Supplementary material data for: Unstable environmental conditions constrain the fine-tune between opsin sensitivity and underwater light in an Amazon forest stream fish
Data files
Jan 03, 2024 version files 26.15 KB
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Forest_stream_blue_light.csv
2.18 KB
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Phylogenetic_relationship_genes.fas
21.66 KB
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README.md
2.31 KB
Abstract
Visual adaptations can stem from variations in amino acid composition, chromophore utilization, and differential opsin gene expression levels, enabling individuals to adjust their light sensitivity to environmental lighting conditions. In stable environments, adaptations often involve amino acid substitutions, whereas in unstable conditions, differential gene expression may be a more relevant mechanism. Amazon forest streams present diverse underwater lighting conditions and experience short-term water colour fluctuations. In these environments, it is less likely for genetic and amino acid sequences to undergo modifications that tailor opsin proteins to the prevailing lighting conditions, particularly in species having several copies of the same gene. The sailfin tetra, Crenuchus spilurus, inhabits black and clear water Amazon forest streams. The long wavelength sensitivity (LWS) is an important component for foraging and courtship. Here, we investigated LWS opsin genes in the sailfin tetra. Three copies of LWS1 and two copies of LWS2 genes were found. The maximum absorbance wavelength (λmax) estimated from the amino acid sequences of LWS1 genes exhibited variation among the different copies. In contrast, the copies of LWS2 genes showed identical expected λmax values. Although the amino acid positions affecting λmax varied among LWS genes, they remained consistent among populations living in different water colours. The relative expression levels of LWS genes differed between gene copies. While not formally tested, our results suggest that in fluctuating environments, visual adaptations may primarily stem from alterations in gene expression profiles and/or chromophore usage rather than precise genetic tuning of protein light sensitivity to environmental lighting conditions.
README: Data for Supplementary Material -
https://doi.org/10.5061/dryad.69p8cz986
Description of the data and file structure
These are the nucleotide sequences used for the phylogenetic relationship among the genes found in our samples with those genes that have been previously described, and the data (values in lux) used to measure the variation in the underwater lighting condition in black and clear water Amazon igarapés.
File = Phylogenetic_relationship_genes.fas
Lines 1 to 13 = NCBI sequence data (starting with the accession number) for each specific opsin gene and species that were used for the phylogenetic relationship among the genes found in our samples and those previously described.
Lines 14 to 19 = Genetic data obtained in the BW1 sample that was used for checking the phylogenetic relationship among the genes found in our samples with those opsin genes that were previously described and are available at NCBI.
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File name = Forest_stream_blue_light.csv
day = day of the year
time = time in which the data was sampled
day_linear = Counting days for the analysis
Acara_bottom = Values measured at the Acara igarape at the bottom (in lux)
Acara_sup = Values measured at the Acara igarape at the surface (in lux)
Bolivia_bottom = Values measured at the Bolivia igarape at the bottom (in lux)
Bolivia_sup = Values measured at the Bolivia igarape at the surface (in lux)
Ipiranga_bottom = Values measured at the Ipiranga igarape at the bottom (in lux)
Ipiranga_sup = Values measured at the Ipiranga igarape at the surface (in lux)
Tinga_bottom = Values measured at the Tinga igarape at the bottom (in lux)
Tinga_sup = Values measured at the Tinga igarape at the surface (in lux)
Bolivia_new = Data for the Bolivia igarape used for the statistical analysis (Transmission of the blue light (%))
Tinga_new = Data for the Tinga igarape used for the statistical analysis (Transmission of the blue light (%))
Ipiranga_new = Data for the Ipiranga igarape used for the statistical analysis (Transmission of the blue light (%))
Acara_new = Data for the Acara igarape used for the statistical analysis (Transmission of the blue light (%))
'NA' cells represent the missing data for that particular variable due to technical issues with the equipment used to take the measurements.
Methods
These are the nucleotide sequences used for the phylogenetic relationship among the genes found in our samples with those genes that have been previously described, and the data used to measure the variation in the underwater lighting condition in black and clear water Amazon streams.