Zebrafish relatives as models for functional comparative genetics and genomics

Irion, U. & Nusslein-Volhard, C. Developmental genetics with model organisms. Proc. Natl Acad. Sci. USA 119, e2122148119 (2022).

Liberali, P. & Schier, A. F. The evolution of developmental biology through conceptual and technological revolutions. Cell 187, 3461–3495 (2024).

Hilgers, L. & Schwarzer, J. The untapped potential of medaka and its wild relatives. eLife 8, e46994 (2019).

Boos, F., Chen, J. & Brunet, A. The African turquoise killifish: a scalable vertebrate model for aging and other complex phenotypes. Cold Spring Harb. Protoc. 2024, 107737 (2024).

Nagy, B. & Watters, B. R. A review of the conservation status of seasonal Nothobranchius fishes (Teleostei: Cyprinodontiformes), a genus with a high level of threat, inhabiting ephemeral wetland habitats in Africa. Aquat. Conserv.: Mar. Freshw. Ecosyst. 32, 199–216 (2022).

Salzburger, W. Understanding explosive diversification through cichlid fish genomics. Nat. Rev. Genet. 19, 705–717 (2018).

Quah, F. X. et al. Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements. Genome Res. 35, 1094–1107 (2025).

Du, K. et al. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat. Commun. 15, 6609 (2024).

Parichy, D. M. & Johnson, S. L. Zebrafish hybrids suggest genetic mechanisms for pigment pattern diversification in Danio. Dev. Genes Evol. 211, 319–328 (2001).

Parichy, D. M. Advancing biology through a deeper understanding of zebrafish ecology and evolution. eLife 4, e05635 (2015).

Bass, A. H. & Perelmuter, J. T. Danionella fishes. Nat. Methods 21, 1767–1769 (2024).

Tang, K. L. et al. Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol. Phylogenetics Evol. 57, 189–214 (2010).

McCluskey, B. M. & Postlethwait, J. H. Phylogeny of zebrafish, a “model species,” within Danio, a “model genus”. Mol. Biol. Evol. 32, 635–652 (2015).

McCluskey, B. M., Batzel, P. & Postlethwait, J. H. The hybrid history of zebrafish. G3 15, jkae299 (2025). Phylogenomic analyses reveal that zebrafish have a hybrid evolutionary origin involving ancient gene flow between distinct Danio lineages.

Lu, J. et al. Genomic and genetic insights into speciation and pigment pattern diversification in Danio fishes. Preprint at bioRxiv https://doi.org/10.1101/2025.10.17.682988 (2025).

Sudasinghe, H. et al. Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations. Preprint at bioRxiv 10.64898/2026.01.14.699467 (2026). This preprint provides a phylogenomic framework for understanding the evolutionary history of Cypriniformes.

Sudasinghe, H. et al. Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes. Preprint at bioRxiv https://doi.org/10.64898/2026.04.20.719654 (2026).

Howe, K. et al. The genome sequence of the zebra danio, Danio rerio (Hamilton, 1822) (Cypriniformes: Danionidae). Wellcome Open Res. 10, 330 (2025).

Ruber, L. et al. The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009). Wellcome Open Res. 9, 194 (2024).

Howe, K. et al. The chromosome-level genome sequences of Danio rerio strains AB, Nadia and Cooch Behar. Wellcome Open Res. 10, 559 (2025).

Howe, K. et al. The genome sequence of the Panther Danio, Danio aesculapii Kullander & Fang, 2009. Wellcome Open Res. 10, 560 (2025).

Howe, K. et al. The genome sequence of the orange-finned danio, Danio kyathit Fang, 1998. Wellcome Open Res. 10, 584 (2025).

Okendo, J. et al. Complete de novo assembly and re-annotation of the zebrafish genome. Preprint at bioRxiv https://doi.org/10.1101/2025.11.17.688901 (2025).

Howe, K. et al. The genome sequences of Danio albolineatus (Blyth, 1860), Danio choprai Hora, 1928, Danio jaintianensis (Sen, 2007) and Danio tinwini [Kullander & Fang], 2009. Wellcome Open Res. 10, 642 (2025).

Howe, K. et al. A trio-binned, haplotype-resolved genome sequence of the zebrafish, Danio rerio Hamilton 1822, SAT strain. Wellcome Open Res. 10, 682 (2025).

Huang, D. et al. Graded BMP signals modulate yellow and red color in fishes, impacting adult pigment patterns and conspecific shoaling behavior. Curr. Biol. 36, 2127–2136 (2026).

Dewar, A. E., Belcher, L. J. & West, S. A. A phylogenetic approach to comparative genomics. Nat. Rev. Genet. 26, 395–405 (2025).

Tatarsky, R. L. et al. Acoustic and postural displays in a miniature and transparent teleost fish, Danionella dracula. J. Exp. Biol. 225, jeb244585 (2022).

Cook, V. et al. Ultrafast sound production mechanism in one of the smallest vertebrates. Proc. Natl Acad. Sci. USA 121, e2314017121 (2024). The authors uncover an ultrafast biomechanical mechanism enabling sound production in Danionella cerebrum.

Groneberg, A. H., Dressler, L. E., Kadobianskyi, M., Muller, J. & Judkewitz, B. Development of sound production in Danionella cerebrum. J. Exp. Biol. 227, jeb247782 (2024).

Veith, J. et al. The mechanism for directional hearing in fish. Nature 631, 118–124 (2024). This study identifies the mechanistic basis of directional hearing in Danionella cerebrum.

Patterson, L. B. & Parichy, D. M. Zebrafish pigment pattern formation: insights into the development and evolution of adult form. Annu. Rev. Genet. 53, 505–530 (2019).

Irion, U. & Nusslein-Volhard, C. The identification of genes involved in the evolution of color patterns in fish. Curr. Opin. Genet. Dev. 57, 31–38 (2019).

Parichy, D. M. Evolution of pigment cells and patterns: recent insights from teleost fishes. Curr. Opin. Genet. Dev. 69, 88–96 (2021).

Meyer, A., Biermann, C. H. & Orti, G. The phylogenetic position of the zebrafish (Danio rerio), a model system in developmental biology: an invitation to the comparative method. Proc. Biol. Sci. 252, 231–236 (1993).

Dehal, P. & Boore, J. L. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3, e314 (2005).

Amores, A. et al. Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711–1714 (1998).

Jaillon, O. et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946–957 (2004).

Pasquier, J. et al. Evolution of gene expression after whole-genome duplication: new insights from the spotted gar genome. J. Exp. Zool. B 328, 709–721 (2017).

Braasch, I. et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat. Genet. 48, 427–437 (2016).

Thompson, A. W. et al. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat. Genet. 53, 1373–1384 (2021).

Ravi, V. & Venkatesh, B. The divergent genomes of teleosts. Annu. Rev. Anim. Biosci. 6, 47–68 (2018).

Nelson, J. S. Fishes of the World 4th edn (Wiley, 2006).

Parey, E. et al. Genome structures resolve the early diversification of teleost fishes. Science 379, 572–575 (2023).

Ruber, L., Kottelat, M., Tan, H. H., Ng, P. K. & Britz, R. Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world’s smallest vertebrate. BMC Evol. Biol. 7, 38 (2007).

Schumer, M., Rosenthal, G. G. & Andolfatto, P. How common is homoploid hybrid speciation? Evolution 68, 1553–1560 (2014).

Bolnick, D. I. et al. Evolutionary Immunology. Annu. Rev. Ecol. Evol. Syst. 56, 27–51 (2025).

Boehm, T. Understanding vertebrate immunity through comparative immunology. Nat. Rev. Immunol. 25, 141–152 (2025).

Teasdale, L. C. et al. Pangenomic context reveals the extent of intraspecific plant NLR evolution. Cell Host Microbe 33, 1291–1305 (2025).

Schafer, Y. et al. Copy number variation and population-specific immune genes in the model vertebrate zebrafish. eLife 13, e98058 (2024). The paper shows that extensive copy number variation contributes to population-specific immune gene diversity in wild and laboratory zebrafish strains.

Suurvali, J. et al. The laboratory domestication of zebrafish: from diverse populations to inbred substrains. Mol. Biol. Evol. 37, 1056–1069 (2020).

Masternak, K. et al. CIITA is a transcriptional coactivator that is recruited to MHC class II promoters by multiple synergistic interactions with an enhanceosome complex. Genes Dev. 14, 1156–1166 (2000).

Graser, R., O’HUigin, C., Vincek, V., Meyer, A. & Klein, J. Trans-species polymorphism of class II Mhc loci in danio fishes. Immunogenetics 44, 36–48 (1996).

Bao, L. S. & Xia, J. L. Global analysis of transcriptome sequences highlights accelerated evolution of immune genes in Danio choprae and Danio albolineatus. Fish Shellfish Immunol. 66, 390–397 (2017).

Backhed, F. et al. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl Acad. Sci. USA 101, 15718–15723 (2004).

Camp, J. G., Jazwa, A. L., Trent, C. M. & Rawls, J. F. Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. PLoS Genet. 8, e1002585 (2012).

Hartwig, J. et al. Temporal control over the initiation of cell motility by a regulator of G-protein signaling. Proc. Natl Acad. Sci. USA 111, 11389–11394 (2014).

Hansen, C. L. & Pelegri, F. Primordial germ cell specification in vertebrate embryos: phylogenetic distribution and conserved molecular features of preformation and induction. Front. Cell Dev. Biol. 9, 730332 (2021).

Hansen, C. L., Chamberlain, T. J., Trevena, R. L., Kurek, J. E. & Pelegri, F. Conserved germ plasm characteristics across the Danio and Devario lineages. Genesis 59, e23452 (2021).

Kitano, J., Ansai, S., Takehana, Y. & Yamamoto, Y. Diversity and convergence of sex-determination mechanisms in teleost fish. Annu. Rev. Anim. Biosci. 12, 233–259 (2024).

Wilson, C. A. et al. Wild sex in zebrafish: loss of the natural sex determinant in domesticated strains. Genetics 198, 1291–1308 (2014).

Wilson, C. A., Batzel, P. & Postlethwait, J. H. Direct male development in chromosomally ZZ zebrafish. Front. Cell Dev. Biol. 12, 1362228 (2024).

Wilson, C. A. & Postlethwait, J. H. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. G3 14, jkae050 (2024).

Liew, W. C. et al. Polygenic sex determination system in zebrafish. PLoS ONE 7, e34397 (2012).

Trevena, R. L., Veire, B. M., Chamberlain, T. J., Moravec, C. E. & Pelegri, F. Embryonic lethality, juvenile growth variation, and adult sterility correlate with phylogenetic distance of danionin hybrids. Evol. Dev. 27, e12495 (2025).

Endoh, M. et al. Hybrid between Danio rerio female and Danio nigrofasciatus male produces aneuploid sperm with limited fertilization capacity. PLoS ONE 15, e0233885 (2020).

Saito, T., Goto-Kazeto, R., Arai, K. & Yamaha, E. Xenogenesis in teleost fish through generation of germ-line chimeras by single primordial germ cell transplantation. Biol. Reprod. 78, 159–166 (2008).

Wong, T. T., Saito, T., Crodian, J. & Collodi, P. Zebrafish germline chimeras produced by transplantation of ovarian germ cells into sterile host larvae. Biol. Reprod. 84, 1190–1197 (2011).

Wang, X. et al. Induced formation of primordial germ cells from zebrafish blastomeres by germplasm factors. Nat. Commun. 14, 7918 (2023).

Presgraves, D. C. The molecular evolutionary basis of species formation. Nat. Rev. Genet. 11, 175–180 (2010).

Frayer, M. E., Robles, N. V., Rodriguez-Barrera, M. J., Coughlan, J. M. & Schumer, M. The molecular evolutionary basis of species formation revisited. Trends Genet. 41, 1068–1095 (2025).

Kullander, S. O., Rahman, M. M., Noren, M. & Mollah, A. R. Devario in Bangladesh: species diversity, sibling species, and introgression within danionin cyprinids (Teleostei: Cyprinidae: Danioninae). PLoS ONE 12, e0186895 (2017).

Podobnik, M. et al. kcnj13 regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between Danio species. Development 150, dev201627 (2023).

Delomas, T. A. & Dabrowski, K. Asymmetric viability in reciprocal crosses of zebrafish Danio rerio and pearl danio Danio albolineatus. J. Fish Biol. 100, 10–14 (2022).

Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B. & Schilling, T. F. Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310 (1995).

Parichy, D. M., Elizondo, M. R., Mills, M. G., Gordon, T. N. & Engeszer, R. E. Normal table of postembryonic zebrafish development: staging by externally visible anatomy of the living fish. Dev. Dyn. 238, 2975–3015 (2009).

Britz, R., Conway, K. W. & Ruber, L. Spectacular morphological novelty in a miniature cyprinid fish, Danionella dracula n. sp. Proc. Biol. Sci. 276, 2179–2186 (2009).

Britz, R., Conway, K. W. & Ruber, L. The emerging vertebrate model species for neurophysiological studies is Danionella cerebrum, new species (Teleostei: Cyprinidae). Sci. Rep. 11, 18942 (2021).

Conway, K. W., K, M. K. & Britz, R. Extreme evolutionary shifts in developmental timing establish the miniature Danionella as a novel model in the neurosciences. Dev. Dyn. 250, 601–611 (2021).

Meyer, B. M., Froehlich, J. M., Galt, N. J. & Biga, P. R. Inbred strains of zebrafish exhibit variation in growth performance and myostatin expression following fasting. Comp. Biochem. Physiol. A 164, 1–9 (2013).

Gurevich, D. B. et al. Asymmetric division of clonal muscle stem cells coordinates muscle regeneration in vivo. Science 353, aad9969 (2016).

Nguyen, P. D. et al. Muscle stem cells undergo extensive clonal drift during tissue growth via Meox1-mediated induction of G2 cell-cycle arrest. Cell Stem Cell 21, 107–119 (2017).

Ratnayake, D. et al. Macrophages provide a transient muscle stem cell niche via NAMPT secretion. Nature 591, 281–287 (2021).

Lu, Y., Ruparelia, A. A. & Currie, P. D. Zebrafish: lessons and insights into skeletal muscle research. Cold Spring Harb. Perspect. Biol. 17, a041515 (2025).

Lu, Y. et al. Divergence in skeletal muscle growth by differential spatial hyperplastic patterning in teleost fishes. Preprint at bioRxiv https://doi.org/10.64898/2026.02.23.707519 (2026). This preprint shows that evolutionary divergence in skeletal muscle growth is associated with species-specific spatial patterns of muscle fibre hyperplasia in zebrafish, Devario malabaricus and Danionella cerebrum.

Jagot, S. et al. Distinct muscle stem cell fates correlated with hyperplasia and hypertrophy during skeletal muscle growth in rainbow trout. Preprint at bioRxiv https://doi.org/10.64898/2026.01.28.702282 (2026).

Cuthill, I. C. et al. The biology of color. Science 357, aan0221 (2017).

Braasch, I., Brunet, F., Volff, J. N. & Schartl, M. Pigmentation pathway evolution after whole-genome duplication in fish. Genome Biol. Evol. 1, 479–493 (2009).

Lorin, T., Brunet, F. G., Laudet, V. & Volff, J. N. Teleost fish-specific preferential retention of pigmentation gene-containing families after whole genome duplications in vertebrates. G3 8, 1795–1806 (2018).

Force, A., Lynch, M., Pickett F. B., Amores, A., Yan, Y. L. & Postlethwait, J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 4, 1531–1545 (1999).

Mills, M. G., Nuckels, R. J. & Parichy, D. M. Deconstructing evolution of adult phenotypes: genetic analyses of kit reveal homology and evolutionary novelty during adult pigment pattern development of Danio fishes. Development 134, 1081–1090 (2007).

McCluskey, B. M., Liang, Y., Lewis, V. M., Patterson, L. B. & Parichy, D. M. Pigment pattern morphospace of Danio fishes: evolutionary diversification and mutational effects. Biol. Open 10, bio058814 (2021).

Patterson, L. B., Bain, E. J. & Parichy, D. M. Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution. Nat. Commun. 5, 5299 (2014).

Spiewak, J. E. et al. Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes. PLoS Genet. 14, e1007538 (2018).

Irion, U., Singh, A. P. & Nusslein-Volhard, C. The developmental genetics of vertebrate color pattern formation: lessons from zebrafish. Curr. Top. Dev. Biol. 117, 141–169 (2016).

Toomey, M. B. et al. A mechanism for red coloration in vertebrates. Curr. Biol. 32, 4201–4214 (2022). This paper identifies a biochemical mechanism underlying red coloration that is conserved between Danio albolineatus and several bird species.

Huang, D. et al. Development and genetics of red coloration in the zebrafish relative Danio albolineatus. eLife 10, e70253 (2021).

Podobnik, M. et al. Evolution of the potassium channel gene kcnj13 underlies colour pattern diversification in Danio fish. Nat. Commun. 11, 6230 (2020). This study provides evidence for repeated and independent divergence of potassium channel gene functions during pigment pattern diversification.

McCluskey, B. M., Uji, S., Mancusi, J. L., Postlethwait, J. H. & Parichy, D. M. A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots. PLoS Genet. 17, e1009364 (2021). The paper reveals that complex genetic architectures underlie stripe and spot pattern differences in closely related Danio species.

Quigley, I. K. et al. Pigment pattern evolution by differential deployment of neural crest and post-embryonic melanophore lineages in Danio fishes. Development 131, 6053–6069 (2004).

Quigley, I. K. et al. Evolutionary diversification of pigment pattern in Danio fishes: differential fms dependence and stripe loss in D. albolineatus. Development 132, 89–104 (2005).

Stern, D. L. Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test. Trends Genet. 30, 547–554 (2014).

Dorner, L., Stratmann, B., Bader, L., Podobnik, M. & Irion, U. Efficient genome editing using modified Cas9 proteins in zebrafish. Biol. Open 13, bio060401 (2024).

Klann, M. et al. Cell-cell communication as underlying principle governing color pattern formation in teleost fishes. Nat. Commun. 17, 2899 (2026). This study corroborates the existence of hotspot genes for pigment pattern diversification in teleost fishes.

Elkin, J., Martin, A., Courtier-Orgogozo, V. & Santos, M. E. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol. Rev. Camb. Philos. Soc. 98, 1250–1277 (2023).

Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009).

Courtier-Orgogozo, V. & Martin, A. The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing. J. Exp. Biol. 223, jeb208934 (2020).

Orteu, A. & Jiggins, C. D. The genomics of coloration provides insights into adaptive evolution. Nat. Rev. Genet. 21, 461–475 (2020).

Poss, K. D. & Tanaka, E. M. Hallmarks of regeneration. Cell Stem Cell 31, 1244–1261 (2024).

Bangru, S., Diegmiller, R., Di Talia, S. & Poss, K. D. Signal control during tissue regeneration in adult animals. Nat. Rev. Mol. Cell Biol. 27, 316–335 (2026).

Lekkos, K. et al. Oxidative phosphorylation is required for cardiomyocyte re-differentiation and long-term fish heart regeneration. Nat. Cardiovasc. Res. 4, 1363–1380 (2025). This study uses intra-species and inter-species data to reveal oxidative phosphorylation as essential for cardiomyocyte re-differentiation and sustained heart regeneration in zebrafish.

Begeman, I. J. et al. Decoding an organ regeneration switch by dissecting cardiac regeneration enhancers. Development 147, dev194019 (2020).

Lafontant, P. J. et al. The giant danio (D. aequipinnatus) as a model of cardiac remodeling and regeneration. Anat. Rec. 295, 234–248 (2012).

Schulze, L. et al. Transparent Danionella translucida as a genetically tractable vertebrate brain model. Nat. Methods 15, 977–983 (2018).

Ruetten, V. M. S. et al. Imaging cellular activity across all organs reveals body-wide circuits. Nature https://doi.org/10.1038/s41586-026-10979-6 (2026). This preprint demonstrates the feasibility of live imaging of calcium flux at the whole-body scale in the adult Danionella cerebrum.

Misyuk, M. et al. In vivo imaging of central nervous system regeneration using Danionella cerebrum. Neural Regen. Res. https://doi.org/10.4103/NRR.NRR-D-25-00948 (2026).

Atabay, K. D. et al. Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration. Preprint at bioRxiv https://doi.org/10.64898/2026.02.03.703562 (2026). This preprint presents a spatially resolved whole-body single-cell atlas of adult Danionella cerebrum.

Lam, P. Y. Longitudinal in vivo imaging of adult Danionella cerebrum using standard confocal microscopy. Dis. Models Mech. 15, dmm049753 (2022).

Munos, J. A. & Lam, P. Y. Calcium signaling in macrophages during a wound response in vivo. Int. J. Mol. Sci. 27, ijms27104463 (2026).

Engert, F. Social behavior: a tiny fish with prodigious skills. Curr. Biol. 35, R62–R64 (2025).

Perelmuter, J. T. & Bass, A. H. Comparative neuroscience: a tale of two fishes. Curr. Biol. 35, R667–R669 (2025).

Rajan, G. et al. Evolutionary divergence of locomotion in two related vertebrate species. Cell Rep. 38, 110585 (2022).

Fouke, K. E., He, Z., Loring, M. D. & Naumann, E. A. Neural circuits underlying divergent visuomotor strategies of zebrafish and Danionella cerebrum. Curr. Biol. 35, 2457–2466 (2025). This study shows that distinct neural circuit architectures underlie different visuomotor strategies between two danionin species.

Demarchi, L. et al. Logarithmic coding leads to adaptive stabilization in the presence of sensorimotor delays. Proc. Natl Acad. Sci. USA 122, e2510385122 (2025).

Zada, D. et al. Development of neural circuits for social motion perception in schooling fish. Curr. Biol. 34, 3380–3391 (2024). The study maps how neural circuits develop to support social motion perception in schooling Danionella cerebrum.

Penalva-Tena, A. et al. Oxytocin-mediated social preference and socially reinforced reward learning in the miniature fish Danionella cerebrum. Curr. Biol. 35, 363–372 (2025). This study demonstrates that oxytocin signalling mediates social behaviour in Danionella cerebrum.

Zada, D., Kadobianskyi, M., Judkewitz, B. & Lovett-Barron, M. Convergent thyroid-ATPase interactions regulate collective behavior in Danionella. Cell Rep. 45, 116730 (2025).

Yu, J. H., Milan, J., Meyerhof, G. T., Napoli, J. L. & Lovett-Barron, M. Neuronal detection of social actions directs collective escape behavior. Preprint at bioRxiv https://doi.org/10.1101/2025.09.24.678087 (2025).

Kadobianskyi, M. et al. Multimodal reference brain atlas of adult Danionella cerebrum. Preprint at bioRxiv https://doi.org/10.64898/2026.03.09.710483 (2026).

Henninger, J. et al. Brain-wide hierarchical and sexually dimorphic tuning for social vocalizations. Preprint at bioRxiv https://doi.org/10.64898/2026.03.04.709502 (2026).

Drew, R. E. et al. Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio). BMC Genom. 13, 323 (2012).

Chow, D. M. et al. Deep three-photon imaging of the brain in intact adult zebrafish. Nat. Methods 17, 605–608 (2020).

Akbari, N. et al. Whole-brain optical access in a small adult vertebrate with two- and three-photon microscopy. iScience 25, 105191 (2022).

Hoffmann, M., Henninger, J., Veith, J., Richter, L. & Judkewitz, B. Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity. Nat. Commun. 14, 8019 (2023).

Akbari, N. et al. Label-free, whole-brain in vivo mapping in an adult vertebrate with third harmonic generation microscopy. J. Comp. Neurol. 532, e25614 (2024).

Beketova, Z. Transparent fish takes center stage in $1 billion neuroscience initiative. Science 393, 18–19 (2026).

Kullander, S. O. & Fang, F. Danio aesculapii, a new species of danio from south-western Myanmar (Teleostei: Cyprinidae). Zootaxa 2164, 41–48 (2009).

Fang, F. Danio kyathit, a new species of cyprinid fish from Myitkyina, northern Myanmar. Ichthyol. Explor. Freshw. 8, 273–280 (1998).

Kullander, S. O. & Fang, F. Danio tinwini, a new species of spotted danio from northern Myanmar (Teleostei: Cyprinidae). Ichthyol. Explor. Freshw. 20, 223 (2009).

Kullander, S. O. Description of Danio flagrans, and redescription of D. choprae, two closely related species from the Ayeyarwaddy River drainage in northern Myanmar (Teleostei: Cyprinidae). Ichthyol. Explor. Freshw. 23, 245 (2012).

Kadobianskyi, M., Schulze, L., Schuelke, M. & Judkewitz, B. Hybrid genome assembly and annotation of Danionella translucida. Sci. Data 6, 156 (2019).

Biga, P. R. & Goetz, F. W. Zebrafish and giant danio as models for muscle growth: determinate vs. indeterminate growth as determined by morphometric analysis. Am. J. Physiol. Regul. Integr. Comp. Physiol. 291, R1327–R1337 (2006).

Froehlich, J. M., Fowler, Z. G., Galt, N. J., Smith, D. L. Jr. & Biga, P. R. Sarcopenia and piscines: the case for indeterminate-growing fish as unique genetic model organisms in aging and longevity research. Front. Genet. 4, 159 (2013).

Poling, K. R. & Brunjes, P. C. Sensory deafferentation and olfactory bulb morphology in the zebrafish and related species. Brain Res. 856, 135–141 (2000).

Folgueira, M. & Clarke, J. D. W. Telencephalic eversion in embryos and early larvae of four teleost species. Evol. Dev. 26, e12474 (2024).

Nelson, H. M. et al. Structure, development, and functional morphology of the cement gland of the giant danio, Devario malabaricus. Dev. Dyn. 248, 1155–1174 (2019).

Kaneko, G. et al. Diversity of lipid distribution in fish skeletal muscle. Zool. Sci. 33, 170–178 (2016).

Shifatu, O. et al. Heart development, coronary vascularization and ventricular maturation in a giant danio (Devario malabaricus). J. Dev. Biol. 6, jdb6030019 (2018).

Hu, Y. et al. Thyroid hormone coordinates developmental trajectories but does not underlie developmental truncation in danionins. Dev. Dyn. 248, 1144–1154 (2019).

Wong, K. Y., Adolph, A. R. & Dowling, J. E. Retinal bipolar cell input mechanisms in giant danio. I. Electroretinographic analysis. J. Neurophysiol. 93, 84–93 (2005).

Biga, P. R. & Meyer, J. Growth hormone differentially regulates growth and growth-related gene expression in closely related fish species. Comp. Biochem. Physiol. A 154, 465–473 (2009).

Froehlich, J. M., Galt, N. J., Charging, M. J., Meyer, B. M. & Biga, P. R. In vitro indeterminate teleost myogenesis appears to be dependent on Pax3. Vitro Cell. Dev. Biol. Anim. 49, 371–385 (2013).

Lewis, V. M. et al. Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores. Proc. Natl Acad. Sci. USA 116, 11806–11811 (2019).

Huang, D. et al. Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish. Proc. Natl Acad. Sci. USA 122, e2424180122 (2025).

Huang, D. et al. Cell type diversification and phenotype convergence underlying white fin-ornamentation of cyprinid fishes. Proc. Natl Acad. Sci. USA 123, e2537571123 (2026).

Tatarsky, R. L., Akbari, N., Wang, K., Xu, C. & Bass, A. H. Label-free multiphoton imaging reveals volumetric shifts across development in sensory-related brain regions of a miniature transparent vertebrate. J. Comp. Neurol. 533, e70048 (2025).

Veith, J., Svanidze, A. & Judkewitz, B. An algorithm underlying directional hearing in fish. Curr. Biol. 36, 1435–1443 (2026).

Zanon, M., Fraser, S. E. & Vallortigara, G. Numerical discrimination in Danionella. iScience 28, 113667 (2025).

McMahon, D. G. & Mattson, M. P. Horizontal cell electrical coupling in the giant danio: synaptic modulation by dopamine and synaptic maintenance by calcium. Brain Res. 718, 89–96 (1996).

Palacios, A. G., Goldsmith, T. H. & Bernard, G. D. Sensitivity of cones from a cyprinid fish (Danio aequipinnatus) to ultraviolet and visible light. Vis. Neurosci. 13, 411–421 (1996).

Chicoli, A. et al. The effects of flow on schooling Devario aequipinnatus: school structure, startle response and information transmission. J. Fish Biol. 84, 1401–1421 (2014).

Mekdara, P. J., Schwalbe, M. A. B., Coughlin, L. L. & Tytell, E. D. The effects of lateral line ablation and regeneration in schooling giant danios. J. Exp. Biol. 221, jeb175166 (2018).

Zhang, Y., Ko, H., Calicchia, M. A., Ni, R. & Lauder, G. V. Collective movement of schooling fish reduces the costs of locomotion in turbulent conditions. PLoS Biol. 22, e3002501 (2024).

Zhang, Y. & Lauder, G. V. Energy conservation by collective movement in schooling fish. eLife 12, e90352 (2024).

Tidswell, B. K., Veliko-Shapko, A. & Tytell, E. D. The role of vision and lateral line sensing for schooling in giant danios (Devario aequipinnatus). J. Exp. Biol. 227, jeb246887 (2024).

Engeszer, R. E., Wang, G., Ryan, M. J. & Parichy, D. M. Sex-specific perceptual spaces for a vertebrate basal social aggregative behavior. Proc. Natl Acad. Sci. USA 105, 929–933 (2008).

Ko, H. et al. Beyond planar: fish schools adopt ladder formations in 3D. Sci. Rep. 15, 20249 (2025).

Coraggioso, M. et al. A sensorimotor instability drives a locomotor transition during fish development. Sci. Adv. 12, eaec6922 (2026).

Rajan, G., Debregeas, G., Orger, M. B. & Del Bene, F. An analysis pipeline to compare explorative locomotion across fish species. STAR Protoc. 3, 101850 (2022).

Spence, R. & Smith, C. The role of early learning in determining shoaling preferences based on visual cues in the zebrafish, Danio rerio. Ethology 113, 62–67 (2007).

Rosenthal, G. G., Ryan & Michael, J. Assortative preferences for stripes in danios. Anim. Behav. 70, 1063–1066 (2005).

Choudhary, V. et al. Eye movement kinematics reveal novel circadian organization of sleep substates. Nat. Commun. 17, 4068 (2026). This study identifies sleep states that are conserved across zebrafish, Danio aesculapii and Danio nigrofasciatus.

Lindemann, N. et al. A comparative analysis of Danionella cerebrum and zebrafish (Danio rerio) larval locomotor activity in a light-dark test. Front. Behav. Neurosci. 16, 885775 (2022).

Lee, T. J. & Briggman, K. L. Visually guided and context-dependent spatial navigation in the translucent fish Danionella cerebrum. Curr. Biol. 33, 5467–5477 (2023).

Kumar, S. et al. TimeTree 5: an expanded resource for species divergence times. Mol. Biol. Evol. 39, msac174 (2022).

Braasch, I. et al. A new model army: emerging fish models to study the genomics of vertebrate Evo-Devo. J. Exp. Zool. B 324, 316–341 (2015).

Parichy, D. M. Evolution of danio pigment pattern development. Heredity 97, 200–210 (2006).

Parichy, D. M. Homology and the evolution of novelty during Danio adult pigment pattern development. J. Exp. Zool. B 308, 578–590 (2007).

Nayak, R., Franek, R., Sindelka, R. & Psenicka, M. Enhancement of zebrafish sperm production via a large body-sized surrogate with germ cell transplantation. Commun. Biol. 6, 412 (2023).

Chernyavskaya, Y., Zhang, X., Liu, J. & Blackburn, J. Long-read sequencing of the zebrafish genome reorganizes genomic architecture. BMC Genom. 23, 116 (2022).

Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).

Mullins, M. C., Hammerschmidt, M., Haffter, P. & Nusslein-Volhard, C. Large-scale mutagenesis in the zebrafish: in search of genes controlling development in a vertebrate. Curr. Biol. 4, 189–202 (1994).

Irion, U., Krauss, J. & Nusslein-Volhard, C. Precise and efficient genome editing in zebrafish using the CRISPR/Cas9 system. Development 141, 4827–4830 (2014).

Kawakami, K. & Shima, A. Identification of the Tol2 transposase of the medaka fish Oryzias latipes that catalyzes excision of a nonautonomous Tol2 element in zebrafish Danio rerio. Gene 240, 239–244 (1999).

Hwang, W. Y. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol. 31, 227–229 (2013).

Meng, F. W. et al. TransTag enables simple and efficient transgene mapping in zebrafish via tagmentation. Cell Rep. Methods 5, 101090 (2025).

Lalonde, R. L. et al. pIGLET: safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. Sci. Adv. 10, eadn6603 (2024).

Moyer, A. J. et al. Genetic context of transgene insertion can influence neurodevelopment in zebrafish. Genetics 231, iyaf195 (2025).

Rosello, M., Serafini, M., Concordet, J. P. & Del Bene, F. Precise mutagenesis in zebrafish using cytosine base editors. Nat. Protoc. 18, 2794–2813 (2023).

Ono, Y. et al. Optimised genome editing for precise DNA insertion and substitution using prime editors in zebrafish. eLife 14, RP107475 (2026).

Rajan, G., Duroure, K. & Del Bene, F. Danionella translucida, a tankful of new opportunities. In Laboratory Fish in Biomedical Research (eds D’angelo, L. & de Girolamo, P.) 409–418 (Elsevier, 2022).

Bradford, Y. M. et al. ZFIN updates to support zebrafish environmental exposure data. Genetics 229, iyaf021 (2025).

Cavalcante, L. D. S., Toner, M., Uygun, K. & Tessier, S. N. Leveraging the zebrafish to model organ transplantation. Curr. Opin. Organ Transpl. 24, 613–619 (2019).

Carmany-Rampey, A. & Moens, C. B. Modern mosaic analysis in the zebrafish. Methods 39, 228–238 (2006).

Demy, D. L. et al. Generating parabiotic zebrafish embryos for cell migration and homing studies. Nat. Methods 10, 256–258 (2013).

Page, D. M. et al. An evolutionarily conserved program of B-cell development and activation in zebrafish. Blood 122, e1–e11 (2013).

Costa, B. et al. Zebrafish Avatar-test forecasts clinical response to chemotherapy in patients with colorectal cancer. Nat. Commun. 15, 4771 (2024).

Groenewoud, A. et al. Patient-derived zebrafish xenografts of uveal melanoma reveal ferroptosis as a drug target. Cell Death Discov. 9, 183 (2023).

Ricemeyer, E. S. et al. Gene conversion empowers natural selection in a clonal fish species. Nature 652, 398–404 (2026).

Reid, K, Bell, M. A. & Veeramah, K. R. Threespine stickleback: a model system for evolutionary genomics. Annu. Rev. Genomics Hum. Genet. 22, 357–383 (2021).

Swaminathan, A., Xia, F. & Rohner, N. From darkness to discovery: evolutionary, adaptive, and translational genetic insights from cavefish. Trends Genet. 40, 24–38 (2024).

Naruse, K., Loosli, F., Ansai, S., Birney, E. & Wittbrodt, J. Medaka: a novel model for analyzing genome-environment interactions. Trends Genet. 42, 350–361 (2026).

Donertas, H. M. & Partridge, L. Evolutionary genetics of ageing. Nat. Rev. Genet. https://doi.org/10.1038/s41576-026-00959-x (2026).

Bedbrook, C. N. et al. Lifelong behavioral screen reveals an architecture of vertebrate aging. Science 391, eaea9795 (2026).

Morabito, G. et al. Spontaneous aging-associated inflammation and genome instability in the immune system of turquoise killifish. Nat. Aging 6, 665–681 (2026).

Schartl, M. & Lu, Y. Validity of Xiphophorus fish as models for human disease. Dis. Models Mech. 17, dmm050382 (2024).

Patton, E. E., Zon, L. I. & Langenau, D. M. Zebrafish disease models in drug discovery: from preclinical modelling to clinical trials. Nat. Rev. Drug Discov. 20, 611–628 (2021).

Yamamoto, S., Kanca, O., Wangler, M. F. & Bellen, H. J. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat. Rev. Genet. 25, 46–60 (2024).

Weiss, J. M. et al. Anatomic position determines oncogenic specificity in melanoma. Nature 604, 354–361 (2022).

Hunter, M. V. et al. Mechanical confinement governs phenotypic plasticity in melanoma. Nature 647, 517–527 (2025).

El-Brolosy, M. A. et al. Genetic compensation triggered by mutant mRNA degradation. Nature 568, 193–197 (2019).

Falcucci, L. et al. Transcriptional adaptation upregulates utrophin in Duchenne muscular dystrophy. Nature 639, 493–502 (2025).