Biology subjects

Schott, R. K.

Publications and source records attributed to Schott, R. K..

8 recordsLinked to original sources

bioRxiv2025

Eyes wide open: Frogs with reduction of auditory communication ability show lower eye, but higher corneal, investment

Vocal communication is the primary mechanism of mate attraction in frogs, but some species have lost the auditory structures needed to hear airborne sounds, raising the question of how they communicate in their absence. We hypothesized that frog species with auditory system reductions have compensated through enhanced visual ability, including through enlarged eyes. To test this trade-off hypothesis, we estimated relative eye and corneal investment across 264 species and tested for correlations with auditory reduction. Contrary to our expectations, we found that species with auditory reductions had smaller eye size and lower eye investment. Instead, we found that non-fossorial species with auditory reductions had significantly greater corneal investment, after controlling for habitat-based variation. Enlarged corneas enhance light sensitivity but are expected to have a lower metabolic cost than larger eyes. Relatively larger corneas may, in combination with other changes, allow frogs with auditory reductions to rely more on vision for communication, while at the same time minimizing energetic costs in small animals that are already metabolically constrained. Our findings suggest that the visual system plays an adaptive role in response to the reduction of auditory communication and highlights the condition of sensory systems as an important factor shaping frog evolution.

evolutionary biology↗

bioRxiv2025

Evolutionary and ontogenetic shifts from aquatic to terrestrial light environments in frogs provide new insights into the vertebrate phototransduction cascade

Evolutionary studies of vertebrate vision have mainly focused on the light-sensitive opsins neglecting the downstream phototransduction cascade. Here, we investigate patterns of gene loss and expression across jawed vertebrates, providing clarity on the evolution of phototransduction. We next focus on an ecologically diverse sample of frogs represented by whole-eye transcriptomes and genomes from 113 species. We tested the hypothesis that phototransduction genes were lost in the common ancestor of frogs due to nocturnality and that functional differences in phototransduction are driven by variation in habitat, activity pattern, and life history. Across frogs, we recovered 38 of 39 vertebrate phototransduction genes, with all but one of these (GUCA1B2) consistently expressed in frog eyes. This contrasts the high level of gene loss found in other ancestrally nocturnal tetrapods (e.g., mammals and snakes) and is more similar to ray-finned fishes. More than other ecological traits, we found that loss of the larval aquatic life stage (direct development) and inhabiting aquatic and semiaquatic habitats as adults were most strongly associated with shifts in selective strength, with widespread signals of both positive and relaxed selection across frog phototransduction genes. These findings suggest that phototransduction is under different functional constraints in aquatic versus terrestrial light environments and that shifts in the use of these environments have played a strong role in frog visual evolution. Collectively, these results reinforce that frogs are of particular interest for vertebrate visual evolution because they span both an evolutionary and an ontogenetic transition from vision underwater to vision on land.

evolutionary biology↗

bioRxiv2022

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

Non-visual opsins are transmembrane proteins expressed in the eyes, skin, and brain of many animals. When paired with a light-sensitive chromophore, non-visual opsins form photopigment systems involved in various non-visual, light-detection functions, including circadian rhythm regulation, light-seeking behavior, and detection of seasonality. Previous research has primarily explored the diversity and function of non-visual opsins in model organisms, with few studies investigating their molecular evolution in non-model species. Here we explored molecular evolution of non-visual opsin genes in anuran amphibians (frogs and toads). With diverse lifestyles ranging from fossorial to aquatic, anurans inhabit a diverse array of light environments, which makes them a compelling system for studying the evolution of light detection mechanisms. Using whole-eye transcriptomes from 79 anuran species, as well as genomes and multi-tissue transcriptomes from an additional 15 species, we 1) identify which non-visual opsin genes are expressed in the eyes of anurans; 2) compare selective constraint ({omega}, or dN/dS) among non-visual opsin genes; and 3) test for potential adaptive evolution by comparing selection between discrete ecological classes in anurans (e.g. diurnal versus non-diurnal). We consistently recovered 14 non-visual opsin genes from anuran eye transcriptomes, compared to 18 genes that we recovered genome wide, and detected positive selection in a subset of these genes. We also found variation in selective constraint between discrete ecological and life-history classes, which may reflect functional adaptation in non-visual opsin genes. Although non-visual opsins remain poorly understood, these findings provide insight into their molecular evolution and set the stage for future research on their potential function across taxa with diverse environmental, developmental, and morphological adaptations.

evolutionary biology↗

bioRxiv2021

Evolutionary analyses of visual opsin genes in anurans reveals diversity and positive selection suggestive of functional adaptation to distinct light environments

Among major vertebrate groups, anurans (frogs and toads) are understudied with regards to their visual systems and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset. We found that anurans consistently express four visual opsin genes (RH1, LWS, SWS1, and SWS2, but not RH2) even though reported photoreceptor complements vary widely among species. We found the first evidence of visual opsin duplication in an amphibian with the duplication of the LWS gene in the African bullfrog, which had distinct LWS copies on the sex chromosomes. The proteins encoded by these genes showed considerable sequence variation among species, including at sites known to shift the spectral sensitivity of visual pigments in other vertebrates and thus mediate dim-light and color vision. Using molecular evolutionary analyses of selection (dN/dS) we found significant evidence for positive selection at a subset of sites in the dim-light rod opsin gene RH1 and the long wavelength sensitive cone opsin gene LWS. The function of sites inferred to be under positive selection are largely unknown, but a few are likely to affect spectral sensitivity and other visual pigment functions based on proximity to previously identified sites in other vertebrates. The observed variation cannot fully be explained by evolutionary relationships among species alone. Taken together, our results suggest that other ecological factors, such as habitat and life history, as well as behaviour, may be driving changes to anuran visual systems.

evolutionary biology↗

bioRxiv2021

Diversity and evolution of amphibian pupil shapes

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes, often among animals that occupy optically similar environments, are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape and the orientation of the constricted pupil across adults of 1293 amphibian species, 72 families, and 3 orders, and additionally for larval life stages for all families of frogs and salamanders with a biphasic ontogeny. Pupil shape is exceptionally diverse in amphibians with evolutionary transitions throughout the amphibian tree of life. For amphibians with a biphasic life history, we found that pupils change in many species that occupy distinct habitats before and after metamorphosis. Finally, we found that non-elongated (round or diamond) constricted pupils were correlated with species inhabiting consistently dim light environments (burrowing and aquatic species) and that elongated pupils (vertical and horizontal) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical, and ecological mechanisms underlying the evolution of pupil shape.

evolutionary biology↗

bioRxiv2021

Genomic and Spectral Visual Adaptation in Southern Leopard Frogs during the Ontogenetic Transition from Aquatic to Terrestrial Light Environments

Many animals have complex life cycles where larval and adult forms have distinct ecologies and habitats that impose different demands on their sensory systems. While the adaptive decoupling hypothesis predicts reduced genetic correlations between life stages, how sensory systems adapt across life stages at the molecular level is not well understood. Frogs are a compelling system to study this question in because most species rely on vision as both aquatic tadpoles and terrestrial adults, but these habitats present vastly different light environments. Here we used whole eye transcriptome sequencing to investigate differential expression between aquatic tadpoles and terrestrial juveniles of the southern leopard frog (Lithobates sphenocephalus). Because visual physiology changes with light levels, we also tested how constant light or dark exposure affected gene expression. We found 42% of genes were differentially expressed in the eyes of tadpoles versus juveniles, versus 5% for light/dark exposure. Analyses targeting a curated set of visual genes revealed significant differential expression between life stages in genes that control aspects of visual function and development, including spectral sensitivity and lens composition. Light/dark exposure had a significant effect on a smaller set of visual genes. Finally, microspectrophotometry of photoreceptors confirmed shifts in spectral sensitivity predicted by the expression results, consistent with adaptation to distinct light environments. Overall, we identified extensive expression-level differences in the eyes of tadpole and juvenile frogs related to observed morphological and physiological changes through metamorphosis, and corresponding adaptive shifts to optimize vision in aquatic versus terrestrial environments.

genomics↗

bioRxiv2019

The tuatara genome: insights into vertebrate evolutionfrom the sole survivor of an ancient reptilian order

The tuatara (Sphenodon punctatus), the only living member of the archaic reptilian order Rhynchocephalia (Sphenodontia) once widespread across Gondwana, is an iconic and enigmatic terrestrial vertebrate endemic to New Zealand. A key link to the now extinct stem reptiles from which dinosaurs, modern reptiles, birds and mammals evolved, the tuatara provides exclusive insights into the ancestral amniotes. The tuatara genome, at [~]5 Gbp, is among the largest vertebrate genomes assembled. Analysis of this genome and comparisons to other vertebrates reinforces the uniqueness of the tuatara. Phylogenetic analyses indicate tuatara diverged from the snakes and lizards [~]250 MYA. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Genome sequence analysis identifies expansions of protein, non-protein-coding RNA families, and repeat elements, the latter of which show an extraordinary amalgam of reptilian and mammalian features. Sequencing of this genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. It also provides important insights into both the technical challenges and the cultural obligations associated with genome sequencing.

genomics↗

bioRxiv2017

Cone-like rhodopsin expressed in the all cone retina of the colubrid pine snake as a potential adaptation to diurnality

Colubridae is the largest and most diverse family of snakes, with visual systems that reflect this diversity, encompassing a variety of retinal photoreceptor organizations. The transmutation theory proposed by Walls postulates that photoreceptors could evolutionarily transition between cell types in squamates, but few studies have tested this theory. Recently, evidence for transmutation and rod-like machinery in an all cone retina has been identified in a diurnal garter snake (Thamnophis), and it appears that the rhodopsin gene at least may be widespread among colubrid snakes. However, functional evidence supporting transmutation beyond the existence of the rhodopsin gene remains rare. We examined the all cone retina of another diurnal colubrid, Pituophis melanoleucus, distantly related to Thamnophis. We found that P. melanoleucus expresses two cone opsins (SWS1, LWS) and rhodopsin (RH1) within the eye. Immunohistochemistry localized rhodopsin to the outer segment of photoreceptors in the all-cone retina of the snake and all opsin genes produced functional visual pigments when expressed in vitro. Consistent with other studies, we found that P. melanoleucus rhodopsin is extremely blue-shifted. Surprisingly, P. melanoleucus rhodopsin reacted with hydroxylamine, a typical cone opsin characteristic. These results support the idea that the rhodopsin-containing photoreceptors of P. melanoleucus are the products of evolutionary transmutation from rod ancestors, and suggests that this phenomenon may be widespread in colubrid snakes. We hypothesize that transmutation may be an adaptation for diurnal, brighter-light vision, which could result in increased spectral sensitivity and chromatic discrimination with the potential for colour vision.\n\nSummary StatementThe all cone retina of the colubrid snake, Pituophis melanoleucus contains a blue-shifted rhodopsin with cone opsin-like properties, which may have been adaptive in diurnal snakes.

evolutionary biology↗