Genetic erosion and escalating extinction risk in frogs with increasing wildfire frequency

In this current wildfire crisis, acknowledge widespread suffering

With climate change causing more extreme weather events globally, climate scientists have argued that societies have three options: mitigation, adaptation or suffering. In recent years, devastating wildfires have caused significant suffering, yet the extent of this suffering has not been defined. To encapsulate this suffering, we determined impacts and effects of extreme wildfires through two systematic literature reviews. Six common themes of wildfire suffering emerged: environmental, social, physical, mental, cultural and resource suffering. These themes varied in scale: from local to regional; from individuals to communities; and from ecosystems to landscapes. We then applied these themes in the Las Maquinas (Chile) and Fort McMurray (Canada) wildfires. This highlighted several adaptation strategies that can reduce suffering, however our exploration indicates these strategies must address social and ecological factors. This analysis concludes that suffering from wildfires is diverse and widespread, and that significant engagement with adaptation strategies is needed if this is going to decrease.

Fire-driven animal evolution in the Pyrocene

Fire regimes are a major agent of evolution in terrestrial animals. Changing fire regimes and the capacity for rapid evolution in wild animal populations suggests the potential for rapid, fire-driven adaptive animal evolution in the Pyrocene. Fire drives multiple modes of evolutionary change, including stabilizing, directional, disruptive, and fluctuating selection, and can strongly influence gene flow and genetic drift. Ongoing and future research in fire-driven animal evolution will benefit from further development of generalizable hypotheses, studies conducted in highly responsive taxa, and linking fire-adapted phenotypes to their underlying genetic basis. A better understanding of evolutionary responses to fire has the potential to positively influence conservation strategies that embrace evolutionary resilience to fire in the Pyrocene.

Complex Organisms Must Deal with Complex Threats: How Does Amphibian Conservation Deal with Biphasic Life Cycles?

The unprecedented rate of global amphibian decline is attributed to The Anthropocene, with human actions triggering the Sixth Mass Extinction Event. Amphibians have suffered some of the most extreme declines, and their lack of response to conservation actions may reflect challenges faced by taxa that exhibit biphasic life histories. There is an urgent need to ensure that conservation measures are cost-effective and yield positive outcomes. Many conservation actions have failed to meet their intended goals of bolstering populations to ensure the persistence of species into the future. We suggest that past conservation efforts have not considered how different threats influence multiple life stages of amphibians, potentially leading to suboptimal outcomes for their conservation. Our review highlights the multitude of threats amphibians face at each life stage and the conservation actions used to mitigate these threats. We also draw attention to the paucity of studies that have employed multiple actions across more than one life stage. Conservation programs for biphasic amphibians, and the research that guides them, lack a multi-pronged approach to deal with multiple threats across the lifecycle. Conservation management programs must recognise the changing threat landscape for biphasic amphibians to reduce their notoriety as the most threatened vertebrate taxa globally.

Drought, fire, and rainforest endemics: A case study of two threatened frogs impacted by Australia's "Black Summer"

Deepening droughts and unprecedented wildfires are at the leading edge of climate change. Such events pose an emerging threat to species maladapted to these perturbations, with the potential for steeper declines than may be inferred from the gradual erosion of their climatic niche. This study focused on two species of amphibians-Philoria kundagungan and Philoria richmondensis (Limnodynastidae)-from the Gondwanan rainforests of eastern Australia that were extensively affected by the "Black Summer" megafires of 2019/2020 and the severe drought associated with them. We sought to assess the impact of these perturbations by quantifying the extent of habitat affected by fire, assessing patterns of occurrence and abundance of calling males post-fire, and comparing post-fire occurrence and abundance with that observed pre-fire. Some 30% of potentially suitable habitat for P. kundagungan was fire affected, and 12% for P. richmondensis. Field surveys revealed persistence in some burnt rainforest; however, both species were detected at a higher proportion of unburnt sites. There was a clear negative effect of fire on the probability of site occupancy, abundance and the probability of persistence for P. kundagungan. For P. richmondensis, effects of fire were less evident due to the limited penetration of fire into core habitat; however, occupancy rates and abundance of calling males were depressed during the severe drought that prevailed just prior to the fires, with the reappearance of calling males linked to the degree of rehydration of breeding habitat post-fire. Our results highlight the possibility that severe negative impacts of climate change for montane rainforest endemics may be felt much sooner than commonly anticipated under a scenario of gradual (decadal-scale) changes in mean climatic conditions. Instead, the increased rate of severe stochastic events places these narrow range species at a heightened risk of extinction in the near-term.

Conservation genomics of an endangered arboreal mammal following the 2019-2020 Australian megafire

The impacts of a changing climate threaten species, populations and ecosystems. Despite these significant and large-scale impacts on threatened species, many remain understudied and have little to no genetic information available. The greater glider, Petauroides volans, is an endangered species highly sensitive to the predicted changes in temperature under a changing climate and was recently severely impacted by a megafire natural disaster (85% estimated population loss). Baseline genetic data is essential for conservation management and for detecting detrimental changes in fire-effected populations. We collected genetic samples within 2 years post the 2019-2020 catastrophic Australian bushfires to examine adaptive potential, baseline genetic diversity and population structure, across their southern range in the state of New South Wales. Population genomic analyses were conducted using 8493 genome-wide SNPs for 86 greater glider individuals across 14 geographic locations. Substantial genetic structure was detected across locations, with low genetic diversity and effective population sizes observed in isolated areas. Additionally, we found signals of putative adaptation in response to temperature in greater gliders using a genotype-environment association analysis. These findings have important implications for the management of greater glider populations by identifying at-risk populations and identifying adaptive potential. We demonstrate the importance of baseline genetic information for endangered species as a practical approach to conservation. This is particularly important given the threat that changes in temperatures and megafire events, as predicted under a changing climate, poses for this species.

Challenges in quantifying genome erosion for conservation

Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.

Using temporal genomics to understand contemporary climate change responses in wildlife

Monitoring the evolutionary responses of species to ongoing global climate change is critical for informing conservation. Population genomic studies that use samples from multiple time points ("temporal genomics") are uniquely able to make direct observations of change over time. Consequently, only temporal studies can show genetic erosion or spatiotemporal changes in population structure. Temporal genomic studies directly examining climate change effects are currently rare but will likely increase in the coming years due to their high conservation value. Here, we highlight four key genetic indicators that can be monitored using temporal genomics to understand how species are responding to climate change. All indicators crucially rely on having a suitable baseline that accurately represents the past condition of the population, and we discuss aspects of study design that must be considered to achieve this.

Factors influencing persistence of a threatened amphibian in restored wetlands despite severe population decline during climate change driven weather extremes

Biodiversity is in global decline during the Anthropocene. Declines have been caused by multiple factors, such as habitat removal, invasive species, and disease, which are often targets for conservation management. However, conservation interventions are under threat from climate change induced weather extremes. Weather extremes are becoming more frequent and devastating and an example of this was the 2019/2020 Australian drought and mega-fires. We provide a case study the impacts of these extreme weather events had on a population of the threatened frog Litoria aurea that occurs in a constructed habitat which was designed to reduce the impact of introduced fish and chytrid-induced disease. We aimed to determine what factors influenced persistence so that the design of wetlands can be further optimised to future-proof threatened amphibians. We achieved this with 4 years (2016-2020) of intensive capture-recapture surveys during austral spring and summer across nine wetlands (n = 94 repeat surveys). As hypothesized, drought caused a sharp reduction in population size, but persistence was achieved. The most parsimonious predictor of survival was an interaction between maximum air temperature and rainfall, indicating that weather extremes likely caused the decline. Survival was positively correlated with wetland vegetation coverage, positing this is an important feature to target to enhance resilience in wetland restoration programs. Additionally, the benefits obtained from measures to reduce chytrid prevalence were not compromised during drought, as there was a positive correlation between salinity and survival. We emphasize that many species may not be able to persist under worse extreme weather scenarios. Despite the potential for habitat augmentation to buffer effects of extreme weather, global action on climate change is needed to reduce extinction risk.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10531-022-02387-9.

Continental risk assessment for understudied taxa post-catastrophic wildfire indicates severe impacts on the Australian bee fauna

The 2019-2020 Australian Black Summer wildfires demonstrated that single events can have widespread and catastrophic impacts on biodiversity, causing a sudden and marked reduction in population size for many species. In such circumstances, there is a need for conservation managers to respond rapidly to implement priority remedial management actions for the most-affected species to help prevent extinctions. To date, priority responses have been biased towards high-profile taxa with substantial information bases. Here, we demonstrate that sufficient data are available to model the extinction risk for many less well-known species, which could inform much broader and more effective ecological disaster responses. Using publicly available collection and GIS datasets, combined with life-history data, we modelled the extinction risk from the 2019-2020 catastrophic Australian wildfires for 553 Australian native bee species (33% of all described Australian bee taxa). We suggest that two species are now eligible for listing as Endangered and nine are eligible for listing as Vulnerable under IUCN criteria, on the basis of fire overlap, intensity, frequency, and life-history traits: this tally far exceeds the three Australian bee species listed as threatened prior to the wildfire. We demonstrate how to undertake a wide-scale assessment of wildfire impact on a poorly understood group to help to focus surveys and recovery efforts. We also provide the methods and the script required to make similar assessments for other taxa or in other regions.

Physical disturbance by recovering sea otter populations increases eelgrass genetic diversity

[Figure: see text].

How fire interacts with habitat loss and fragmentation

Biodiversity faces many threats and these can interact to produce outcomes that may not be predicted by considering their effects in isolation. Habitat loss and fragmentation (hereafter 'fragmentation') and altered fire regimes are important threats to biodiversity, but their interactions have not been systematically evaluated across the globe. In this comprehensive synthesis, including 162 papers which provided 274 cases, we offer a framework for understanding how fire interacts with fragmentation. Fire and fragmentation interact in three main ways: (i) fire influences fragmentation (59% of 274 cases), where fire either destroys and fragments habitat or creates and connects habitat; (ii) fragmentation influences fire (25% of cases) where, after habitat is reduced in area and fragmented, fire in the landscape is subsequently altered because people suppress or ignite fires, or there is increased edge flammability or increased obstruction to fire spread; and (iii) where the two do not influence each other, but fire interacts with fragmentation to affect responses like species richness, abundance and extinction risk (16% of cases). Where fire and fragmentation do influence each other, feedback loops are possible that can lead to ecosystem conversion (e.g. forest to grassland). This is a well-documented threat in the tropics but with potential also to be important elsewhere. Fire interacts with fragmentation through scale-specific mechanisms: fire creates edges and drives edge effects; fire alters patch quality; and fire alters landscape-scale connectivity. We found only 12 cases in which studies reported the four essential strata for testing a full interaction, which were fragmented and unfragmented landscapes that both span contrasting fire histories, such as recently burnt and long unburnt vegetation. Simulation and empirical studies show that fire and fragmentation can interact synergistically, multiplicatively, antagonistically or additively. These cases highlight a key reason why understanding interactions is so important: when fire and fragmentation act together they can cause local extinctions, even when their separate effects are neutral. Whether fire-fragmentation interactions benefit or disadvantage species is often determined by the species' preferred successional stage. Adding fire to landscapes generally benefits early-successional plant and animal species, whereas it is detrimental to late-successional species. However, when fire interacts with fragmentation, the direction of effect of fire on a species could be reversed from the effect expected by successional preferences. Adding fire to fragmented landscapes can be detrimental for species that would normally co-exist with fire, because species may no longer be able to disperse to their preferred successional stage. Further, animals may be attracted to particular successional stages leading to unexpected responses to fragmentation, such as higher abundance in more isolated unburnt patches. Growing human populations and increasing resource consumption suggest that fragmentation trends will worsen over coming years. Combined with increasing alteration of fire regimes due to climate change and human-caused ignitions, interactions of fire with fragmentation are likely to become more common. Our new framework paves the way for developing a better understanding of how fire interacts with fragmentation, and for conserving biodiversity in the face of these emerging challenges.

Density Dependence and Adult Survival Drive Dynamics in Two High Elevation Amphibian Populations

Amphibian conservation has progressed from the identification of declines to mitigation, but efforts are hampered by the lack of nuanced information about the effects of environmental characteristics and stressors on mechanistic processes of population regulation. Challenges include a paucity of long-term data and scant information about the relative roles of extrinsic (e.g., weather) and intrinsic (e.g., density dependence) factors. We used a Bayesian formulation of an open population capture-recapture model and >30 years of data to examine intrinsic and extrinsic factors regulating two adult boreal chorus frogs (Pseudacris maculata) populations. We modelled population growth rate and apparent survival directly, assessed their temporal variability, and derived estimates of recruitment. Populations were relatively stable (geometric mean population growth rate >1) and regulated by negative density dependence (i.e., higher population sizes reduced population growth rate). In the smaller population, density dependence also acted on adult survival. In the larger population, higher population growth was associated with warmer autumns. Survival estimates ranged from 0.30–0.87, per-capita recruitment was <1 in most years, and mean seniority probability was >0.50, suggesting adult survival is more important to population growth than recruitment. Our analysis indicates density dependence is a primary driver of population dynamics for P. maculata adults.

Genetic evidence supports three previously described species of greater glider, Petauroides volans, P. minor, and P. armillatus

The identification and classification of species are essential for effective conservation management. This year, Australia experienced a bushfire season of unprecedented severity, resulting in widespread habitat loss and mortality. As a result, there has been an increased focus on understanding genetic diversity and structure across the range of individual species to protect resilience in the face of climate change. The greater glider (Petauroides volans) is a large, gliding eucalypt folivore. This nocturnal arboreal marsupial has a wide distribution across eastern Australia and is considered the sole extant member of the genus Petauroides. Differences in morphology have led to suggestions that the one accepted species is actually three. This would have substantial impacts on conservation management, particularly given a recent history of declining populations, coupled with extensive wildfires. Until now, genetic evidence to support multiple species has been lacking. For the first time, we used DArT sequencing on greater glider tissue samples from multiple regions and found evidence of three operational taxonomic units (OTUs) representing northern, central and southern groups. The three OTUs were also supported by our morphological data. These findings have important implications for greater glider management and highlight the role of genetics in helping to assess conservation status.

A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks

Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta-analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied river systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.

Integrating functional connectivity and fire management for better conservation outcomes

Globally, the mean abundance of terrestrial animals has fallen by 50% since 1970, and populations face ongoing threats associated with habitat loss, fragmentation, climate change, and disturbance. Climate change can influence the quality of remaining habitat directly and indirectly by precipitating increases in the extent, frequency, and severity of natural disturbances, such as fire. Species face the combined threats of habitat clearance, changing climates, and altered disturbance regimes, each of which may interact and have cascading impacts on animal populations. Typically, conservation agencies are limited in their capacity to mitigate rates of habitat clearance, habitat fragmentation, or climate change, yet fire management is increasingly used worldwide to reduce wildfire risk and achieve conservation outcomes. A popular approach to ecological fire management involves the creation of fire mosaics to promote animal diversity. However, this strategy has 2 fundamental limitations: the effect of fire on animal movement within or among habitat patches is not considered and the implications of the current fire regime for long-term population persistence are overlooked. Spatial and temporal patterns in fire history can influence animal movement, which is essential to the survival of individual animals, maintenance of genetic diversity, and persistence of populations, species, and ecosystems. We argue that there is rich potential for fire managers to manipulate animal movement patterns; enhance functional connectivity, gene flow, and genetic diversity; and increase the capacity of populations to persist under shifting environmental conditions. Recent methodological advances, such as spatiotemporal connectivity modeling, spatially explicit individual-based simulation, and fire-regime modeling can be integrated to achieve better outcomes for biodiversity in human-modified, fire-prone landscapes. Article impact statement: Land managers may conserve populations by using fire to sustain or enhance functional connectivity.

Marine Heatwave Drives Cryptic Loss of Genetic Diversity in Underwater Forests

Extreme events have profound ecological impacts on species and ecosystems, including range contractions and collapse of entire ecosystems. Although theory predicts that extreme events cause loss of genetic diversity, empirical demonstrations are rare, obscuring implications for future adaptive capacity of species and populations. Here, we use rare genetic data from before an extreme event to empirically demonstrate massive and cryptic loss of genetic diversity across ∼800 km of underwater forests following the most severe marine heatwave on record. Two forest-forming seaweeds (Sargassum fallax and Scytothalia dorycarpa) lost ∼30%-65% of average genetic diversity within the 800-km footprint of the heatwave and up to 100% of diversity at some sites. Populations became dominated by single haplotypes that were often not dominant or present prior to the heatwave. Strikingly, these impacts were cryptic and not reflected in measures of forest cover used to determine ecological impact of the heatwave. Our results show that marine heatwaves can drive strong loss of genetic diversity, which may compromise adaptability to future climatic change.