Understanding how environmental variation interacts with gene flow to shape population genomic patterns is a central goal in evolutionary biology. We investigated how geographic and environmental differences impact genetic variation in the clouded sulfur butterfly (Colias philodice eriphyle) by conducting whole-genome resequencing across replicated transects consisting of paired high- and low-elevation sites on both sides of a major mountain range. Despite sampling across steep environmental gradients, we found no evidence of discrete population structure, providing support for high connectivity across the region or recent divergence with limited drift. Nonetheless, significant isolation by distance-strongest in eastern populations-revealed that geographic distance may impose limits on gene flow, and genetic diversity was also elevated in the east. Genotype-environment association analyses identified more than 16,000 loci associated with elevation, precipitation, and solar radiation. Our redundancy analysis identified precipitation as the strongest predictor of adaptive genomic differentiation, and candidate genes included those linked to melanization and thermoregulation (e.g., TH and yellow). These results demonstrate that even in a largely panmictic population, environmental variation can maintain regional-scale signals of local adaptation. Because insects are declining globally and remain underrepresented in genomic monitoring, conducting whole-genome analyses in a widespread species provides valuable context for assessing how insects today persist across such diverse landscapes and their potential for withstanding future environmental change.

Conservation success depends on translating theory into practical guidance and tools that are relevant and useful for non-scientists. While the complexity of population genetics has challenged the usage of straightforward metrics for conservation, several practical guidelines have been advanced, such as those regarding effective population size (N e ). Allendorf et al. highlight limitations of N e as a metric for practical use. Specifically, they demonstrate that while N e is sufficient for predicting heterozygosity, it is not predictive of the number of alleles, another key variable in conservation genetics. This has important implications for N e -based metrics, such as the N e 500 indicator recently adopted in the Convention on Biological Diversity's Kunming-Montreal Global Biodiversity Framework. As developers and advocates of the N e 500 indicator, we agree with this assessment, and acknowledge that N e does not comprehensively predict changes in allelic variation. In this article we briefly summarize several major points in Allendorf et al. and provide practical suggestions to better account for allelic variation during indicator assessments. These suggestions include reporting major declines in N c as part of genetic assessments, clearly articulating the intention and caveats of the N e 500 indicator, integrating simulations into genetic assessments, and assessing the number of genetically distinct populations. We conclude that the N e 500 indicator remains a valuable metric uniquely capable of capturing critical aspects of a species' genetic status while remaining accessible and interpretable to policymakers and other non-geneticists. By acknowledging the limitations of focusing solely on N e and providing options for more thorough and nuanced understandings of genetic diversity, we hope to guide future usage of the N e 500 indicator and help bridge the gap between conservation genetics theory and practice.

Identifying populations at highest risk from climate change is a critical component of conservation efforts. However, vulnerability assessments are usually applied at the species level, even though intraspecific variation in exposure, sensitivity and adaptive capacity play a crucial role in determining vulnerability. Genomic data can inform intraspecific vulnerability by identifying signatures of local adaptation that reflect population-level variation in sensitivity and adaptive capacity. Here, we address the question of local adaptation to temperature and the genetic basis of thermal tolerance in two stream frogs (Ascaphus truei and A. montanus). Building on previous physiological and temperature data, we used whole-genome resequencing of tadpoles from four sites spanning temperature gradients in each species to test for signatures of local adaptation. To support these analyses, we developed the first annotated reference genome for A. truei. We then expanded the geographic scope of our analysis using targeted capture at an additional 11 sites per species. We found evidence of local adaptation to temperature based on physiological and genomic data in A. montanus and genomic data in A. truei, suggesting similar levels of sensitivity (i.e., susceptibility) among populations regardless of stream temperature. However, invariant thermal tolerances across temperatures in A. truei suggest that populations occupying warmer streams may be most sensitive. We identified high levels of evolutionary potential in both species based on genomic and physiological data. While further integration of these data is needed to comprehensively evaluate spatial variation in vulnerability, this work illustrates the value of genomics in identifying spatial patterns of climate change vulnerability.

Conservation science and policy are geared primarily toward the preservation of species and habitats, with priority often given to the rarest, most vulnerable or most charismatic forms. This pattern-based approach has broad appeal and offers a pragmatic short-cut for targeting conservation action. However, the long-term efficacy of species and landscape conservation programs remains highly uncertain, amid growing evidence that sustainable conservation action requires an increased emphasis on preserving ecological and evolutionary processes. This reframing of conservation goals was first proposed 50 y ago, but the concept has struggled to gain traction, particularly in terms of translation into policy. Nonetheless, recent events have shifted the narrative, with multiple interlinked global challenges-including biological invasions, food security, disease, and climate change-putting ecological processes firmly back on the agenda. Concurrently, conservation finance is changing rapidly, driven in part by the 2022 Kunming-Montreal Global Biodiversity Framework, which prioritized actions to enhance and restore ecosystem stability, connectivity, and resilience. These ecosystem properties are fundamentally process-driven and appear to create an operational gulf between current conservation practice and the targets of international agreements. We describe how new approaches can be used to close this gap by redirecting conservation attention toward processes at the heart of ecosystem function, including adaptation, gene flow, dispersal, and trophic interactions. Wider adoption of these approaches is urgently needed to forge a deeper connection between conservation practice and policy targets, thereby ensuring that ongoing investment in biodiversity conservation goes beyond damage limitation and instead leaves a lasting legacy of resilient ecosystems.

Genetic diversity is fundamental to biological diversity, vital for species’ health and adaptation to environmental change. Under the recently adopted Kunming-Montreal Global Biodiversity Framework (GBF), 196 Parties committed to report the status of genetic diversity for both wild and domesticated species. For this, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: ensuring that populations are large enough to maintain genetic diversity (effective population size Ne 500 indicator) and maintaining genetically distinct populations (populations maintained, PM indicator). A third indicator focuses on the number of species being monitored using DNA-based methods. Adopted by 196 CBD Parties in December 2022, GBF integrated Ne 500 and PM as headline and complementary indicators, respectively. To aid nations in quantifying these indicators, a detailed set of guideline materials was developed, encompassing species selection, data compilation, and indicator computation. These guidelines draw from the collaborative efforts of the first multinational assessment of genetic diversity indicators that was recently completed and that will be refined continually through a versioning system, as more experience is gained and shared. The materials aim to support the global monitoring framework established by the CBD and are accessible online for utilization and updates. The guidelines are available at this link.

In December 2022, the United Nations Convention on Biological Diversity (CBD) adopted the Kunming-Montreal Global Biodiversity Framework, in which 196 Parties, for the first time, committed to report on the status of genetic diversity for all species. To facilitate this reporting, three genetic diversity indicators were developed, two of which focus on the processes contributing to genetic diversity loss: the loss of genetically distinct populations (measured by complementary indicator “proportion of populations maintained within species”) and populations being too small to maintain genetic diversity (measured by headline indicator A4, “The proportion of populations within species with an effective population size > 500”). The major advantage of these indicators is that they can be estimated without DNA-based data. However, demonstrating the feasibility of this approach to all Parties for their national reporting, requires addressing methodological challenges of using empirical data gathered from diverse sources, across diverse taxonomic groups and for countries of varying socio-economic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5,271 populations across nine countries, including megadiverse and developing economies. Data were available to calculate indicators for each country and taxonomic group (765 taxa [83%] had data for at least one indicator). Additionally, 41% of taxa (n=518) have lost at least one-tenth of their populations (complementary indicator [populations maintained] value < 0.9), while 58% of taxa (n=568) have all populations too small to sustain genetic diversity (headline indicator [Ne 500] value = 0). By comparing taxon indicator values to their GlobalRed List status, range size, and other factors, we found the loss of genetic diversity shown by these indicators would go unnoticed by other biodiversity assessments, highlighting the critical importance of monitoring and conserving genetic diversity using these indicators.

Genetic diversity is essential for maintaining healthy populations and ecosystems. Several approaches have recently been developed to evaluate population genetic trends without necessarily collecting new genetic data. Such “genetic diversity indicators” enable rapid, large-scale evaluation across dozens to thousands of species. Empirical genetic studies, when available, provide detailed information that is important for management, such as estimates of gene flow, inbreeding, genetic erosion and adaptation. In this article, we argue that the development and advancement of genetic diversity indicators is a complementary approach to genetic studies in conservation biology, but not a substitute. Genetic diversity indicators and empirical genetic data can provide different information for conserving genetic diversity. Genetic diversity indicators enable affordable tracking, reporting, prioritization and communication, although, being proxies, do not provide comprehensive evaluation of the genetic status of a species. Conversely, genetic methods offer detailed analysis of the genetic status of a given species or population, although they remain challenging to implement for most species globally, given current capacity and resourcing. We conclude that indicators and genetic studies are both important for genetic conservation actions and recommend they be used in combination for conserving and monitoring genetic diversity.

Temporally variable climates are expected to drive the evolution of thermal physiological traits that enable performance across a wider range of temperatures (i.e. climate variability hypothesis, CVH). Spatial thermal variability, however, may mediate this relationship by providing ectotherms with the opportunity to behaviourally select preferred temperatures (i.e. the Bogert effect). These antagonistic forces on thermal physiological traits may explain the mixed support for the CVH within species despite strong support among species at larger geographical scales. Here, we test the CVH as it relates to plasticity in physiological upper thermal limits (critical thermal maximum—CTmax) among populations of coastal tailed frogs ( Ascaphus truei ). We targeted populations that inhabit spatially homogeneous environments, reducing the potentially confounding effects of behavioural thermoregulation. We found that populations experiencing greater temporal thermal variability exhibited greater plasticity in CTmax, supporting the CVH. Interestingly, we identified only one site with spatial temperature variability and tadpoles from this site demonstrated greater plasticity than expected, suggesting the opportunity for behavioural thermoregulation can reduce support for the CVH. Overall, our results demonstrate one role of climate variability in shaping thermal plasticity among populations and provide a baseline understanding of the impact of the CVH in spatially homogeneous thermal landscapes.

Abstract Global change is impacting biodiversity across all habitats on earth. New selection pressures from changing climatic conditions and other anthropogenic activities are creating heterogeneous ecological and evolutionary responses across many species' geographic ranges. Yet we currently lack standardised and reproducible tools to effectively predict the resulting patterns in species vulnerability to declines or range changes. We developed an informatic toolbox that integrates ecological, environmental and genomic data and analyses (environmental dissimilarity, species distribution models, landscape connectivity, neutral and adaptive genetic diversity, genotype‐environment associations and genomic offset) to estimate population vulnerability. In our toolbox, functions and data structures are coded in a standardised way so that it is applicable to any species or geographic region where appropriate data are available, for example individual or population sampling and genomic datasets (e.g. RAD‐seq, ddRAD‐seq, whole genome sequencing data) representing environmental variation across the species geographic range. To demonstrate multi‐species applicability, we apply our toolbox to three georeferenced genomic datasets for co‐occurring East African spiny reed frogs (Afrixalus fornasini, A. delicatus and A. sylvaticus) to predict their population vulnerability, as well as demonstrating that range loss projections based on adaptive variation can be accurately reproduced from a previous study using data for two European bat species (Myotis escalerai and M. crypticus). Our framework sets the stage for large scale, multi‐species genomic datasets to be leveraged in a novel climate change vulnerability framework to quantify intraspecific differences in genetic diversity, local adaptation, range shifts and population vulnerability based on exposure, sensitivity and landscape barriers.

In late December 1973, the United States enacted what some would come to call “the pitbull of environmental laws.” In the 50 years since, the formidable regulatory teeth of the Endangered Species Act (ESA) have been credited with considerable successes, obliging agencies to draw upon the best available science to protect species and habitats. Yet human pressures continue to push the planet toward extinctions on a massive scale. With that prospect looming, and with scientific understanding ever changing, Science invited experts to discuss how the ESA has evolved and what its future might hold. —Brad Wible

Abstract Adaptive plasticity in thermal tolerance traits may buffer organisms against changing temperatures, making such responses of particular interest in the face of global climate change. Although population variation is integral to the evolvability of this trait, many studies inferring proxies of physiological vulnerability from thermal tolerance traits extrapolate data from one or a few populations to represent the species. Estimates of physiological vulnerability can be further complicated by methodological effects associated with experimental design. We evaluated how populations varied in their acclimation capacity (i.e., the magnitude of plasticity) for critical thermal maximum (CTmax) in two species of tailed frogs (Ascaphidae), cold‐stream specialists. We used the estimates of acclimation capacity to infer physiological vulnerability to future warming. We performed CTmax experiments on tadpoles from 14 populations using a fully factorial experimental design of two holding temperatures (8 and 15°C) and two experimental starting temperatures (8 and 15°C). This design allowed us to investigate the acute effects of transferring organisms from one holding temperature to a different experimental starting temperature, as well as fully acclimated responses by using the same holding and starting temperature. We found that most populations exhibited beneficial acclimation, where CTmax was higher in tadpoles held at a warmer temperature, but populations varied markedly in the magnitude of the response and the inferred physiological vulnerability to future warming. We also found that the response of transferring organisms to different starting temperatures varied substantially among populations, although accounting for acute effects did not greatly alter estimates of physiological vulnerability at the species level or for most populations. These results underscore the importance of sampling widely among populations when inferring physiological vulnerability, as population variation in acclimation capacity and thermal sensitivity may be critical when assessing vulnerability to future warming.

The complexity of global anthropogenic change makes forecasting species responses and planning effective conservation actions challenging. Additionally, important components of a species’ adaptive capacity, such as evolutionary potential, are often not included in quantitative risk assessments due to lack of data. While genomic proxies for evolutionary potential in at-risk species are increasingly available, they have not yet been included in extinction risk assessments at a species-wide scale. In this study, we used an individual-based, spatially explicit, dynamic eco-evolutionary simulation model to evaluate the extinction risk of an endangered desert songbird, the southwestern willow flycatcher (Empidonax traillii extimus), in response to climate change. Using data from long-term demographic and habitat studies in conjunction with genome-wide ecological genomics research, we parameterized simulations that include 418 sites across the breeding range, genomic data from 225 individuals, and climate change forecasts spanning 3 generalized circulation models and 3 emissions scenarios. We evaluated how evolutionary potential, and the lack of it, impacted population trajectories in response to climate change. We then investigated the compounding impact of drought and warming temperatures on extinction risk through the mechanism of increased nest failure. Finally, we evaluated how rapid action to reverse greenhouse gas emissions would influence population responses and species extinction risk. Our results illustrate the value of incorporating evolutionary, demographic, and dispersal processes in a spatially explicit framework to more comprehensively evaluate the extinction risk of threatened and endangered species and conservation actions to promote their recovery.

Wildlife diseases are a major global threat to biodiversity. Boreal toads (Anaxyrus [Bufo] boreas) are a state-endangered species in the southern Rocky Mountains of Colorado and New Mexico, and a species of concern in Wyoming, largely due to lethal skin infections caused by the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). We performed conservation and landscape genomic analyses using single nucleotide polymorphisms from double-digest, restriction site-associated DNA sequencing in combination with the development of the first boreal toad (and first North American toad) reference genome to investigate population structure, genomic diversity, landscape connectivity, and adaptive divergence. Genomic diversity (π=0.00034–0.00040) and effective population sizes (Ne=8.9 –38.4) were low, likely due to post-Pleistocene founder effects and Bd-related population crashes over the last three decades, respectively. Population structure was also low, likely due to formerly-high connectivity among a higher density of geographically-proximate populations. Boreal toad gene flow was facilitated by low precipitation, cold minimum temperatures, less tree canopy cover, low heat load, and less urbanization. We also found >8X more putatively-adaptive loci related to Bd intensity than to all other environmental factors combined, as well as evidence for genes under selection related to immune response, heart development and regulation, and skin function. These data suggest boreal toads in habitats with Bd have experienced stronger selection pressure from disease than from other, broad-scale environmental variation. These findings can now be used by managers to conserve and recover the species through actions such as reintroduction and supplementation of populations that have declined due to Bd.

Identifying adaptive responses to the environment is key for understanding and predicting the ability of species to respond to human-induced global changes, such as climate change, land-use change, pollution and disease outbreaks. Adaptive responses can be studied using a variety of observational, experimental and modelling methods. The genomic revolution has led to the development of new approaches and refinement of existing approaches to identify the genomic basis of adaptive responses to the environment and environmental change. These methods often involve the application of statistical techniques that relate variation at the genomic level to environmental conditions or phenotypic variability in order to detect candidate adaptive genetic loci. The past decade has seen a proliferation of studies employing these tools in a variety of applications from informing conservation management, agricultural production and the management of invasive species, to understanding disease dynamics and modelling vulnerability to future global changes. Experimental and functional validation of these statistical inferences represents an area of increasing importance in this rapidly evolving field. Emerging approaches look beyond the organism's genome to its interactions with its associated bacterial metagenomes, at epigenetic variation and the structure of the genome itself.

1. Critical thermal limits represent an important component of an organism's capacity to cope with future temperature changes. Understanding the drivers of variation in these traits may uncover patterns in physiological vulnerability to climate change. Local temperature extremes have emerged as a major driver of thermal limits, although their effects can be mediated by the exploitation of fine-scale spatial variation in temperature through behavioural thermoregulation.2. Here, we investigated thermal limits along elevation gradients within and between two cold-water frog species (Ascaphus spp.), one with a coastal distribution (A. truei) and the other with a continental range (A. montanus). We quantified thermal limits for over 700 tadpoles, representing multiple populations from each species. We combined local temporal and fine-scale spatial temperature data to quantify local thermal landscapes (i.e., thermalscapes), including the opportunity for behavioural thermoregulation.3. Lower thermal limits for either species could not be reached experimentally without the water freezing, suggesting that cold tolerance is <0.3 degrees C. By contrast, upper thermal limits varied among populations, but this variation only reflected local temperature extremes in A. montanus, perhaps as a consequence of the greater variation in stream temperatures across its range. Lastly, we found minimal fine-scale spatial variability in temperature, suggesting limited opportunity for behavioural thermoregulation and thus increased vulnerability to warming for all populations.4. By quantifying local thermalscapes, we uncovered different trends in the relative vulnerability of populations across elevation for each species. In A. truei, physiological vulnerability decreased with elevation, whereas in A. montanus, all populations were equally physiologically vulnerable. These results highlight how similar environments can differentially shape physiological tolerance and patterns of vulnerability of species, and in turn impact their vulnerability to future warming.

Morphological variation is often maintained by complex and interrelated factors, complicating the identification of underlying drivers. Tadpole oral morphology is one such trait that may be driven by the independent and interacting effects of the environment and variation in developmental processes. Although many studies have investigated tadpole oral morphological diversity among species, few have sought to understand the drivers that underlie intraspecific variation. In this study, we investigated potential drivers of labial tooth number variation among populations of two species of tailed frogs, the Rocky Mountain Tailed Frog (Ascaphus montanus) and the Coastal Tailed Frog (A. truei). We counted labial teeth from 240 tadpoles collected across elevation (both species) and latitudinal (A. truei) gradients, providing a natural temperature gradient. We tested the effects of developmental stage and local temperature conditions on labial tooth number. We found that labial tooth number variation was independently affected by both developmental stage and local temperature, as well as the interacting effects of these two variables (pseudo-R2 5 67–77%). Our results also uncovered consistent patterns in labial tooth row formula across the ranges of both species; however, tadpoles of A. truei from northern British Columbia had a unique bifurcation of a posterior tooth row. This study highlights the diversity in intraspecific tadpole oral morphology and the interacting processes that drive it.

Temperature is a critical driver of ectotherm life-history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life-history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) can help uncover the molecular mechanisms of temperature-driven variation in growth, longevity and senescence. However, our understanding of these mechanisms is still limited, which reduces our ability to predict the response of non-model ectotherms to global temperature change. In this study, we examined the potential role of thermal adaptation in clinal shifts of life-history traits (i.e. life span, senescence rate and recruitment) in the Columbia spotted frog Rana luteiventris along a broad temperature gradient in the western United States. We took advantage of extensive capture-recapture datasets of 20,033 marked individuals from eight populations surveyed annually for 14-18 years to examine how mean annual temperature and precipitation influenced demographic parameters (i.e. adult survival, life span, senescence rate, recruitment and population growth). After showing that temperature was the main climatic predictor influencing demography, we used RAD-seq data (50,829 SNPs and 6,599 putative CNVs) generated for 352 individuals from 31 breeding sites to identify the genomic signatures of thermal adaptation. Our results showed that temperature was negatively associated with annual adult survival and reproductive life span and positively associated with senescence rate. By contrast, recruitment increased with temperature, promoting the long-term viability of most populations. These temperature-dependent demographic changes were associated with strong genomic signatures of thermal adaptation. We identified 148 SNP candidates associated with temperature including three SNPs located within protein-coding genes regulating resistance to cold and hypoxia, immunity and reproduction in ranids. We also identified 39 CNV candidates (including within 38 transposable elements) for which normalized read depth was associated with temperature. Our study indicates that both SNPs and structural variants are associated with temperature and could eventually be found to play a functional role in clinal shifts in senescence rate and life-history strategies in R. luteiventris. These results highlight the potential role of different sources of molecular variation in the response of ectotherms to environmental temperature variation in the context of global warming.