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 fro..., , # Seeing in the deep: evolution of the opsin gene expression in Bermin crater lake cichlids Dataset DOI: [10.5061/dryad.zw3r228km](10.5061/dryad.zw3r228km) ## Description of the data and file structure README – Dataset for Seeing in the deep: evolution of the opsin gene expression in Bermin crater lake cichlids Contact Email: [[e-mail]](mailto:[e-mail]) Project Description: This dataset supports a study on opsin gene expression and visual sensitivity in the 13 endemic Coptodon species flock from Lake Bermin (Cameroon), exploring depth-related and seasonal variation in retinal visual systems. ### Files and variables #### File: Coptodon_OpsinExpression_BetaRegression.csv **Description:** ##### Variables * gene: Opsin gene: sws1, sws2b, sws2a, rh2b, rh2aβ, rh2aα, lws * species: Scientific name of the cichlid species * sex: Biological sex of the individual: male or female * depth: Habitat depth classification: `deep` or `shallow` * season: Sampl..., ,本研究聚焦喀麦隆伯明火山口湖（Bermin crater lake）的口孵非鲫属（Coptodon）物种群视觉系统演化，该类群包含13个物种（其中9个已正式定名，4个尚未被描述）。研究利用109份视网膜转录组（retina transcriptome），分析视蛋白（opsin）基因序列与表达模式，以评估迁徙物种饰带口孵非鲫（Coptodon imbrifernus）在深度梯度与季节变化下的视觉系统差异。 将双端测序读段（paired-end reads）比对至7个视锥视蛋白基因（sws1、sws2b、sws2a、rh2b、rh2aβ、rh2aα、lws），并使用Geneious 9.1.4软件计算相对表达量。我们分别针对单视锥与双视锥视蛋白计算了比例化表达量，并采用贝塔回归（beta regression，R包betareg v3.2-1）比较深水物种（深渊口孵非鲫Coptodon bythobates、饰带口孵非鲫Coptodon imbrifernus、海绵口孵非鲫Coptodon spongotroktis）与浅水物种的表达差异，同时分析饰带口孵非鲫的季节表达差异。 为估算整体视网膜感光敏感性，我们参考Hofmann等人（2009b）的方法，基于实验测得的λmax值计算加权平均视锥感光灵敏度…… # 深海视物：伯明火山口湖慈鲷的视蛋白基因表达演化 数据集DOI: [10.5061/dryad.zw3r228km](10.5061/dryad.zw3r228km) ## 数据与文件结构说明 README —— 题为“深海视物：伯明火山口湖慈鲷的视蛋白基因表达演化”的数据集说明文档 联系邮箱: [[e-mail]](mailto:[e-mail]) 项目概述: 本数据集支撑一项针对喀麦隆伯明湖13种特有口孵非鲫属物种群的视蛋白基因表达与视觉敏感性研究，旨在探索视网膜视觉系统的深度相关与季节变化差异。 ### 文件与变量 #### 文件: Coptodon_OpsinExpression_BetaRegression.csv **描述:** ##### 变量 * gene: 视蛋白基因，涵盖sws1、sws2b、sws2a、rh2b、rh2aβ、rh2aα、lws * species: 慈鲷物种的学名 * sex: 个体的生物学性别：雄性（male）或雌性（female） * depth: 栖息深度分类：`deep`（深水）或`shallow`（浅水） * season: 采样季节……