Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments.

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.

Expression patterns of melanin-related genes are linked to crypsis and conspicuousness in a pumpkin toadlet.

Colour signals play pivotal roles in different communication systems, and the evolution of these characters has been associated with behavioural ecology, integumentary production processes and perceptual mechanisms of the species involved. Here, we present the first insight into the molecular and histological basis of skin colour polymorphism within a miniaturized species of pumpkin toadlet, potentially representing the lowest size threshold for colour polytypism in tetrapods. Brachycephalus actaeus exhibits a coloration ranging from cryptic green to conspicuous orange skin, and our findings suggest that colour morphs differ in their capability to be detected by potential predators. We also found that the distribution and abundance of chromatophores are variable in the different colour morphs. The expression pattern of coloration related genes was predominantly associated with melanin synthesis (including dct, edn1, mlana, oca2, pmel, slc24a5, tyrp1 and wnt9a). Up-regulation of melanin genes in grey, green and brown skin was associated with higher melanophore abundance than in orange skin, where xanthophores predominate. Our findings provide a significant foundation for comparing and understanding the diverse pathways that contribute to the evolution of pigment production in the skin of amphibians.

Multiple contact zones and karyotypic evolution in a neotropical frog species complex.

Previous studies of DNA sequence and karyotypic data have revealed high genetic diversity in the Physalaemus cuvieri - Physalaemus ephippifer species complex-a group of small leptodactylid frogs in South America. To date, seven major genetic lineages have been recognized in this group, with species delimitation tests supporting four to seven of them as valid species. Among these, only P. ephippifer shows heteromorphic sex chromosomes, but the implications of cytogenetic divergence for the evolution of this group are unknown. We analyzed karyotypic, mitochondrial DNA, and 3RAD genomic data to characterize a putative contact zone between P. ephippifer and P. cuvieri Lineage 1, finding evidence for admixture and karyotypic evolution. We also describe preliminary evidence for admixture between two other members of this species complex-Lineage 1 and Lineage 3 of P. cuvieri. Our study sheds new light on evolutionary relationships in the P. cuvieri - P. ephippifer species complex, suggesting an important role of karyotypic divergence in its evolutionary history and underscoring the importance of hybridization as a mechanism of sex chromosome evolution in amphibians.

Host-associated helminth diversity and microbiome composition contribute to anti-pathogen defences in tropical frogs impacted by forest fragmentation.

Habitat fragmentation can negatively impact wildlife populations by simplification of ecological interactions, but little is known about how these impacts extend to host-associated symbiotic communities. The symbiotic communities of amphibians play important roles in anti-pathogen defences, particularly against the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). In this study, we analyse the role of macroparasitic helminth communities in concert with microbial communities in defending the host against Bd infection within the context of forest fragmentation. We found that skin microbial and helminth communities are disrupted at fragmented habitats, while gut microbiomes appear more resilient to environmental change. We also detected potential protective roles of helminth diversity and anti-pathogen microbial function in limiting Bd infection. Microbial network analysis revealed strong patterns of structure in both skin and gut communities, with helminths playing central roles in these networks. We reveal consistent roles of microbial and helminth diversity in driving host-pathogen interactions and the potential implications of fragmentation on host fitness.

From genes to ecosystems: a synthesis of amphibian biodiversity research in Brazil / De genes a ecossistemas: uma síntese da pesquisa em biodiversidade de anfíbios no Brasil

Abstract Here, we summarize examples of significant advances in amphibian research supported by the São Paulo Research Foundation (FAPESP), focusing on recent discoveries in the fields of community ecology, habitat change, infection diseases, and multipurpose DNA sequencing. We demonstrated that FAPESP has been fundamental not only by directly funding research projects and scholarships, but also through its science training policy, fostering international collaborations with world-class research institutions, improving and consolidating new lines of research that often depended on a synergetic combination of different knowledge and complex tools. We emphasized that future studies will continue to focus on basic questions, such as description of new species, as well as taxonomic and systematic corrections. Furthermore, we also expect that there will be a strong integration among different disciplines using novel bioinformatics tools and modeling approaches, such as machine learning. These new approaches will be critical to further develop our understanding of foundational questions of amphibian life-history trait variation, disease transmission, community assembly, biogeography, and population forecasts under different global change scenarios such as agricultural expansion, agrochemical use, habitat loss, and climate change.

Resumo No presente estudo apresentamos exemplos de avanços significativos nas pesquisas com anfíbios financiadas pela Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), focando em descobertas recentes nos campos de ecologia de comunidades, modificação do habitat, doenças infecciosas e o sequenciamento de DNA com múltiplos propósitos. Demonstramos que a FAPESP tem sido fundamental não somente pelo financiamento direto de projetos de pesquisa e bolsas de estudo, mas também através de sua política de formação científica, fomentando colaborações internacionais com instituições de pesquisa de excelência mundial, melhorando e consolidando novas linhas de pesquisa que frequentemente dependem da combinação sinérgica entre diferentes linhas de conhecimento e ferramentas complexas. Enfatizamos que futuros estudos continuem com foco em questões básicas, como a descrição de novas espécies, bem como correções taxonômicas e sistemáticas. Além disso, esperamos uma forte integração entre diferentes disciplinas usando novas ferramentas de bioinformática e abordagens de modelagem, como o aprendizado de máquina. Essas novas abordagens serão críticas para desenvolver ainda mais nossa compreensão a respeito de questões fundamentais sobre as características da história de vida dos anfíbios, transmissão de doenças, estrutura de comunidades, biogeografia e previsões populacionais em diferentes cenários de mudanças globais, como a expansão da agricultura, uso de agrotóxicos, perda de habitat e mudanças climáticas.

Reproductive activity and vocalizations of Leptodactylus labyrinthicus (Anura: Leptodactylidae) in southeastern Brazil

Durante os meses de junho de 2001 a fevereiro de 2003 foram estudados os tipos de vocalizações e a atividade reprodutiva de duas populações de Leptodactylus labyrinthicus no Estado de São Paulo. As observações iniciaram-se antes do ocaso e terminaram por volta de 23:00 h. Ocasionalmente, indivíduos foram monitorados durante toda a madrugada. Dados sobre período reprodutivo, sítios de canto, comprimento rostro-cloacal dos adultos (CRC), sítios de desova e período de desova foram coletados. Leptodactylus labyrinthicus apresentou padrão reprodutivo prolongado associado ao período de chuvas na região. Os machos foram encontrados vocalizando às margens de corpos d'água temporários ou permanentes, começaram suas atividades de vocalização ao entardecer e cessaram entre 23:00 e 24:00 h. Durante o pico da estação de vocalização (dezembro a janeiro) a atividade de vocalização cessou por volta de 04:00 e 05:00 h. Foram gravados três tipos de vocalizações com fins reprodutivos: canto de anúncio, canto territorial e canto de corte. O canto de anúncio foi a vocalização mais comumente emitida. Não foi observado dimorfismo sexual quanto ao CRC. No entanto, machos de uma das populações apresentaram CRC significantemente maior do que o de machos da outra população estudada. Provavelmente esta diferença deve-se a atividade de caça à espécie realizada em uma das áreas e os machos maiores poderiam estar sendo exterminados da população. As desovas foram encontradas às margens de corpos d'água temporários, protegidas por vegetação, durante os meses de outubro e novembro de 2001/2002. Nas desovas o número de óvulos fertilizados correspondeu a aproximadamente 6,5% do total de óvulos. Os óvulos não fertilizados possivelmente são usados pelos girinos como fonte de alimento. O diâmetro médio dos ninhos de espuma foi de 25,5 cm e a altura média de 11,4 cm.

Recognition and distribution of Leptodactylus mystaceus (Anura; Leptodactylidae) in the State of São Paulo, Southeastern Brazil

Leptodactylus mystaceus, a widespread species over South America, is diagnosed based on specimens from the State of São Paulo, its southernmost geographic distribution limit. Here we present the first record of this species for Southeastern Brazil, extending its distribution for approximately 1,300 km to the southeast. We also include a description of its advertisement call, natural history data, photograph in life and morphological illustrations that make easier the identification of the species.

Leptodactylus mystaceus, uma espécie com ampla distribuição geográfica pela América do Sul, é diagnosticada com base em exemplares do Estado de São Paulo, seu limite meridional de distribuição geográfica. Apresentamos aqui o primeiro registro da espécie para o Sudeste do Brasil, ampliando sua distribuição conhecida em cerca de 1.300 km ao sudeste. Também incluímos a descrição da vocalização de anúncio, informações sobre história natural, fotografia em vida e desenhos de caracteres morfológicos que auxiliam na identificação desta espécie.