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Seeing in the deep: evolution of the opsin gene expression in Bermin crater lake cichlids

Kłodawska, Monika1; Indermaur, Adrian2; Bitja Nyom, Arnold Roger34; Omelchenko, Dmytro1; Bartoš, Oldřich15; Musilova, Zuzana1

Published Apr 15, 2026 on Dryad. https://doi.org/10.5061/dryad.zw3r228km

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Abstract

This study examines visual system evolution in the Bermin crater lake species flock in Cameroon, comprising 13 Coptodon species (9 valid, 4 undescribed). Using 109 retina transcriptomes, we analyzed opsin gene sequences and expression to assess variation across depth gradients and seasonal shifts in the migrating species Coptodon imbrifernus. Paired-end reads were mapped to seven cone opsin genes (sws1, sws2b, sws2a, rh2b, rh2aβ, rh2aα, lws), and relative expression was calculated using Geneious 9.1.4. We computed proportional opsin expression separately for single- and double-cone opsins, and used beta regression (R package betareg v3.2-1) to compare deep water species (Coptodon bythobates, Coptodon imbrifernus, Coptodon spongotroktis) with shallow-water species, as well as seasonal differences in C. imbrifernus. To estimate overall retinal sensitivity, we calculated weighted average cone sensitivities following Hofmann et al. (2009b), using experimentally measured λmax values from tilapia (Spady et al., 2006). We also compared the overall visual sensitivity profiles of Bermin species with those of the Barombi Mbo cichlid flock, based on opsin gene expression. Our results reveal depth-related differences in opsin gene expression, suggesting that visual adaptation in this system occurs primarily at the level of gene expression.