DOI: 10.5061/dryad.zw3r2289j
title: Supplementary data for: Selection on visual opsin genes in diurnal Neotropical frogs and loss of the SWS2 opsin in poison frogs

description: Amphibians are ideal for studying visual system evolution because their
 biphasic (aquatic and terrestrial) life history and ecological diversity
 expose them to a broad range of visual conditions. Here we evaluate
 signatures of selection on visual opsin genes across Neotropical anurans
 and focus on three diurnal clades that are well-known for the concurrence
 of conspicuous colors and chemical defense (i.e., aposematism): poison
 frogs (Dendrobatidae), Harlequin toads (Bufonidae: Atelopus), and pumpkin
 toadlets (Brachycephalidae: Brachycephalus). We found evidence of positive
 selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes,
 of which one in LWS and two in RH1 have been previously identified as
 spectral tuning sites in other vertebrates. Given that anurans have mostly
 nocturnal habits, the patterns of selection revealed new sites that might
 be important in spectral tuning for frogs, potentially for adaptation to
 diurnal habits and for color-based intraspecific communication.
 Furthermore, we provide evidence that SWS2, normally expressed in rod
 cells in frogs and some salamanders, has likely been lost in the ancestor
 of Dendrobatidae, suggesting that under low-light levels, dendrobatids
 have inferior wavelength discrimination compared to other frogs. This loss
 might follow the origin of diurnal activity in dendrobatids and could have
 implications for their chemical ecology, biodiversity, and behavior. Our
 analyses show that assessments of opsin diversification in understudied
 groups could expand our understanding of the role of sensory system
 evolution in ecological adaptation.
description: Please see the accompanying paper (Wan et al. 2023) for descriptions of the methods and analyses used to produce these data. Briefly, we obtained sequences of opsin genes from amphibians through RNAseq, public databases, and target-enrichment sequencing. We verified the gene identity of each sequence by estimating gene trees (Data S3). These data suggested that the <em>SWS2</em> gene was missing from dendrobatid poison frogs, so we wrote a set of scripts to verify that blast fails to identify an <em>SWS2</em> ortholog in <em>Oophaga</em> <em>pumilio</em> (Data S4). Then, we demonstrate that a short region upstream of <em>LWS</em> is present in <em>Oophaga pumilio</em>, even though the <em>SWS2</em> gene appears to be absent (Data S2). Finally, we used CODEML and four types of site-based selection analyses from HyPhy version 2.5.14, on our frog opsin sequences: FEL, which estimates the rate of synonymous (dS) and non-synonymous (dN) substitutions per site with maximum likelihood and compares them using likelihood ratio tests; MEME, a mixed-effects maximum likelihood approach, to test for episodic or diversifying selection; contrast-FEL, tests for differences in selective pressures at individual sites among clades and groups of branches; and FUBAR, tests for nonsynonymous (dN) and synonymous (dS) substitution rates on a per-site basis using a Bayesian approach (Data S1).