Zebrafish Pigment Pattern Formation: Insights into the Development and Evolution of Adult Form
Abstract
Vertebrate pigment patterns are diverse and fascinating adult traits that allow animals to recognize conspecifics, attract mates, and avoid predators. Pigment patterns in fish are among the most amenable traits for studying the cellular basis of adult form, as the cells that produce diverse patterns are readily visible in the skin during development. The genetic basis of pigment pattern development has been most studied in the zebrafish, Danio rerio. Zebrafish adults have alternating dark and light horizontal stripes, resulting from the precise arrangement of three main classes of pigment cells: black melanophores, yellow xanthophores, and iridescent iridophores. The coordination of adult pigment cell lineage specification and differentiation with specific cellular interactions and morphogenetic behaviors is necessary for stripe development. Besides providing a nice example of pattern formation responsible for an adult trait of zebrafish, stripe-forming mechanisms also provide a conceptual framework for posing testable hypotheses about pattern diversification more broadly. Here, we summarize what is known about lineages and molecular interactions required for pattern formation in zebrafish, we review some of what is known about pattern diversification in Danio, and we speculate on how patterns in more distant teleosts may have evolved to produce a stunningly diverse array of patterns in nature.
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Wild-type hybrids between D. rerio and other Danio species generally display a pattern of horizontal stripes, similar to the D. rerio pattern, with stripe aberrations sometimes evident likely depending on genetic backgrounds of different species isolates.
“Wild-type hybrids between D. rerio and other Danio species generally display a pattern of horizontal stripes6,9,46,47, similar to the D. rerio pattern, with stripe aberrations sometimes evident likely depending on !genetic backgrounds of different species isolates, as depicted here for D. tinwini and D. albolineatus hybrids (Fig. 5A).”
From Genomic and genetic insights into speciation and pigment pattern diversification in <i>Danio</i> fishes (2025) · cites this paper as [6]
In this model, latent progenitors associated with the peripheral nervous system that have transited to the skin during the larva-to-adult transformation expand clonally as early iridoblasts-not specified to subtype-and subsequently differentiate according to cues in the microenvironment they encounter.
“In this model, latent progenitors associated with the peripheral nervous system that have transited to the skin during the larva-to-adult transformation3 expand clonally as early iridoblasts—not specified to subtype—and subsequently differentiate according to cues in the microenvironment they encounter”
From In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning (2020) · cites this paper as [3]
In zebrafish, interactions among chromatophores generate and maintain a pattern of dark and light horizontal stripes.
“In the teleost most studied for its pigmentation, zebrafish Danio rerio, interactions among chromatophores generate and maintain a pattern of dark and light horizontal stripes (4)”
From Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish (2025) · cites this paper as [4]
The mechanisms documented here further highlight the role of positional information in generating a pigmentary phenotype, even in a species that provides a premier example of self-organization by pigment cells during body stripe formation.
“The mechanisms documented here further highlight the role of positional information in generating a pigmentary phenotype, even in a species that provides a premier example of self-organization by pigment cells during body stripe formation (4, 5).”
From Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish (2025) · cites this paper as [4]
Cites
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Thyroid hormone regulates distinct paths to maturation in pigment cell lineages
Saunders, L. M., Mishra, A. K., Aman, A. J., Lewis, V. M., Toomey, M. B., Packer, J. S., Qiu, X., McFaline-Figueroa, J. L., Corbo, J. C., Trapnell, C., et al. (2019) · eLife · doi:10.7554/elife.45181 · Cited by 170 · see citing works
Self-citationPetratou, K., Subkhankulova, T., Lister, J. A., Rocco, A., Schwetlick, H., & Kelsh, R. N. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007402 · Cited by 69 · see citing works
An ongoing role for<i>Wnt</i>signaling in differentiating melanocytes in vivo
Vibert, L., Aquino, G., Gehring, I., Subkankulova, T., Schilling, T. F., Rocco, A., & Kelsh, R. N. (2017) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12568 · Cited by 35 · see citing works
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Thyroid hormone regulates distinct paths to maturation in pigment cell lineages
Saunders, L. M., Mishra, A. K., Aman, A. J., Lewis, V. M., Toomey, M. B., Packer, J. S., Qiu, X., McFaline-Figueroa, J. L., Corbo, J. C., Trapnell, C., et al. (2019) · eLife · doi:10.7554/elife.45181 · Cited by 170 · see citing works
Self-citationIn situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning
Gur, D., Bain, E. J., Johnson, K. R., Aman, A. J., Pasolli, H. A., Flynn, J. D., Allen, M. C., Deheyn, D. D., Lee, J. C., Lippincott-Schwartz, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20088-1 · Cited by 69 · see citing works
Self-citationHuang, D., Kapadia, E. H., Liang, Y., Shriver, L. P., Dai, S., Patti, G. J., Humbel, B. M., Laudet, V., & Parichy, D. M. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2424180122 · Cited by 15 · see citing works
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Self-citationZebrafish relatives as models for functional comparative genetics and genomics
Podobnik, M., Lu, Y., Irion, U., & Currie, P. D. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-01007-4 · Cited by 1 · see citing works
- Authors
- Patterson, L. B., & Parichy, D. M.
- Affiliations
- Rhode Island College (US)
- University of Virginia (US)
- Corresponding author
- Patterson, Larissa B.
- ORCID
- Parichy, David M.
- Venue
- Annual Review of Genetics
- Publisher
- Annual Reviews
- Published
- 2019-12-03
- Volume
- 53
- Issue
- 1
- Pages
- 505-530
- ISSN
- 0066-4197 (ISSN-L)
- 1545-2948
- OpenAlex
- W2973095164
- Cited by
- 151
- References
- 4
- Citations by year
- 2026: 19 · 2025: 20 · 2024: 18 · 2023: 32 · 2022: 18 · 2021: 26 · 2020: 14 · 2019: 4
- FWCI
- 1.82
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Genetics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (P20GM103430, R35GM122471)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Zebrafish Biomedical Research Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- zebrafish, pigment pattern formation, melanophores, xanthophores, iridophores
- MeSH terms
- Animals, Biological Evolution, Melanophores, Neural Crest, Pigmentation, Zebrafish, Cell Lineage, Paracrine Communication, Zebrafish Proteins
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