David William Pfennig

Convergence in color patterns among venomous coral snakes and various nonvenomous snake species has long fascinated evolutionary biologists. The prevailing view is that these patterns serve as warning signals to predators and that multiple coral snake species benefit from converging on the same signal. Nonvenomous species are similarly thought to gain protection from predation by mimicking coral snake coloration. Consistent with this hypothesis, field experiments in North and Central America have found that predators avoid snake replicas bearing coral snake coloration. However, similar experiments in South America have produced ambiguous results. Clarifying whether coral snake color patterns deter predation in South America is vital because the much greater coral snake species richness and pattern diversity there might affect predator deterrence differently than in North and Central America. Using methods comparable to those in North and Central America, we tested whether coral snake color patterns deter predation in Ecuador and Colombia. We found no evidence that coral snake patterns consistently reduced predation in either study area. However, the coral snake patterns that experienced the lowest predation were also most closely resembled by nonvenomous species, suggesting that color patterns are under predator-mediated selection. Thus, in species-rich communities, phenotypic convergence among venomous species and between venomous and nonvenomous species may involve complex dynamics that warrant further investigation.

Phenotypic plasticity––the ability of organisms to adjust their traits in response to changes in their environment––has long been thought to prevent extinction in novel or changing environments. However, there are few tests linking plasticity to population persistence. Here, we show that plasticity promotes population persistence in replicate populations of rotifers. We experimentally exposed 33 clonal lines that varied in plasticity to over 20 novel environments for up to 40 overlapping generations. We found that clonal populations expressing plasticity in morphology and life history traits persisted longer and were less likely to go extinct in novel environments than populations not expressing such plasticity. These results directly link plasticity to population persistence in novel environments and suggest that plasticity can buy time for organisms in a changing world. Teaser: A multigenerational experiment finds that environmentally induced traits allow populations to persist in novel environments.

Resource polyphenisms result in the production of environmentally induced morphs with differential niche use. These striking examples of phenotypic plasticity are taxonomically widespread and ecologically important. However, cannibalism is a frequent repercussion of resource polyphenisms. Despite some benefits, cannibalism is always costly to victims and sometimes costly to the cannibal. Therefore, we here evaluate how morphological and behavioral plastic strategies to minimize these costs may evolve. To better understand the evolution and consequences of cannibalistic polyphenisms, we tested whether rotifers Asplanchna brightwellii possess effective morphological defenses against cannibalism and the ability to discriminate by genetic relationship. We found that small humps produced by vulnerable A. brightwellii limit cannibalism. We also found that cannibals were less likely to attack clonemates than non-kin. The rotifer genus Asplanchna comprises species with varying degrees of resource polyphenism, cannibalism, induced morphological defenses, and behavioral kin discrimination. The observed induced defense and kin discrimination in Asplanchna brightwellii likely represent evolutionary intermediates facilitating the evolution of a unique trimorphic resource polyphenism in congeners.

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 genomic 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 genomic 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 essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess 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 emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address 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, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. 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 call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.

Organisms can react to environmental variation by altering their phenotype, and such phenotypic plasticity is often adaptive. This plasticity contributes to the diversity of phenotypes across the tree of life. Generally, the production of these phenotypes must be preceded by assessment, where the individual acquires information about its environment and phenotype relative to that environment, and then determines if and how to respond with an alternative phenotype. The role of assessment in adaptive plasticity is, therefore, crucial. In this Review, we (1) highlight the need for explicitly considering the role of assessment in plasticity; (2) present two different models for how assessment and the facultative production of phenotypes are related; and (3) describe an overarching framework for how assessment evolves. In doing so, we articulate avenues of future work and suggest that explicitly considering the role of assessment in the evolution of plasticity is key to explaining how and when plasticity occurs. Moreover, we emphasize the need to understand the role of assessment in adaptive versus maladaptive plasticity, which is an issue that will become increasingly important in a rapidly changing world.

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 genomic 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 genomic 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 essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess 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 emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address 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, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. 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 call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.

Many organisms facultatively produce different phenotypes depending on their environment, yet relatively little is known about the genetic bases of such plasticity in natural populations. In this study, we describe the genetic variation underlying an extreme form of plasticity––resource polyphenism––in Mexican spadefoot toad tadpoles, Spea multiplicata. Depending on their environment, these tadpoles develop into one of two drastically different forms: a carnivore morph or an omnivore morph. We collected both morphs from two ponds that differed in which morph had an adaptive advantage and performed genome-wide association studies of phenotype (carnivore vs. omnivore) and adaptive plasticity (adaptive vs. maladaptive environmental assessment). We identified four quantitative trait loci associated with phenotype and nine with adaptive plasticity, two of which exhibited signatures of minor allele dominance and two of which (one phenotype locus and one adaptive plasticity locus) did not occur as minor allele homozygotes. Investigations into the genetics of plastic traits in natural populations promise to provide novel insights into how such complex, adaptive traits arise and evolve.

Novel forms of phenotypic plasticity may evolve by lineage‐specific changes or by co‐opting mechanisms from more general forms of plasticity. Here, we evaluated whether a novel resource polyphenism in New World spadefoot toads (genus Spea) evolved by co‐opting mechanisms from an ancestral form of plasticity common in anurans—accelerating larval development rate in response to pond drying. We compared overlap in differentially expressed genes between alternative trophic morphs constituting the polyphenism in Spea versus those found between tadpoles of Old World spadefoot toads (genus Pelobates) when experiencing different pond‐drying regimes. Specifically, we (1) generated a de novo transcriptome and conducted differential gene expression analysis in Spea multiplicata, (2) utilized existing gene expression data and a recently published transcriptome for Pelobates cultripes when exposed to different drying regimes, and (3) identified unique and overlapping differentially expressed transcripts. We found thousands of differentially expressed genes between S. multiplicata morphs that were involved in major developmental reorganization, but the vast majority of these were not differentially expressed in P. cultripes. Thus, S. multiplicata's novel polyphenism appears to have arisen primarily through lineage‐specific changes in gene expression and not by co‐opting existing patterns of gene expression involved in pond‐drying plasticity. Therefore, although ancestral stress responses might jump‐start evolutionary innovation, substantial lineage‐specific modification might be needed to refine these responses into more complex forms of plasticity.