State of the Amphibia 2020: A Review of Five Years of Amphibian Research and Existing Resources

Womack, Molly C.; Steigerwald, Emma; Blackburn, David C.; Cannatella, David C.; Catenazzi, Alessandro; Che, Jing; Koo, Michelle S.; McGuire, Jimmy A.; Ron, Santiago R.; Spencer, Carol; Vredenburg, Vance T.; Tarvin, Rebecca D.

doi:10.1643/h2022005

Cited by 34 publications

(17 citation statements)

References 188 publications

(187 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…These results will serve as a base for future studies adopting a deep-learning approach to monitoring anuran reproduction. This method reduces the time required for data analysis and allows researchers to handle long-term recordings (Womack et al, 2022). Moreover, the existing databases are mostly of focal species recordings, which may perform poorly when applied to omnidirectional soundscape recordings (Kahl et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…This method reduces the time required for data analysis and allows researchers to handle long-term recordings from multiple sites in a standardized manner. One of the main challenges would be the limited availability of open acoustic databases, especially for Asian frogs (Womack et al, 2022). Moreover, the existing databases are mostly of focal species recordings, which may perform poorly when applied to omnidirectional soundscape recordings (Kahl et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Evaluation of Deep Learning-Based Monitoring of Frog Reproductive Phenology

Kimura,

Sota

2023

Ichthyology & Herpetology

View full text Add to dashboard Cite

To evaluate the utility of a deep-learning approach for monitoring amphibian reproduction, we examined the classification accuracy of a trained model and tested correlations between calling intensity and frog abundance. Field recording and count surveys were conducted at two sites in Kyoto City, Japan. A convolutional neural network (CNN) model was trained to classify the calls of five anuran species. The model achieved 91-100% precision and 75-98% recall per species, with relatively lower performance on less abundant species. Computational experiments investigating the effects of the number and seasonality of the training samples showed that models trained on larger datasets from broader recording seasons performed better. Calling activity was high when males were abundant (Pearson's r 5 0.45-0.66), although correlations between the calling activity and the number of pairs in amplexus were generally weaker. Our results suggest that deep learning is an effective tool for reconstructing the reproductive phenology of male anurans from field recordings. However, caution is required when applying to rare species and when inferring female reproductive activity.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Evaluation of Deep Learning-Based Monitoring of Frog Reproductive Phenology

Kimura,

Sota

2023

Ichthyology & Herpetology

View full text Add to dashboard Cite

show abstract

“…For example, bacteria present in amphibian and bat microbiomes can inhibit the growth of fungal pathogens that have caused severe population declines in both groups of vertebrates [3,5,23,24]. Amphibians nowadays are considered the most vulnerable group of vertebrates due to habitat reduction, introduction of invasive species, and the emergence of infectious diseases such as chytridiomycosis [3,[25][26][27]. This disease is caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) [28] and B. salamandrivorans (Bsal) [29], and it has been linked to population declines of more than 500 amphibian species worldwide [3].…”

Section: Introductionmentioning

confidence: 99%

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

Martínez-Ugalde,

Ávila-Akerberg,

González Martínez

et al. 2024

Microbial Genomics

View full text Add to dashboard Cite

Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.

show abstract

“…However, morphological and genetic divergence are not always tightly correlated, as evidenced by morphologically similar species and highly variable species, resulting in lumping or splitting of a morphospecies-based taxonomy when genetic data become available. Indeed, the rise of genomic-scale data has the potential to resolve many cryptic species complexes and to stimulate the identification of new species (Womack et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Deep Divergences Among Inconspicuously Colored Clades ofEpipedobatesPoison Frogs

Lopez-Hervas

Santos

Ron

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuous (cryptic) and considered non-aposematic.Epipedobatesis among the youngest genus-level clades of Dendrobatidae that includes both aposematic and cryptic species. Using mitochondrial and nuclear markers, we demonstrate deep genetic divergences among cryptic species ofEpipedobatesbut relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the cryptic lineages typically identified asE. boulengeriandE. espinosai, which reveals two putative new species, one in west-central Colombia (E.sp. 1) and the other in north-central Ecuador (E.aff.espinosai). We conclude thatE. darwinwallaceiis a junior subjective synonym ofE. espinosai. We also clarify the geographic distributions of crypticEpipedobatesspecies including the widespreadE. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of cryptic species. We conclude thatEpipedobatescontains eight known valid species, six of which are cryptic. A relaxed molecular clock analysis suggests that the most recent common ancestor ofEpipedobatesis ~11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador.

show abstract

State of the Amphibia 2020: A Review of Five Years of Amphibian Research and Existing Resources

Abstract: BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses.

Cited by 34 publications

References 188 publications

Evaluation of Deep Learning-Based Monitoring of Frog Reproductive Phenology

Evaluation of Deep Learning-Based Monitoring of Frog Reproductive Phenology

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

Deep Divergences Among Inconspicuously Colored Clades ofEpipedobatesPoison Frogs

Contact Info

Product

Resources

About