Insertion of an invading retrovirus regulates a novel color trait in swordtail fish

Haghani, N.; Dodge, T. O.; Baczenas, J. J.; Gunn, T.; He, Q.; Pangburn, W.; Sood, R.; Du, K.; Fascinetto-Zago, P.; Kaatmann, A.; Ou, Z.; Dougan, S.; Olmos-Santiago, N. S.; Preising, G. A.; Payne, C. Y.; Haase Cox, S. K.; Hunnicutt, K. E.; Madrzyk, M.; Moran, B. M.; Stigloher, C.; Powell, D. L.; Schartl, M.; Gifford, C.; Han, G. z.; Schumer, M.

doi:10.1101/2025.11.07.687308

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bioRxiv · 10.1101/2025.11.07.687308

Insertion of an invading retrovirus regulates a novel color trait in swordtail fish

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Abstract

For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable within and between species and can serve as an important window into the mechanisms of adaptation. Here, we map the genetic basis of a newly described iridescence trait in swordtail fish to a single locus. Individuals with this trait appear to sparkle as they move through the water. We find that the trait is driven by the recent endogenization of a retrovirus that inserted near the gene alkal2a. This insertion is associated with changes in the chromatin landscape, upregulation of alkal2a, and accumulation of iridescent cells that adhere to the scales. Rather than causing diseases, our results demonstrate that invading endogenous retroviruses can also regulate novel trait variation in the host. Moreover, we find that this coloration trait may act as an important signal in interactions between fish and their predators in the natural environment.

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Haghani, N., Dodge, T. O., Baczenas, J. J., Gunn, T., He, Q., Pangburn, W., Sood, R., Du, K., Fascinetto-Zago, P., Kaatmann, A., Ou, Z., Dougan, S., Olmos-Santiago, N. S., Preising, G. A., Payne, C. Y., Haase Cox, S. K., Hunnicutt, K. E., Madrzyk, M., Moran, B. M., Stigloher, C., Powell, D. L., Schartl, M., Gifford, C., Han, G. z., Schumer, M.. 2025-11-11. Insertion of an invading retrovirus regulates a novel color trait in swordtail fish. https://doi.org/10.1101/2025.11.07.687308

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