Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality

Vision evolves in response to species’ light environments and ecological needs. The transition to fossoriality may relax constraints on vision, leading to reduced visual capabilities. Caecilians (Gymnophiona)—specialized fossorial amphibians—possess reduced eyes covered by skin or bone. These traits, together with the assumption of a single photoreceptor type expressing one opsin gene, have long been interpreted as evidence of limited vision, including an inability to focus or perceive color. Here we provide genomic, transcriptomic, and anatomical data that challenge some of these assumptions. We identified the long-wavelength-sensitive (LWS) opsin gene in 13 caecilian species spanning 8 of 10 recognized families, with alignments showing no frame-shift mutations or premature stop codons, consistent with maintained functionality. Molecular evidence further demonstrates that LWS is transcribed in the eye of Caecilia orientalis. Selection analyses indicate that LWS is broadly under purifyi..., Morphology and search for cone photoreceptors
Histology: The examined sections are archival material accessioned in the MVZ that were originally prepared by MHW in the 1980s. Details on sample preparation, staining, and storage are provided in Supplementary Methods section 2.2.1. The file is also accompaning this submission. Sampling was opportunistic, representing all species with available histological sections suitable for visualizing eye morphology. More information about these species and accession information can be found in Supplementary Table 2. 
Photomicrography: Eyes were observed with a Laxco microscope, where we examined sections with intact photoreceptors and retina. Photographs were taken at standard low, medium, and high magnifications using a Laxco SeBaCam5C digital microscope camera, and rendered using SeBaView software v3.7 (Laxco, Inc.). A stage micrometer was used for measurements and to calibrate scale bars. A total of 282 photomicrographs of retinae representi..., , # Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality

[https://doi.org/10.5061/dryad.h18931zxf](https://doi.org/10.5061/dryad.h18931zxf)

## Description of the data and file structure

The dataset deposited here contains the raw data and control files necessary to replicate the analyses presented in the submission titled: Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality. Additionally, we have included the output files, log files, and summary results from all analyses for reference.

The raw data includes *LWS* and *RH1* sequences from caecilian species, obtained through genome mining from NCBI and public repositories (N=4). Additionally, we present *LWS* sequences obtained via PCR amplification (568 bp, N=11) and transcriptome sequencing of the eye from one caecili...,