Amphibians are an ideal model 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 of five Neotropical diurnal frog groups, with a focus on three conspicuously colored and chemically defended (i.e., aposematic) clades: poison frogs (Dendrobatidae), Harlequin toads (Bufonidae:Atelopus), and pumpkin toadlets (Brachycephalidae:Brachycephalus). We found evidence of positive selection on 15 amino acid sites inLWS, SWS1, SWS2, andRH1opsin genes, of which one inLWShas been previously identified as important for spectral tuning in other vertebrates. Patterns of selection reveal that the evolution of diurnality was important in shaping the vision of focal frog groups; whether conspicuous coloration has played a role remains unclear, as no support was found but inferences may have been statistically limited by sample size. Furthermore, we provide evidence that theSWS2gene, normally expressed in rod cells in amphibians, 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 might coincide with the diurnal activity of dendrobatids and could have implications for opsin evolution in this clade. Our analyses show that studies of opsin diversification could expand our understanding of how adaptations for diel habits evolve and how visual tuning alters the sensory landscape of animals.
Background: Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and >1,000 described species, encompassing ~15% of all named frog species. The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among three recent phylogenomic studies utilizing 95, 389, and 2,214 nuclear loci, respectively. In this paper, we re-evaluate relationships within Terraranae using a novel genomic dataset for 16 ingroup species representing most terraranan families and subfamilies. Results: The preferred data matrix consisted of 2,665 nuclear loci from ultraconserved elements (UCEs), with a total of 743,419 aligned base pairs and 57% missing data. Concatenated likelihood analyses and coalescent-based species-tree analyses both recovered strong statistical support for the following relationships among terraranan families: (Brachycephalidae, (Eleutherodactylidae, (Craugastoridae + “Strabomantidae”))). Our placement of Brachycephalidae agrees with two previous phylogenomic studies but conflicts with another. Our results place Strabomantis (of the Strabomantidae) with (or within) Craugastor (Craugastoridae) rather than with other strabomantid genera, rendering Strabomantidae paraphyletic with respect to Craugastoridae. Conclusions: Our results suggest that Strabomantidae should be placed in the synonymy of the older Craugastoridae. Furthermore, our results suggest that Pristimantinae is paraphyletic with respect to Holoadeninae and should be subsumed into the older Holoadeninae. We also found that using matrices of UCE loci with less missing data (and concomitantly fewer loci) generally decreased support for most nodes on the tree. Overall, our results help resolve controversial relationships within one of the largest clades of frogs, with a dataset containing ~7 times more loci than previous studies focused on this clade.
The present work provides a logical account for translating caste concepts in social insects to an ontology-based data model, which can be used by researchers for describing and organizing entities belonging to non-human societies, as well as for the provision of evidential criteria for evaluating constitutive explanations of social entities. We establish the top-level category for the concept of caste and give examples on how to accommodate some subcategories (e.g. workers) in the ontology, following a domain granularity framework for the life sciences. We also provide accounts on current limitations in automated reasoning, current practices for caste conceptualization, and improvements needed to be addressed in future works.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.