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Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual 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 nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual 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. [ABSTRACT FROM AUTHOR]

New World mabuyine skinks are a diverse radiation of morphologically cryptic lizards with unique reproductive biologies. Recent studies examining population-level data (morphological, ecological, and genomic) have uncovered novel biodiversity and phenotypes, including the description of dozens of new species and insights into the evolution of their highly complex placental structures. Beyond the potential for this diverse group to serve as a model for the evolution of viviparity in lizards, much of the taxonomic diversity is concentrated in regions experiencing increasing environmental instability from climate and anthropogenic change. Consequently, a better understanding of genome structure and diversity will be an important tool in the adaptive management and conservation of this group. Skinks endemic to Caribbean islands are particularly vulnerable to global change with several species already considered likely extinct and several remaining species either endangered or threatened. Combining PacBio long-read sequencing, Hi-C, and RNAseq data, here we present the first genomic resources for this group by describing new chromosome-level reference genomes for the Puerto Rican Skink Spondylurus nitidus and the Culebra Skink S. culebrae. Results indicate two high quality genomes, both ∼1.4 Gb, assembled nearly telomere to telomere with complete mitochondrion assembly and annotation. [ABSTRACT FROM AUTHOR]

Species whose ranges encompass substantial environmental variation should experience heterogeneous selection, potentially resulting in local adaptation. Repeated covariation between phenotype and environment across ecologically similar species inhabiting similar environments provides strong evidence for adaptation. Lesser Antillean anoles present an excellent system in which to study repeated local adaptation because most species are widespread generalists occurring throughout environmentally heterogenous island landscapes. We leveraged this natural replication to test the hypothesis that intraspecific variation in phenotype (coloration and morphology) is consistently associated with environment across 9 species of bimaculatus series anoles. We measured dorsal coloration from 173 individuals from 6 species and 16 morphological traits from 883 individuals from 9 species, spanning their island ranges. We identified striking, but incomplete, parallelism in dorsal coloration associated with annual precipitation in our study species. By contrast, we observed significant patterns of morphological isolation-by-environment in only 2 species and no signal of parallel morphological evolution. Collectively, our results reveal strong divergent natural selection by environment on dorsal coloration but not morphology. [ABSTRACT FROM AUTHOR]

The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size using 179 micro X-ray computed tomography scans of 126 biphasic anuran species and tested for correlations with life stage, environmental transitions, adult habits and adult activity patterns. Across broad phylogenetic diversity, tadpole lenses are more spherical than those of adults. Biphasic species with aquatic larvae and terrestrial adults typically undergo ontogenetic changes in lens shape, whereas species that remain aquatic as adults tend to retain more spherical lenses after metamorphosis. Further, adult lens shape is influenced by adult habit; notably, fossorial adults tend to retain spherical lenses following metamorphosis. Finally, lens size relative to eye size is smaller in aquatic and semiaquatic species than other adult ecologies. Our study demonstrates how ecology shapes visual systems, and the power of non-invasive imaging of museum specimens for studying sensory evolution. [ABSTRACT FROM AUTHOR]

The spectral characteristics of vertebrate ocular lenses affect the image of the world that is projected onto the retina, and thus help shape diverse visual capabilities. Here, we tested whether amphibian lens transmission is driven by adaptation to diurnal activity (bright light) and/or scansorial habits (complex visual environments).Spectral transmission through the lenses of 79 species of frogs and six species of salamanders was measured, and data for 29 additional frog species compiled from published literature. Phylogenetic comparative methods were used to test ecological explanations of variation in lens transmission and to test for selection across traits.Lenses of diurnal (day‐active) and scansorial (climbing) frogs transmitted significantly less shortwave light than those of non‐diurnal or non‐scansorial amphibians, and evolutionary modelling suggested that these differences have resulted from differential selection.The presence of shortwave‐transparent lenses was common among the sampled amphibians, which implies that many are sensitive to shortwave light to some degree even in the absence of visual pigments maximally sensitive in the UV. This suggests that shortwave light, including UV, could play an important role in amphibian behaviour and ecology.Shortwave‐absorbing lens pigments likely provide higher visual acuity to diurnally active frogs of multiple ecologies and to nocturnally active scansorial frogs. This new mechanistic understanding of amphibian visual systems suggests that shortwave‐filtering lenses are adaptive not only in daylight conditions but also in those scotopic conditions where high acuity is advantageous. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The fungal pathogen Batrachochytrium dendrobatidis ( Bd) infects hundreds of amphibian species and is implicated in global amphibian declines. Bd is comprised of several lineages that differ in pathogenicity, thus, identifying which Bd strains are present in a given amphibian community is essential for understanding host-pathogen dynamics. The presence of Bd has been confirmed in Central Africa, yet vast expanses of this region have not yet been surveyed for Bd prevalence, and the genetic diversity of Bd is largely unknown in this part of the world. Using retrospective surveys of museum specimens and contemporary field surveys, we estimated the prevalence of Bd in Central African island and continental amphibian assemblages, and genotyped strains of Bd present in each community. Our sampling of museum specimens included just a few individuals collected in the Gulf of Guinea archipelago prior to 1998, yet one of these individuals was Bd-positive indicating that the pathogen has been on Bioko Island since 1966. We detected Bd across all subsequent sample years in our study and found modest support for a relationship between host life history and Bd prevalence, a positive relationship between prevalence and host community species richness, and no significant relationship between elevation and prevalence. The Global Panzootic Lineage ( Bd GPL) was present in all the island and continental amphibian communities we surveyed. Our results are consistent with a long-term and widespread distribution of Bd in amphibian communities of Gabon and the Gulf of Guinea archipelago. [ABSTRACT FROM AUTHOR]

The article examines the presence of Ranavirus in anurans from two national parks in Gabon, revealing no evidence of the virus in the sampled amphibian populations. Topics discussed include the methods used for detecting Ranavirus Deoxyribonucleic Acid (DNA), the challenges in assessing virus prevalence due to potential limitations in the detection techniques, and the implications for future research and surveillance in Africa.

The article offers information on frog specie Hyperolius adspersus, and mentions about predation of a Leptopelis brevirostris tree frog by a wandering spider (Ctenidae), both in Cameroon.

Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size using 179 micro X-ray computed tomography scans of 126 biphasic anuran species and tested for correlations with life stage, environmental transitions, adult habits and adult activity patterns. Across broad phylogenetic diversity, tadpole lenses are more spherical than those of adults. Biphasic species with aquatic larvae and terrestrial adults typically undergo ontogenetic changes in lens shape, whereas species that remain aquatic as adults tend to retain more spherical lenses after metamorphosis. Further, adult lens shape is influenced by adult habit; notably, fossorial adults tend to retain spherical lenses following metamorphosis. Finally, lens size relative to eye size is smaller in aquatic and semiaquatic species than other adult ecologies. Our study demonstrates how ecology shapes visual systems, and the power of non-invasive imaging of museum specimens for studying sensory evolution.