DOI: 10.5061/dryad.mgqnk98vx
title: Data from: Visual pigment evolution in Characiformes: The dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning

description: Vision represents an excellent model for studying adaptation, given the
 genotype-to-phenotype-map that has been characterized in a number of taxa.
 Fish possess a diverse range of visual sensitivities and adaptations to
 underwater light making them an excellent group to study visual system
 evolution. In particular, some speciose but understudied lineages can
 provide a unique opportunity to better understand aspects of visual system
 evolution such as opsin gene duplication and neofunctionalization. In this
 study, we showcase the visual system evolution of neotropical
 Characiformes and the spectral tuning mechanisms they exhibit to modulate
 their visual sensitivities. Such mechanisms are gene duplications and
 losses, gene conversion, opsin amino acid sequence and expression
 variation, and A1/A2-chromophore shifts. The Characiforms we studied
 utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1).
 However, the characiform’s entire opsin gene repertoire is a product of
 dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS,
 RH1). The LWS- and RH1-duplicates originated from a teleost specific
 whole-genome duplication as well as characiform-specific duplication
 events. Both LWS-opsins exhibit gene conversion and, through substitutions
 in key tuning sites, one of the LWS-paralogs has acquired spectral
 sensitivity to green light. These sequence changes suggest reversion and
 parallel evolution of key tuning sites. In addition, characiforms
 exhibited species-specific differences in opsin expression. Finally, we
 found interspecific and intraspecific variation in the use of
 A1/A2-chromophores correlating with the light environment. These multiple
 mechanisms may be a result of the highly diverse visual environments where
 Characiformes have evolved.
description: # Data from: Visual pigment evolution in Characiformes: The dynamic
 interplay of teleost whole-genome duplication, surviving opsins and
 spectral tuning
 [https://doi.org/10.5061/dryad.mgqnk98vx](https://doi.org/10.5061/dryad.mgqnk98vx) ## Description of the data and file structure This is a guide for understanding the files names and content.  Because some of these alignments were for PAML, many of them were trimmed at the end to have an alignment with equal length, no stop codons and no ambiguities in the sequences.  1. Teleost alignment of LWS opsin, nucleotide, in phy format 2. Teleost alignment of LWS opsin, amino acid, in phy format 3. Teleost alignment of RH1-RH2 opsin, amino acid, in phy format 4. Teleost alignment of LWS opsin, nucleotide, in phy format 5. Teleost alignment of SWS opsin, amino acid, in phy format 6. Teleost alignment of SWS opsin, nucleotide, in phy format 7. Concatenated alignment of Characins of 5 genes (mitochondrial/nuclear) 8. Opsin alignments, nucleotide, for PAML ancestral reconstruction analysis 9. Tree result of PAML ancestral reconstruction analysis (pdf) 10. Tree result of PAML ancestral reconstruction analysis (txt) ### Files and variables #### File: 2\_Teleosts\_LWS\_AAII.phy **Description:** Teleost alignment of LWS opsin, amino acid, in phy format #### File: 3\_Teleosts\_RH1\_RH2\_AA\_alignment.phy **Description:** Teleost alignment of RH1-RH2 opsin, amino acid, in phy format #### File: 1\_Teleost\_LWS\_nucl.phy **Description:** Teleost alignment of LWS opsin, nucleotide, in phy format #### File: 5\_Teleosts\_SWS\_AA.phy **Description:** Teleost alignment of SWS opsin, amino acid, in phy format #### File: 4\_Teleosts\_RH1\_RH2\_nucl\_alignment.phy **Description:** Teleost alignment of LWS opsin, nucleotide, in phy format #### File: 6\_Teleosts\_SWS\_nucl.phy **Description:** Teleost alignment of SWS opsin, nucleotide, in phy format #### File: 9\_Ancestral\_seq\_tree\_PAML.pdf **Description:** Tree result of PAML ancestral reconstruction analysis (pdf) #### File: 8\_Nucl\_LWS\_algmnt\_PAML.txt **Description:** Opsin alignments, nucleotide, for PAML ancestral reconstruction analysis #### File: 10\_PAML\_ancestral\_rec\_results.txt **Description:** Tree result of PAML ancestral reconstruction analysis (txt) **File: 7_FINAL_concatenated_characins.phy** **Description:** Concatenated alignment of Characins of 5 genes (mitochondrial/nuclear)