PMC

Musilová  Z  et al.  Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon. Mol Ecol. 2019b:28:5010–5031. 10.1111/mec.15217. PubMed DOI

Musilová  Z, Cortesi  F. The evolution of the green-light-sensitive visual opsin genes (RH2) in teleost fishes. Vision Res.  2023:206:108204. 10.1016/j.visres.2023.108204. PubMed DOI

Musilova  Z, Cortesi  F. An (omics) perspective on the evolution of vision in deep-sea fishes reveals exceptional adaptations to life in the extreme. Funct Ecol. 2025:39: 2601–2610. 10.1111/1365-2435.70074. DOI

Musilová  Z, Salzburger  W, Cortesi  F. The visual opsin gene repertoires of teleost fishes: evolution, ecology, and function. Annu Rev Cell Dev Biol. 2021:37:441–468. 10.1146/annurev-cellbio-120219-024915. PubMed DOI

Nandamuri  SP, Yourick  MR, Carleton  KL. Adult plasticity in African cichlids: rapid changes in opsin expression in response to environmental light differences. Mol Ecol. 2017:26:6036–6052. 10.1111/mec.14357. PubMed DOI PMC

Naylor  A, Hopkins  A, Hudson  N, Campbell  M. Tight junctions of the outer blood retina barrier. Int J Mol Sci. 2019:21:211. 10.3390/ijms21010211. PubMed DOI PMC

O’Quin  KE, Hofmann  CM, Hofmann  HA, Carleton  KL. Parallel evolution of opsin gene expression in African cichlid fishes. Mol Biol Evol. 2010:27:2839–2854. 10.1093/molbev/msq171. PubMed DOI

Parry  JW  et al.  Mix and match color vision: tuning spectral sensitivity by differential opsin gene expression in Lake Malawi cichlids. Curr Biol. 2005:15:1734–1739. 10.1016/j.cub.2005.08.010. PubMed DOI

Quinlan  AR, Hall  IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010:26:841–842. 10.1093/bioinformatics/btq033. PubMed DOI PMC

Rheaume  BA  et al.  Single-cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes. Nat Commun. 2018:9:2759. 10.1038/s41467-018-05134-3. PubMed DOI PMC

Ricci  V, Ronco  F, Boileau  N, Salzburger  W. Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika. Sci Adv. 2023:9:eadag6568. 10.1126/sciadv.adg6568. PubMed DOI PMC

Ricci  V, Ronco  F, Musilova  Z, Salzburger  W. Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika. Mol Ecol. 2022:31:2882–2897. 10.1111/mec.16429. PubMed DOI PMC

Roesti  M, Salzburger  W, Berner  D. Uninformative polymorphisms bias genome scans for signatures of selection. BMC Evol Biol. 2012:12:94. 10.1186/1471-2148-12-94. PubMed DOI PMC

Ronco  F  et al.  Drivers and dynamics of a massive adaptive radiation in cichlid fishes. Nature. 2021:589:76–81. 10.1038/s41586-020-2930-4. PubMed DOI

Ronquist  F  et al.  Mrbayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012:61:539–542. 10.1093/sysbio/sys029. PubMed DOI PMC

Rozas  J  et al.  DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol Evol. 2017:34:3299–3302. 10.1093/molbev/msx248. PubMed DOI

Sahu  A, Devi  S, Jui  J, Goldman  D. Notch signaling via Hey1 and Id2b regulates Müller glia's regenerative response to retinal injury. Glia. 2021:69:2882–2898. 10.1002/glia.24075. PubMed DOI PMC

Salvatore  S, Vingolo  EM. Endothelin-1 role in human eye: a review. J Ophthalmol. 2010:2010:354645. 10.1155/2010/354645. PubMed DOI PMC

Salzburger  W. Understanding explosive diversification through cichlid fish genomics. Nat Rev Genet. 2018:19:705–717. 10.1038/s41576-018-0043-9. PubMed DOI

Schedel  FDB, Musilová  Z, Schliewen  UK. East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation. BMC Evol Biol. 2019:19:1–25. 10.1186/s12862-019-1417-0. PubMed DOI PMC

Schliewen  U  et al.  Genetic and ecological divergence of a monophyletic cichlid species pair under fully sympatric conditions in Lake Ejagham, Cameroon. Mol Ecol. 2001:10:1471–1488. 10.1046/j.1365-294X.2001.01276.x. PubMed DOI

Schliewen  UK, Tautz  D, Paabo  S. Sympatric speciation suggested by monophyly of crater lake cichlids. Nature. 1994:368:629–632. 10.1038/368629a0. PubMed DOI

Seehausen  O  et al.  Speciation through sensory drive in cichlid fish. Nature. 2008:455:620–626. 10.1038/nature07285. PubMed DOI

Seehausen  O, van Alphen  JJ, Witte  F. Cichlid fish diversity threatened by eutrophication that curbs sexual selection. Science. 1997:277:1808–1811. 10.1126/science.277.5333.1808. DOI

Shao  YT  et al.  Androgens increase lws opsin expression and red sensitivity in male three-spined sticklebacks. PLoS One. 2014:9:e100330. 10.1371/journal.pone.0100330. PubMed DOI PMC

Shaughnessy  A, Cortesi  F. Coral reef fish visual adaptations to a changing world. Funct Ecol. 2024:39:2561–2572. 10.1111/1365-2435.14668. DOI

Spady  TC  et al.  Evolution of the cichlid visual palette through ontogenetic subfunctionalization of the opsin gene arrays. Mol Biol Evol. 2006:23:1538–1547. 10.1093/molbev/msl014. PubMed DOI

Stager  JC  et al.  On the age and origin of Lake Ejagham, Cameroon, and its endemic fishes. Quat Res. 2018:89:21–32. 10.1017/qua.2017.37. DOI

Stiassny  MLJ, Schliewen  UK, Dominey  WJ. A new species flock of cichlid fishes from Lake Bermin, Cameroon with a description of eight new species of Tilapia (Labroidei: Cichlidae). Ichthyol Explor Freshwat. 1992:3:311–346.

Stieb  SM  et al.  Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes. Mol Ecol. 2023:32:1656–1672. 10.1111/mec.16831. PubMed DOI PMC

Stieb  SM, Carleton  KL, Cortesi  F, Marshall  NJ, Salzburger  W. Depth-dependent plasticity in opsin gene expression varies between damselfish (Pomacentridae) species. Mol Ecol.  2016:25:3645–3661. 10.1111/mec.13712. PubMed DOI

Talbi  M, Turner  GF, Malinsky  M. Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko. Evolution. 2025:79:364–379. 10.1093/evolut/qpae169. PubMed DOI

Temple  SE  et al.  Seasonal cycle in vitamin A1/A2-based visual pigment composition during the life history of coho salmon (Oncorhynchus kisutch). J Comp Physiol A. 2006:192:301–313. 10.1007/s00359-005-0068-3. PubMed DOI

Terai  Y  et al.  Visual adaptation in Lake Victoria cichlid fishes: depth-related variation of color and scotopic opsins in species from sand/mud bottoms. BMC Evol Biol. 2017:17:200. 10.1186/s12862-017-1040-x. PubMed DOI PMC

Tettamanti  V, de Busserolles  F, Lecchini  D, Marshall  NJ, Cortesi  F. Visual system development of the spotted unicornfish, Naso brevirostris (Acanthuridae). J Exp Biol. 2019:222:jeb209916. 10.1242/jeb.209916. PubMed DOI

Thieme  ML  et al.  Freshwater ecoregions of Africa and Madagascar: a conservation assessment. Island Press; 2005. p. 58–60.

Torres-Dowdall  J  et al.  Rapid and parallel adaptive evolution of the visual system of Neotropical Midas cichlid fishes. Mol Biol Evol. 2017:34:2469–2485. 10.1093/molbev/msx143. PubMed DOI

Torres-Dowdall  J, Karagic  N, Härer  A, Meyer  A. Diversity in visual sensitivity across Neotropical cichlid fishes via differential expression and intraretinal variation of opsin genes. Mol Ecol. 2021:30:1880–1891. 10.1111/mec.15855. PubMed DOI

Trewavas  E, Green  J, Corbet  SA. Ecological studies on crater lakes in West Cameroon: fishes of Barombi Mbo. J Fish Zool. 1972:167:41–95. 10.1111/j.1469-7998.1972.tb01722.x. DOI

Tseng  WH  et al.  Opsin gene expression regulated by testosterone level in a sexually dimorphic lizard. Sci Rep. 2018:8:16055. 10.1038/s41598-018-34284-z. PubMed DOI PMC

Turner  GF. Adaptive radiation of cichlid fish. Curr Biol. 2007:17:R827–R831. 10.1016/j.cub.2007.07.026. PubMed DOI

van der Meer  HJ, Bowmaker  JK. Interspecific variation of photoreceptors in four co-existing haplochromine cichlid fishes. Brain Behav Evol. 1995:45:232–240. 10.1159/000113552. PubMed DOI

Vaney  DI, Sivyer  B, Taylor  WR. Direction selectivity in the retina: symmetry and asymmetry in structure and function. Nat Rev Neurosci. 2012:13:194–208. 10.1038/nrn3165. PubMed DOI

Wagner  CE  et al.  Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol Ecol. 2013:22:787–798. 10.1111/mec.12023. PubMed DOI

Wu  RX  et al.  Transcriptomic analysis reveals circadian rhythm homeostasis in pearl gentian grouper under acute hypoxia. Fishes. 2023:8:358. 10.3390/fishes8070358. DOI

Yan  Y. 2021. ggvenn: draw Venn diagram by ggplot2. R package version 0.1.9. [accessed 2023 Jan]. https://CRAN.R-project.org/package=ggvenn

Yokoyama  R, Yokoyama  S. Convergent evolution of the red- and green-like visual pigment genes in fish, Astyanax fasciatus, and human. Proc Natl Acad Sci U S A.  1990:87:9315–9318. 10.1073/pnas.87.23.9315. PubMed DOI PMC

Yokoyama  S. Molecular evolution of vertebrate visual pigments. Prog Retin Eye Res. 2000:19:385–419. 10.1016/S1350-9462(00)00002-1. PubMed DOI

Yokoyama  S. Evolution of dim-light and color vision pigments. Annu Rev Genomics Hum Genet. 2008:9:259–282. 10.1146/annurev.genom.9.081307.164228. PubMed DOI

Yokoyama  S, Radlwimmer  B. The “five-sites” rule and the evolution of red and green color vision in mammals. Mol Biol Evol. 1998:15:560–567. 10.1093/oxfordjournals.molbev.a025956. PubMed DOI

Yourick  MR  et al.  Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Mol Ecol Resour. 2019:19:1447–1460. 10.1111/1755-0998.13062. PubMed DOI PMC