DOI: 10.5061/dryad.vhhmgqp2c
title: Data from: Light environment and seasonal variation in the visual system of the red shiner (Cyprinella lutrensis)

description: The light environment under water can vary dramatically over space and
 time, challenging the visual systems of aquatic organisms. To meet these
 challenges, many species shift their spectral sensitivities through
 changes in visual pigment chromophore and opsin expression. The red shiner
 (Cyprinella lutrensis) is a cyprinid minnow species that has rapidly
 expanded its range throughout North America and inhabits a wide range of
 aquatic habitats. We hypothesized that visual system plasticity has
 contributed to the red shiner’s success. We investigated plasticity in
 chromophore usage and opsin expression by collecting red shiners from
 three Oklahoma creeks that vary in turbidity throughout the year. We
 characterized the light environment by spectroradiometry, measured
 chromophore composition of the eyes with high-performance liquid
 chromatography, characterized CYP27C1 enzyme function through heterologous
 expression, and examined ocular gene expression by RNA sequencing and de
 novo transcriptome assembly. We observed significantly higher proportions
 of the long-wavelength shifted A2 chromophore in the eyes of fish from the
 turbid site and in samples collected in winter suggesting that there may
 be a temperature-dependent trade-off between chromophore-based spectral
 tuning and chromophore-related noise. Opsin expression varied between
 turbid and clear creeks, but did not align with light environment as
 expected and the magnitude of these differences was limited compared to
 the differences in chromophore composition. We confirmed that red shiner
 CYP27C1 catalyzes the conversion of A1 to A2, but the ocular expression of
 CYP27C1 not well correlated with A2 levels in the eye suggesting
 conversion may be occurring outside of the eye.
description: # Light environment and seasonal variation in the visual system of the red
 shiner (Cyprinella lutrensis)
 [https://doi.org/10.5061/dryad.vhhmgqp2c](https://doi.org/10.5061/dryad.vhhmgqp2c) This archive contains complete scripts and datasets for all analyses of ocular chromophore composition, opsin and enzyme gene expression, and visual system performance in the red shiner in relation to light environment and season that are presented in Foster et. al 2025.  ## Description of the data and file structure This archive consists of thirteen files:  * **Statisitcal_analyses_and_plotting_Mar25.rmd** - An R markdown file with the scripts for the complete statistical analyses and data plotting of the results presented in the manuscript: Light environment and seasonal variation in the visual system of the red shiner (*Cyprinella lutrensis*). The HTML rendered document is also available: **Statisitcal_analyses_and_plotting_Mar25.html** * **chromophore_site_season.csv** * *Fish.ID* - Sample identification code  * *Site.Name* - Site that each sample was collected from * *Date* - Date of sample collection in MM/DD/YYYY format * *A2.Prop.1.2* - The proportion of the total ocular retinoid profile that consisted of A2 retinoids * *Eye.Size -* Eye diameter measured in mm.  * *Sex -* The sex of each sample: M - Males, F - female, or U - unkown * *Body.Length* - Body length of each sample in mm measured from the tip of the snout to fork of the tail * *Season -* Meteorological season each sample was collected * *Year* - the year each sample was collected * **gene_expression.csv** * *ext_gene -* the gene symbol   * *sample* - Sample identification code  * *tpm* - gene expression measures as transcripts per million calculated with [Kallisto](https://pachterlab.github.io/kallisto)  * *site* - Site that each sample was collected from: LCV = Lightning Creek, BCV = Big Creek, PCJ = Polecat Creek * *season* - Meteorological season each sample was collected * **spectrum_site_season.csv** * *SiteDate* - An identifier indicating the site and date the measures were made * *rep* - letters A-E denoting replicate spectral measurements at a given site and season * *prop_red* - the ratio of transmittance in the red (550-650 nm) vs. blue portions (350-450 nm) of the light spectrum * *Site* - Site that each was measured: LCV = Lightning Creek, BCV = Big Creek, PCJ = Polecat Creek * *Season* - Meteorological season each spectrum was measured * **transmittance_site_season.csv** * *SiteDate* - An identifier indicating the site and date the measures were made * ``` *rep* - letters A-E denoting replicate spectral measurements at a given site and season ``` * *trans* - the ratio of total irradiance at 20 cm depth vs. total irradiance at measured at the water surface * *Site* - Site that each was measured: LCV = Lightning Creek, BCV = Big Creek, PCJ = Polecat Creek * *Season* - Meteorological season each spectrum was measured * **turbidity_site_season.csv** * *Site.Name -* Name of the sampling site * *Latitude* - Latitude of the sampling location in decimal degrees * *Longitude* -  Longitude of the sampling location in decimal degrees * *Date - Date of measurement  *in MM/DD/YYYY format * *Time* - Time of measurement in Hr:Min:Sec in a 12 Hr format  * *NTU* - turbidity measured as nephelometric turbidity units * *season - *Meteorological season each measurement was taken * **A2_to_TPM.csv** * *sample* - Sample identification code * *tpm* - The expression of *CYP27c1* measured as transcripts per kilobase million * *site* - Site that each sample was collected: LCV = Lightning Creek, BCV = Big Creek, PCJ = Polecat Creek * *season* - Meteorological season each spectrum was measured * *A2_prop* - The proportion of the total ocular retinoid profile that consisted of A2 retinoids * **IRR_sub.csv** * *wavelength* - wavelength in nanometers * columns 2:15 - normalized irradiance spectra measured at 20 cm depth. These columns are labeled - [site name] [sample date] [replicate] * **gf_cornea.csv** * *x* - wavelength in nanometers * *y* - the transmission spectrum of the lens of the goldfish reported in: * Douglas, R. H. (1989). The spectral transmission of the lens and cornea of the brown trout (Salmo trutta) and goldfish (Carassius auratus)--effect of age and implications for ultraviolet vision. Vision Res. 29, 861–869. * **C_luterensis_transcriptome_assembly_Apr23.fa** - The transcriptome assembly generated from RNA sequencing of whole eye. This included *de novo* assembled transcripts created with [Trininty](https://github.com/trinityrnaseq/trinityrnaseq/wiki) and supplemented with manual curation of *opsin* and *CYP27c1* transcripts as described in the accompanying manuscript.  * **C_luterensis_selected_transcripts_Apr23.fa** - A FASTA format file containing the transcript sequences of the manually curated *opsins* and *CYP27c1* ## Sharing/Access information Raw RNA-seq reads are available in the NCBI short-read archive (BioProject ID: PRJNA1076457)