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 purifying selection, which may explain its
persistence despite hundreds of millions of years of fossoriality, but
also show evidence of relaxed constraint, suggesting reduced reliance on
canonical cone-mediated vision. The specific photoreceptor type expressing
LWS remains uncertain: rod phototransduction genes are largely intact,
whereas cone pathway genes display a mosaic pattern of losses. Further,
anatomical surveys across five families did not conclusively identify
cone-like cells, though organized retinal layers were observed even in
species with highly reduced eyes. The datasets in this submission include:
(i) alignments of phototransduction and opsin genes; (ii) histological
photographs from several caecilian species; and (iii) input, output, and
summary files from codeml selection analyses. Together, these resources
support further exploration of gene integrity, phototransduction pathways,
and the evolution of vision in fossorial vertebrates.