Diversity and molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs

John L Boyette; Rayna C Bell; Matthew K Fujita; Kate N Thomas; Jeffrey W Streicher; David J Gower; Ryan K Schott

doi:10.1093/molbev/msae090

Diversity and molecular evolution of non-visual opsin genes across environmental, developmental, and morphological adaptations in frogs

Mol Biol Evol. 2024 May 13:msae090. doi: 10.1093/molbev/msae090. Online ahead of print.

Authors

John L Boyette^{1

2

3

4}, Rayna C Bell^{3

4}, Matthew K Fujita⁵, Kate N Thomas^{5

6}, Jeffrey W Streicher⁶, David J Gower⁶, Ryan K Schott^{3

7}

Affiliations

¹ Department of Biological Sciences, The Pennsylvania State University, State College, Pennsylvania, USA.
² Department of Biology, Berry College, Rome, Georgia, USA.
³ Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC, USA.
⁴ Department of Herpetology, California Academy of Sciences, San Francisco, California, USA.
⁵ Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA.
⁶ Department of Life Sciences, Natural History Museum, London, UK.
⁷ Department of Biology & Centre for Vision Research, York University, Toronto, Ontario, CAN.

PMID: 38736374
DOI: 10.1093/molbev/msae090

Abstract

Non-visual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, non-visual opsins form photopigments involved in various non-visual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here we investigate the molecular evolution of non-visual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of non-visual opsins due to nocturnal ancestry and potential functional differences in non-visual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multi-tissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which non-visual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate non-visual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 non-visual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on non-visual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many non-visual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.

Keywords: Amphibia; Anura; eyes; selection; transcriptome; visual ecology.