The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti- predator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to "leap" to the next level.

Calling to the collective: contact calling rates within groups of disc-winged bats do not vary by kinship or association.

Many group-living animals coordinate social behaviours using contact calls, which can be produced for all group members or targeted at specific individuals. In the disc-winged bat, Thyroptera tricolor, group members use 'inquiry' and 'response' calls to coordinate daily movements into new roosts (furled leaves). Rates of both calls show consistent among-individual variation, but causes of within-individual variation remain unknown. Here, we tested whether disc-winged bats produce more contact calls towards group members with higher kinship or association. In 446 experimental trials, we recorded 139 random within-group pairs of one flying bat (producing inquiry calls for roost searching) and one roosting bat (producing response calls for roost advertising). Using generalized linear mixed-effect models (GLMM), we assessed how response and inquiry calling rates varied by sender, receiver, genetic kinship and co-roosting association rate. Calling rates varied consistently across senders but not by receiver. Response calling was influenced by inquiry calling rates, but neither calling rate was higher when the interacting pair had higher kinship or association. Rather than dyadic calling rates indicating within-group relationships, our findings are consistent with the hypothesis that bats produce contact calls to maintain contact with any or all individuals within a group while collectively searching for a new roost site. This article is part of the theme issue 'The power of sound: unravelling how acoustic communication shapes group dynamics'.

Visual environment of rearing sites affects larval response to perceived risk in poison frogs.

Turbidity challenges the visual performance of aquatic animals. Here, we use the natural diversity of ephemeral rearing sites occupied by tadpoles of two poison frog species to explore the relationship between environments with limited visibility and individual response to perceived risk. To compare how species with diverse natural histories respond to risk after developing in a range of photic environments, we sampled wild tadpoles of (1) Dendrobates tinctorius, a rearing-site generalist with facultatively cannibalistic tadpoles and (2) Oophaga pumilio, a small-pool specialist dependent on maternal food-provisioning. Using experimental arenas, we measured tadpole activity and space use first on a black and white background, and then on either black or white backgrounds where tadpoles were exposed to potentially predatory visual stimuli. The effects of rearing environment on D. tinctorius tadpoles were clear: tadpoles from darker pools were less active than tadpoles from brighter pools and did not respond to the visual stimuli, whereas tadpoles from brighter pools swam more when paired with conspecifics versus predatory insect larvae, suggesting that tadpoles can visually discriminate between predators. For O. pumilio, tadpoles were more active on experimental backgrounds that more closely matched the luminosity of their rearing sites, but their responses to the two visual stimuli did not differ. Larval specialisation associated with species-specific microhabitats may underlie the observed responses to visual stimuli. Our findings demonstrate that light availability in wild larval rearing conditions influences risk perception in novel contexts, and provides insight into how visually guided animals may respond to sudden environmental disturbances.

What Amphibians Can Teach Us About the Evolution of Parental Care.

Parenting is considered a key evolutionary innovation that contributed to the diversification and expansion of vertebrates. However, we know little about how such diversity evolved. Amphibians are an ideal group in which to identify the ecological factors that have facilitated or constrained the evolution of different forms of parental care. Among, but also within, the three amphibian orders-Anura, Caudata, and Gymnophiona-there is a high level of variation in habitat use, fertilization mode, mating systems, and parental sex roles. Recent work using broad phylogenetic, experimental, and physiological approaches has helped to uncover the factors that have selected for the evolution of care and transitions between different forms of parenting. Here, we highlight the exceptional diversity of amphibian parental care, emphasize the unique opportunities this group offers for addressing key questions about the evolution of parenting, and give insights into promising novel directions of research.

Correction: Integrating tropical research into biology education is urgently needed.

[This corrects the article DOI: 10.1371/journal.pbio.3001674.].

Meta-analysis of tadpole taste tests: consumption of anuran prey across development and predator strategies.

The risk of predation and the costs and benefits of diverse anti-predator strategies can shift across the life stages of an organism. Yet, empirical examples of ontogenetic switches in defense mechanisms are scarce. Anurans represent an alleged exception; previous meta-analytic work suggests that unpalatability of developing anurans is "rare", whereas adult anurans in many lineages are well defended by toxic and/or unpalatable skin secretions. Here, we revisit the question of the unpalatability of anuran young in a meta-analysis of the relative proportion of prey consumed within 922 predation tests, including 135 anuran species. We tested the hypotheses that a predator's propensity to consume anuran young depends on (1) prey family, (2) predator manipulation strategy, and (3) prey ontogenetic stage. We used a binomial mixed model approach with considerations for multiple effect sizes within studies to evaluate the log odds ratio of the proportion of prey consumed by individual predators. Prey consumption was highly variable, but toads (Bufonidae) were consumed in lower proportions. Chewing invertebrates consumed more anuran prey than biting vertebrates. Late stage tadpoles were more vulnerable to predation than other stages of anuran ontogeny. However, more studies are needed to unravel the roles of development and evolutionary history in the chemical ecology of anuran young. This synthesis provides clear meta-analytic evidence that relative unpalatability is an important component in the anti-predator defenses of young in some anuran families, calling into question the degree to which chemically defended anuran families undergo ontogenetic switches in anti-predator strategies.

Integrating tropical research into biology education is urgently needed.

Understanding tropical biology is important for solving complex problems such as climate change, biodiversity loss, and zoonotic pandemics, but biology curricula view research mostly via a temperate-zone lens. Integrating tropical research into biology education is urgently needed to tackle these issues.

High Efficacy of Therapeutic Equine Hyperimmune Antibodies Against SARS-CoV-2 Variants of Concern.

SARS-CoV-2 variants of concern show reduced neutralization by vaccine-induced and therapeutic monoclonal antibodies; therefore, treatment alternatives are needed. We tested therapeutic equine polyclonal antibodies (pAbs) that are being assessed in clinical trials in Costa Rica against five globally circulating variants of concern: alpha, beta, epsilon, gamma and delta, using plaque reduction neutralization assays. We show that equine pAbs efficiently neutralize the variants of concern, with inhibitory concentrations in the range of 0.146-1.078 µg/mL, which correspond to extremely low concentrations when compared to pAbs doses used in clinical trials. Equine pAbs are an effective, broad coverage, low-cost and a scalable COVID-19 treatment.

Whispers from vestigial nubbins: Arrested development provokes trait loss in toads.

Despite the use of acoustic communication, many species of toads (family Bufonidae) have lost parts of the tympanic middle ear, representing at least 12 independent evolutionary occurrences of trait loss. The comparative development of the tympanic middle ear in toads is poorly understood. Here, we compared middle ear development among two pairs of closely related toad species in the genera Atelopus and Rhinella that have (eared) or lack (earless) middle ear structures. We bred toads in Peru and Ecuador, preserved developmental series from tadpoles to juveniles, and examined ontogenetic timing and volume of the otic capsule, oval window, operculum, opercularis muscle, columella (stapes), and extracolumella in three-dimensional histological reconstructions. All species had similar ontogenesis of the otic capsule, oval window, operculum, and opercularis muscle. Moreover, cell clusters of primordial columella in the oval window appeared just before metamorphosis in both eared and earless lineages. However, in earless lineages, the cell clusters either remained as small nubbins or cell buds in the location of the columella footplate within the oval window or disappeared by juvenile and adult stages. Thus, columella growth began around metamorphosis in all species but was truncated and/or degenerated after metamorphosis in earless species, leaving earless adults with morphology typical of metamorphic anurans. Shifts in the timing or expression of biochemical pathways that regulate the extension or differentiation of the columella after metamorphosis may be the developmental mechanism underlying convergent trait loss among toad lineages.

Correction: Male principal investigators (almost) don't publish with women in ecology and zoology.

[This corrects the article DOI: 10.1371/journal.pone.0218598.].

Developments in Amphibian Parental Care Research: History, Present Advances, and Future Perspectives.

Despite rising interest among scientists for over two centuries, parental care behavior has not been as thoroughly studied in amphibians as it has in other taxa. The first reports of amphibian parental care date from the early 18th century, when Maria Sibylla Merian went on a field expedition in Suriname and reported frog metamorphs emerging from their mother's dorsal skin. Reports of this and other parental behaviors in amphibians remained descriptive for decades, often as side notes during expeditions with another purpose. However, since the 1980s, experimental approaches have proliferated, providing detailed knowledge about the adaptive value of observed behaviors. Today, we recognize more than 30 types of parental care in amphibians, but most studies focus on just a few families and have favored anurans over urodeles and caecilians. Here, we provide a synthesis of the last three centuries of parental care research in the three orders comprising the amphibians. We draw attention to the progress from the very first descriptions to the most recent experimental studies, and highlight the importance of natural history observations as a source of new hypotheses and necessary context to interpret experimental findings. We encourage amphibian parental care researchers to diversify their study systems to allow for a more comprehensive perspective of the behaviors that amphibians exhibit. Finally, we uncover knowledge gaps and suggest new avenues of research using a variety of disciplines and approaches that will allow us to better understand the function and evolution of parental care behaviors in this diverse group of animals.

Male principal investigators (almost) don't publish with women in ecology and zoology.

Representation of women in science drops substantially at each career stage, from early student to senior investigator. Disparities in opportunities for women to contribute to research metrics, such as distinguished speaker events and authorship, have been reported in many fields in the U.S.A. and Europe. However, whether female representation in scientific contributions differs in other regions, such as Latin America, is not well understood. In this study, in order to determine whether female authorship is influenced by gender or institutional location of the last (senior) author or by subfield within ecology, we gathered author information from 6849 articles in ten ecological and zoological journals that publish research articles either in or out of Latin America. We found that female authorship has risen marginally since 2002 (27 to 31%), and varies among Latin American countries, but not between Latin America and other regions. Last author gender predicted female co-authorship across all journals and regions, as research groups led by women published with over 60% female co-authors whereas those led by men published with less than 20% female co-authors. Our findings suggest that implicit biases and stereotype threats that women face in male-led laboratories could be sources of female withdrawal and leaky pipelines in ecology and zoology. Accordingly, we encourage every PI to self-evaluate their lifetime percentage of female co-authors. Female role models and cultural shifts-especially by male senior authors-are crucial for female retention and unbiased participation in science.

Prolonged middle ear development in Rhinella horribilis.

Despite the benefit of the tympanic middle ear to airborne hearing sensitivity, anurans range in how soon they develop functional middle ears after transitioning to life on land. Previous evidence suggested that bufonids had particularly slow middle ear developmental rates, but precise timelines have not yet been published for this family. Here, we provide the first age-verified middle ear development timeline for a true toad species (family Bufonidae). We find that although middle ear development begins during metamorphosis in Rhinella horribilis, the middle ear remains incomplete 15 weeks after the transition from aquatic tadpole to land-dwelling toadlet. Using this new middle ear timeline, we discuss commonalities and differences in middle ear development among bufonids, as well as among Anura.

Poison frogs.

Stynoski et al. introduce the dendrobatids, a charismatic group of frogs known for their colourful and often poisonous skin.

Maternally derived chemical defences are an effective deterrent against some predators of poison frog tadpoles (Oophaga pumilio).

Parents defend their young in many ways, including provisioning chemical defences. Recent work in a poison frog system offers the first example of an animal that provisions its young with alkaloids after hatching or birth rather than before. But it is not yet known whether maternally derived alkaloids are an effective defence against offspring predators. We identified the predators of Oophaga pumilio tadpoles and conducted laboratory and field choice tests to determine whether predators are deterred by alkaloids in tadpoles. We found that snakes, spiders and beetle larvae are common predators of O. pumilio tadpoles. Snakes were not deterred by alkaloids in tadpoles. However, spiders were less likely to consume mother-fed O. pumilio tadpoles than either alkaloid-free tadpoles of the red-eyed treefrog, Agalychnis callidryas, or alkaloid-free O. pumilio tadpoles that had been hand-fed with A. callidryas eggs. Thus, maternally derived alkaloids reduce the risk of predation for tadpoles, but only against some predators.

Evidence of maternal provisioning of alkaloid-based chemical defenses in the strawberry poison frog Oophaga pumilio.

Many organisms use chemical defenses to reduce predation risk. Aposematic dendrobatid frogs sequester alkaloid-based chemical defenses from a diet of arthropods, but research on these defenses has been limited to adults. Herein, we investigate chemical defense across development in a dendrobatid frog, Oophaga pumilio. This species displays complex parental care: at hatching, mothers transport tadpoles to phytotelmata, and then return to supply them with an obligate diet of nutritive eggs for about six weeks. We collected eggs, tadpoles, juveniles, and adults of O. pumilio, and detected alkaloids in all life stages. The quantity and number of alkaloids increased with frog and tadpole size. We did not detect alkaloids in the earliest stage of tadpoles, but alkaloids were detected as trace quantities in nutritive eggs and as small quantities in ovarian eggs. Tadpoles hand-reared with eggs of an alkaloid-free heterospecific frog did not contain alkaloids. Alkaloids that are sequestered from terrestrial arthropods were detected in both adults and phytotelm-dwelling tadpoles that feed solely on nutritive eggs, suggesting that this frog may be the first animal known to actively provision post-hatch offspring with chemical defenses. Finally, we provide experimental evidence that maternally derived alkaloids deter predation of tadpoles by a predatory arthropod.