Supplementary data for: Selection on visual opsin genes in diurnal Neotropical frogs and loss of the SWS2 opsin in poison frogs

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.两栖动物是研究视觉系统演化的理想类群，其兼具双相（水生与陆生）生活史且生态多样性丰富，因此暴露于广泛的视觉环境中。本研究对新热带区无尾两栖类的视觉视蛋白基因的选择信号进行了评估，重点关注三个因兼具醒目体色与化学防御（即警戒色（aposematism））而闻名的日行支系：箭毒蛙科（Dendrobatidae）毒蛙、蟾蜍科（Bufonidae）彩蟾属（Atelopus）花斑蟾蜍，以及短头蟾科（Brachycephalidae）短头蟾属（Brachycephalus）南瓜小蟾。我们在长波长敏感视蛋白（LWS）、短波敏感视蛋白1（SWS1）、短波敏感视蛋白2（SWS2）与视紫红质1（RH1）的44个氨基酸位点中检测到正选择信号，其中LWS上的1个位点与RH1上的2个位点此前已在其他脊椎动物中被鉴定为光谱调谐位点。鉴于无尾两栖类多为夜行性，本次选择模式分析揭示了新的可能对蛙类光谱调谐至关重要的位点，这或许与它们适应日行性生活及基于体色的种内交流相关。此外，我们发现原本在蛙类与部分蝾螈的视杆细胞中表达的SWS2基因，很可能在箭毒蛙科的祖先类群中发生了丢失，这表明在低光照条件下，箭毒蛙科物种的波长辨别能力相较于其他蛙类更弱。该基因丢失事件可能伴随箭毒蛙科日行性活动的起源，且可能对其化学生态、生物多样性及行为产生影响。我们的分析表明，对研究不足类群的视蛋白多样性进行评估，可拓展我们对感官系统演化在生态适应中所扮演角色的认知。