Evolutionary principles guiding amphibian conservation

Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity

Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared with forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact nonurban areas on both recent and older timescales.

Discovering the diversity of tadpoles in the mid-north Brazil: morphological and molecular identification, and characterization of the habitat

Brazil stands out for presenting the highest amphibian anuran diversity in the world. However, taxonomic studies that address characteristic of larval stage of anurans are incipient, representing only 62% of known species. We assess the species diversity of tadpoles from eastern Maranhão state, mid-northern region of Brazil based on morphological and molecular identification (i.e., 16S rRNA gene fragment), and we also provide characteristics of the habitats occupied by each species. We carried out 30 field samplings during 13 months in 16 environments along an ecotonal area, over five cities inside the limits of state of Maranhão, between the Maranhão Babaçu Forest and Cerrado ecoregions. We searched for tadpoles in a variety of water bodies, and the tadpoles that reached the developmental stage between 34 to 40 Gosner were morphologically identified. The tadpoles collected herein represent 26 species belonging to five families. The external morphology enabled the identification of 24 species, while the molecular data recognized 22 unique evolutionary units. The most represented family was Hylidae (Hylinae 11 spp., Phyllomedusinae one spp.) followed by Leptodactylidae (Leptodactylinae seven spp., Leiuperinae three spp.), Microhylidae (Gastrophryninae two spp.), and Bufonidae (two spp.). Our results show that oral morphology was the most important character for identifying tadpoles based on morphology, and the specific 16S rRNA primer was suitable for molecular identification. This study pioneers the use of both morphological and molecular data to identify tadpoles in the state of Maranhão. It also provides, for the first-time, habitat characteristic for the species. Our study reveals a high number of anuran species sampled at the larval stage in the region, identifies species that require further taxonomic and systematic attention, and extends the geographic distribution of six species, three of which represent new occurrences for the state. Our results strengthen the hypothesis that the diversity of amphibians from Maranhão is underestimated and highlight the importance of herpetological inventories in poorly sampled areas, decentralizing the knowledge of biodiversity.

Importance of Genetic-Fitness Correlations for the Conservation of Amphibians

Endangered animals suffer from isolation of their habitats. Isolation leads to a reduction in population size as well as a decrease in genetic diversity and a concomitant increase in the risk of extinction. Amphibians are the most endangered vertebrate class. Besides habitat loss, fragmentation and isolation, amphibians are threatened by emerging diseases e.g., chytrid fungus or Ranavirus. By employing experiments, researchers investigate whether changes in genetic diversity within or among isolated populations affect amphibian fitness. While genetic diversity estimates are based on molecular markers, typically microsatellites, fitness is mostly measured as tadpole performance in rearing experiments often under varying environmental conditions. Tadpole performances (e.g., body mass, growth rate and survival) have been found to be negatively affected by low genetic diversity, as several studies have found a positive association between genetic diversity and these fitness traits. Moreover, infection with pathogens also seems to be more likely in individuals or populations with lower genetic diversity. Overall, these genetic-fitness correlations seem to be more pronounced or detectable in smaller, declining populations but not in larger populations. Genomic studies, which sample a larger fraction of the genome, are still scarce in the conservation genetic literature on amphibians. These are likely to increase in upcoming years and may reveal adaptive variants that protect against dangerous pathogens or environmental changes. Altogether, genetic-fitness correlation studies should be a priority in order to develop effective management plans for the genetic rescue of isolated, imperilled amphibian populations.

Population dynamics in newts of the Carpathian Mountains

Rarity, range restriction, and narrow endemism tend to carry dire and urgent conservation implications for imperilled species. What is also clear is that human-associated extinction risk factors such as urbanization and deforestation pose overwhelming threats to range-restricted species. In this issue of Molecular Ecology, Antunes et al. (2022) demonstrate that these threats can also impact widespread species. By comparing newts in the genus Lissotriton that co-occur in the same geographical region, they expose the distinctness of risks facing species with different habitat preferences. Their study emphasizes the importance of local-scale landscape genetics to reveal the nuances of population connectivity that might otherwise be missed by studying a broader spatial scale.

Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris)

Ecologically distinct species may respond to landscape changes in different ways. In addition to basic ecological data, the extent of the geographic range has been successfully used as an indicator of species sensitivity to anthropogenic landscapes, with widespread species usually found to be less sensitive compared to range-restricted species. In this study, we investigate connectivity patterns of two closely related but ecologically distinct newt species - the range-restricted, Lissotriton montandoni and the widespread, L. vulgaris - using genomic data, a highly replicated setting (six geographic regions per species), and tools from landscape genetics. Our results show the importance of forest for connectivity in both species, but at the same time suggest differential use of forested habitat, with L. montandoni and L. vulgaris showing the highest connectivity at forest-core and forest-edges, respectively. Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased resistance in both species, but the effect was one to three orders of magnitude stronger in L. montandoni than in L. vulgaris. This result is consistent with a view of L. vulgaris as an ecological generalist. Even so, currently, the negative impact of anthropogenic landscapes is mainly seen in connectivity among L. vulgaris populations, which show significantly stronger isolation and lower effective sizes relative to L. montandoni. Overall, this study emphasizes how habitat destruction is compromising genetic connectivity not only in endemic, range-restricted species of conservation concern but also in widespread generalist species, despite their comparatively lower sensitivity to anthropogenic landscape changes.

Assessment of the threat status of the amphibians in Vietnam - Implementation of the One Plan Approach

The current decline in global biodiversity is most evident in amphibians with 41% percent of all species worldwide classified as threatened with extinction. Hence, a major challenge in amphibian conservation is the high number of threatened species, leading to a common approach of identifying priority species and regions for conservation efforts. As a part of one of 36 globally designated biodiversity hotspots, Vietnam is considered to be of particular importance for conservation action. To improve amphibian conservation in Vietnam, this study provides an updated species list and assesses their threat status by compiling data from a variety of sources. Furthermore, a Zoological Information Management System (ZIMS) analysis was conducted to determine the representation of extant amphibians from Vietnam in zoos worldwide. The batrachofauna of Vietnam is characterized by a high level of species richness and local endemism as well as a high rate of new discoveries, with more than half of the endemic species reported exclusively from their type locality, making them especially vulnerable to extinction. Up to 18% of all amphibians extant in Vietnam and 28% of endemic species are classified as threatened with extinction by the IUCN. In many cases, the IUCN Red List status is either missing or outdated, highlighting the urgent need of action. Around 14% of endemic amphibian species have been recorded exclusively from unprotected areas, suggesting prioritization for further research and conservation measures. The continuing decline in many species remains an unresolved problem. As a guide for future research and conservation measures, a list of the top 57 species was compiled. In addition, according to the ZIMS analysis, only 8% of threatened and 3% of endemic amphibian taxa from Vietnam are currently kept in zoos worldwide, and a richness analysis revealed that the highest density of husbandries is found in Europe and North America. To achieve maximum outcome for the conservation of threatened species, this study recommends a general shift by zoos towards maintaining species in greater need of captive assurance populations and breeding programs to support integrative strategies that combine in situ and ex situ conservation efforts following the IUCN’s One Plan Approach.

Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri

Briefly considered extinct in the wild, the future of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.

Early Development Drives Variation in Amphibian Vulnerability to Global Change

Understanding how natural selection determines species’ life histories can reveal their resilience or sensitivity to anthropogenic changes. For example, the safe harbor hypothesis posits that natural selection will favor life histories that maximize the time spent in the safest life stages; a second theoretical prediction suggests that species with complex life histories will maximize the growth potential of a life stage relative to its safety. Amphibians exhibit complex life histories, with a diversity of developmental strategies occurring across taxa. Many strategies involve the complete elimination of a particular life stage, and thus provide an excellent opportunity to evaluate the main tenets of the safe harbor hypothesis and understand the consequences of this developmental variation for conservation of threatened amphibians. We develop a general framework for understanding developmental life histories of amphibians – including the special cases of paedomorphism, direct development, and viviparity – based on the relative growth potential and safety offered by aquatic and terrestrial habitat, which we tested using a global trait database. We then compare the IUCN Red List status of species differing in developmental mode, revealing that most fully aquatic species and species with an aquatic larval stage are currently of Least Concern, despite the fact that freshwater habitats are being lost at a much faster rate compared with terrestrial ecosystems. The higher proportion of direct developing and viviparous species that are threatened can be attributed to their smaller ranges, the fact that they are more likely to be found in rainforest habitats, and their relatively slow life histories. We conclude that an amphibian’s developmental mode reflects the relative costs and benefits of different habitats, and that this could contribute to the resilience or vulnerability of amphibians to future anthropogenic change.

Quantifying the Effect of Land-cover Change on the Endangered Farmland Green Treefrog (Zhangixalus arvalis) in an Agricultural Landscape: Implications for Conservation

Habitat loss and fragmentation have a significant negative effect on amphibian species, particularly those with specialized habitat requirements. The endangered farmland green treefrog (Zhangixalus arvalis) primarily inhabits woodlands of agricultural landscapes in central Taiwan. Recently, due to increased demands for pineapple products, many woodlands, particularly bamboo plantations, were converted to pineapple fields. This study aimed to quantify the effect of habitat loss and fragmentation on Z. arvalis due to changes in land cover in an agricultural landscape. The study area contained 34,243 50 m × 50 m grids. In 2006 and 2014-2015, we used acoustic surveys to survey the occurrence of Z. arvalis in each grid. We obtained satellite images of the study area for 2006 and 2014, and we assigned the land-cover type of each grid to one of the following six types: woodland, brushland, cropland, bareland, manmade structures and water body. We examined whether Z. arvalis preferred a certain land-cover type by comparing the proportion of cover types available and the proportion of cover types used by the frogs. Furthermore, we used occurrence records for 2006 and 2014-2015 and applied the Maximum Entropy Model to predict suitable habitat for the respective years. We mapped the loss of suitable habitat and used six indices to quantify habitat fragmentation within the 8 years. We also tested the prediction that the occupancy rate of Z. arvalis in different-sized habitat patches was a function of patch size. Zhangixalus arvalis exhibited a strong preference for woodland, but avoided cropland and manmade structures. From 2006 to 2014-2015, the suitable habitat decreased 4.1%, and all six indices showed an increase in habitat fragmentation. The occupancy rate of different-sized woodland patches was positively correlated with patch size. Mapping suitable habitat and identifying the potential gaps in functional habitat connectivity can be used to guide effective measures for conserving Z. arvalis.

Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population

Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance and direction, these individual-level decisions further modulate the demography, relatedness and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a great crested newt (Triturus cristatus) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across an SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.

Pesticide-induced multigenerational effects on amphibian reproduction and metabolism

Underlying drivers of species extinctions need to be better understood for effective conservation of biodiversity. Nearly half of all amphibian species are at risk of extinction, and pollution may be a significant threat as seasonal high-level agrochemical use overlaps with critical windows of larval development. The potential of environmental chemicals to reduce the fitness of future generations may have profound ecological and evolutionary implications. This study characterized effects of male developmental exposure to environmentally relevant concentrations of the anti-androgenic pesticide linuron over two generations of offspring in Xenopus tropicalis frogs. The adult male offspring of pesticide-exposed fathers (F1) showed reduced body size, decreased fertility, and signs of endocrine system disruption. Impacts were further propagated to the grand-offspring (F2), providing evidence of transgenerational effects in amphibians. The adult F2 males demonstrated increased weight and fat body palmitoleic-to-palmitic acid ratio, and decreased plasma glucose levels. The study provides important cross-species evidence of paternal epigenetic inheritance and pollutant-induced transgenerational toxicity, supporting a causal and complex role of environmental contamination in the ongoing species extinctions, particularly of amphibians.

Balancing selection and drift in a polymorphic salamander metapopulation

Understanding how genetic variation is maintained in a metapopulation is a longstanding problem in evolutionary biology. Historical resurveys of polymorphisms have offered efficient insights about evolutionary mechanisms, but are often conducted on single, large populations, neglecting the more comprehensive view afforded by considering all populations in a metapopulation. Here, we resurveyed a metapopulation of spotted salamanders (Ambystoma maculatum) to understand the evolutionary drivers of frequency variation in an egg mass colour polymorphism. We found that this metapopulation was demographically, phenotypically and environmentally stable over the last three decades. However, further analysis revealed evidence for two modes of evolution in this metapopulation-genetic drift and balancing selection. Although we cannot identify the balancing mechanism from these data, our findings present a clear view of contemporary evolution in colour morph frequency and demonstrate the importance of metapopulation-scale studies for capturing a broad range of evolutionary dynamics.

Single infection with Batrachochytrium dendrobatidis or Ranavirus does not increase probability of co-infection in a montane community of amphibians

Understanding the occurrence and consequence of co-infections can be useful in designing disease management interventions. Amphibians are the most highly threatened vertebrates, and emerging pathogens are a serious threat to their conservation. The amphibian chytrid fungus and the viruses of the Ranavirus genus are already widely distributed, causing disease outbreaks and population declines worldwide. However, we lack information about the occurrence and consequences of coinfection with these pathogens across age-classes of amphibian hosts. Here, we analyze the occurrence of infection of the amphibian chytrid fungus and ranaviruses during one season in two susceptible amphibian species at two different locations at which outbreaks have occurred. We found that the co-occurrence of both pathogens in a particular host is not common except in highly susceptible life-stages, and that single infections are the most common situation. Moreover, we found that the occurrence of one pathogen in a particular host did not predict the occurrence of the other. We attribute these results to the niches in which both pathogens proliferate in amphibian hosts.

The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.

Bioinformatic Analysis of 1000 Amphibian Antimicrobial Peptides Uncovers Multiple Length-Dependent Correlations for Peptide Design and Prediction

Amphibians are widely distributed on different continents, except for the polar regions. They are important sources for the isolation, purification and characterization of natural compounds, including peptides with various functions. Innate immune antimicrobial peptides (AMPs) play a critical role in warding off invading pathogens, such as bacteria, fungi, parasites, and viruses. They may also have other biological functions such as endotoxin neutralization, chemotaxis, anti-inflammation, and wound healing. This article documents a bioinformatic analysis of over 1000 amphibian antimicrobial peptides registered in the Antimicrobial Peptide Database (APD) in the past 18 years. These anuran peptides were discovered in Africa, Asia, Australia, Europe, and America from 1985 to 2019. Genomic and peptidomic studies accelerated the discovery pace and underscored the necessity in establishing criteria for peptide entry into the APD. A total of 99.9% of the anuran antimicrobial peptides are less than 50 amino acids with an average length of 24 and a net charge of +2.5. Interestingly, the various amphibian peptide families (e.g., temporins, brevinins, esculentins) can be connected through multiple length-dependent relationships. With an increase in length, peptide net charge increases, while the hydrophobic content decreases. In addition, glycine, leucine, lysine, and proline all show linear correlations with peptide length. These correlations improve our understanding of amphibian peptides and may be useful for prediction and design of new linear peptides with potential applications in treating infectious diseases, cancer and diabetes.