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

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.