CPD photolyase evolution supports amphibian UV-sensitivity hypothesis

The UV-sensitivity hypothesis for amphibian decline proposes that interspecific variation in cyclobutane pyrimidine dimer (CPD) photolyase activity determines species' UV sensitivity, which is linked to their natural history and population trends. Here, to shed light on the molecular basis of UV resistance variation, we investigated the evolutionary dynamics of CPD photolyases in amphibians focusing on regions and sites relevant to protein function. Our evolutionary analyses revealed that amino acids critical for CPD photolyase function are highly conserved and their codons have been evolving under purifying selection. Three tryptophan residues, critical for light-dependent repair and potentially for dark repair, are highly conserved in CPD photolyases across species. Nevertheless, we identified variations in functionally relevant CPD photolyase amino acids across amphibian clades, some of which are predicted to contract the active site and destabilize the protein structure. Caudata CPD photolyases contain functionally relevant variations likely linked to the high UV sensitivity of salamanders and newts. In Gymnophiona, we found relaxed purifying selection in CPD photolyase codons, as well as functionally relevant amino acid variations, likely reflecting the fossorial, dark-dwelling lifestyle of caecilians. Strikingly, most amphibian species with decreasing populations exhibit CPD photolyases with functionally relevant amino acid variations, and this pattern is even stronger for variations that disrupt protein structure. For example, two structurally disruptive, functionally relevant amino acid variations co-occur in CPD photolyases of species from the genera Bombina (Anura) and Ambystoma (Caudata), most of which exhibit declining populations. This study shows that species-specific differences in CPD photolyases underscore the UV-sensitivity hypothesis in amphibian ecology and conservation.