Opportunities and challenges in assessing climate change vulnerability through genomics.

By investigating how past selection has affected allele frequencies across space, genomic tools are providing new insights into adaptive evolutionary processes. Now researchers are considering how this genomic information can be used to predict the future vulnerability of species under climate change. Genomic vulnerability assessments show promise, but challenges remain.

Conservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species.

About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.

Acclimation to warmer temperatures can protect host populations from both further heat stress and the potential invasion of pathogens.

Thermal acclimation can provide an essential buffer against heat stress for host populations, while acting simultaneously on various life-history traits that determine population growth. In turn, the ability of a pathogen to invade a host population is intimately linked to these changes via the supply of new susceptible hosts, as well as the impact of warming on its immediate infection dynamics. Acclimation therefore has consequences for hosts and pathogens that extend beyond simply coping with heat stress-governing both population growth trajectories and, as a result, an inherent propensity for a disease outbreak to occur. The impact of thermal acclimation on heat tolerances, however, is rarely considered simultaneously with metrics of both host and pathogen population growth, and ultimately fitness. Using the host Daphnia magna and its bacterial pathogen, we investigated how thermal acclimation impacts host and pathogen performance at both the individual and population scales. We first tested the effect of maternal and direct thermal acclimation on the life-history traits of infected and uninfected individuals, such as heat tolerance, fecundity, and lifespan, as well as pathogen infection success and spore production. We then predicted the effects of each acclimation treatment on rates of host and pathogen population increase by deriving a host's intrinsic growth rate (rm) and a pathogen's basic reproductive number (R0). We found that direct acclimation to warming enhanced a host's heat tolerance and rate of population growth, despite a decline in life-history traits such as lifetime fecundity and lifespan. In contrast, pathogen performance was consistently worse under warming, with within-host pathogen success, and ultimately the potential for disease spread, severely hampered at higher temperatures. Our results suggest that hosts could benefit more from warming than their pathogens, but only by linking multiple individual traits to population processes can the full impact of higher temperatures on host and pathogen population dynamics be realised.

Within population plastic responses to combined thermal-nutritional stress differ from those in response to single stressors, and are genetically independent across traits in both males and females.

Phenotypic plasticity helps animals to buffer the effects of increasing thermal and nutritional stress created by climate change. Plastic responses to single and combined stressors can vary among genetically diverged populations. However, less is known about how plasticity in response to combined stress varies among individuals within a population or whether such variation changes across life-history traits. This is important because individual variation within populations shapes population-level responses to environmental change. Here, we used isogenic lines of Drosophila melanogaster to assess plasticity of egg-to-adult viability and sex-specific body size for combinations of two temperatures (25°C or 28°C) and three diets (standard diet, low caloric diet, or low protein:carbohydrate ratio diet). Our results reveal substantial within-population genetic variation in plasticity for egg-to-adult viability and wing size in response to combined thermal-nutritional stress. This genetic variation in plasticity was a result of cross-environment genetic correlations that were often < 1 for both traits, as well as changes in the expression of genetic variation across environments for egg-to-adult viability. Cross-sex genetic correlations for body size were weaker when the sexes were reared in different conditions, suggesting that the genetic basis of traits may change with the environment. Further, our results suggest that plasticity in egg-to-adult viability is genetically independent from plasticity in body size. Importantly, plasticity in response to diet and temperature individually differed from plastic shifts in response to diet and temperature in combination. By quantifying plasticity and the expression of genetic variance in response to combined stress across traits, our study reveals the complexity of animal responses to environmental change, and the need for a more nuanced understanding of the potential for populations to adapt to ongoing climate change.

Within-population variation in body size plasticity in response to combined nutritional and thermal stress is partially independent from variation in development time.

Ongoing climate change has forced animals to face changing thermal and nutritional environments. Animals can adjust to such combinations of stressors via plasticity. Body size is a key trait influencing organismal fitness, and plasticity in this trait in response to nutritional and thermal conditions varies among genetically diverse, locally adapted populations. The standing genetic variation within a population can also influence the extent of body size plasticity. We generated near-isogenic lines from a newly collected population of Drosophila melanogaster at the mid-point of east coast Australia and assayed body size for all lines in combinations of thermal and nutritional stress. We found that isogenic lines showed distinct underlying patterns of body size plasticity in response to temperature and nutrition that were often different from the overall population response. We then tested whether plasticity in development time could explain, and therefore regulate, variation in body size to these combinations of environmental conditions. We selected five genotypes that showed the greatest variation in response to combined thermal and nutritional stress and assessed the correlation between response of developmental time and body size. While we found significant genetic variation in development time plasticity, it was a poor predictor of body size among genotypes. Our results therefore suggest that multiple developmental pathways could generate genetic variation in body size plasticity. Our study emphasizes the need to better understand genetic variation in plasticity within a population, which will help determine the potential for populations to adapt to ongoing environmental change.

Testing evolutionary adaptation potential under climate change in invertebrates (mostly Drosophila): findings, limitations and directions.

A (quite) large set of experiments has been undertaken to assess the potential for evolutionary changes in invertebrates under current and future climate change conditions. These experimental studies have established some key principles that could affect climate change adaptation, yet there remain substantial obstacles in reaching a meaningful predictive framework. This Review starts with exploring some of the traits considered in individuals and approaches used in assessing evolutionary adaptation relevant to climate, and some of the core findings and their substantial limitations, with a focus on Drosophila. We interpret results in terms of adaptive limits based on population processes versus fundamental mechanistic limits of organisms. We then consider the challenges in moving towards a predictive framework and implications of the findings obtained to date, while also emphasizing the current limited context and the need to broaden it if links to changes in natural populations are to be realized.

Sexual dimorphism in phenotypic plasticity and persistence under environmental change: An extension of theory and meta-analysis of current data.

Populations must adapt to environmental changes to remain viable. Both evolution and phenotypic plasticity contribute to adaptation, with plasticity possibly being more important for coping with rapid change. Adaptation is complex in species with separate sexes, as the sexes can differ in the strength or direction of natural selection, the genetic basis of trait variation, and phenotypic plasticity. Many species show sex differences in plasticity, yet how these differences influence extinction susceptibility remains unclear. We first extend theoretical models of population persistence in changing environments and show that persistence is affected by sexual dimorphism for phenotypic plasticity, trait genetic architecture, and sex-specific selection. Our models predict that female-biased adaptive plasticity-particularly in traits with modest-to-low cross-sex genetic correlations-typically promotes persistence, though we also identify conditions where sexually monomorphic or male-biased plasticity promotes persistence. We then perform a meta-analysis of sex-specific plasticity under manipulated thermal conditions. Although examples of sexually dimorphic plasticity are widely observed, systematic sex differences are rare. An exception-cold resistance-is systematically female-biased and represents a trait wherein sexually dimorphic plasticity might elevate population viability in changing environments. We discuss our results in light of debates about the roles of evolution and plasticity in extinction susceptibility.

Phylogenetic and environmental patterns of sex differentiation in physiological traits across Drosophila species.

Sex-based differences in physiological traits may be influenced by both evolutionary and environmental factors. Here we used male and female flies from >80 Drosophila species reared under common conditions to examine variance in a number of physiological traits including size, starvation, desiccation and thermal tolerance. Sex-based differences for desiccation and starvation resistance were comparable in magnitude to those for size, with females tending to be relatively more resistant than males. In contrast thermal resistance showed low divergence between the sexes. Phylogenetic signal was detected for measures of divergence between the sexes, such that species from the Sophophora clade showed larger differences between the sexes than species from the Drosophila clade. We also found that sex-based differences in desiccation resistance, body size and starvation resistance were weakly associated with climate (annual mean temperature/precipitation seasonality) but the direction and association with environment depended on phylogenetic position. The results suggest that divergence between the sexes can be linked to environmental factors, while an association with phylogeny suggests sex-based differences persist over long evolutionary time-frames.

Thermal limits in the face of infectious disease: How important are pathogens?

The frequency and severity of both extreme thermal events and disease outbreaks are predicted to continue to shift as a consequence of global change. As a result, species persistence will likely be increasingly dependent on the interaction between thermal stress and pathogen exposure. Missing from the intersection between studies of infectious disease and thermal ecology, however, is the capacity for pathogen exposure to directly disrupt a host's ability to cope with thermal stress. Common sources of variation in host thermal performance, which are likely to interact with infection, are also often unaccounted for when assessing either the vulnerability of species or the potential for disease spread during extreme thermal events. Here, we describe how infection can directly alter host thermal limits, to a degree that exceeds the level of variation commonly seen across species large geographic distributions and that equals the detrimental impact of other ecologically relevant stressors. We then discuss various sources of heterogeneity within and between populations that are likely to be important in mediating the impact that infection has on variation in host thermal limits. In doing so we highlight how infection is a widespread and important source of variation in host thermal performance, which will have implications for both the persistence and vulnerability of species and the dynamics and transmission of disease in a more thermally extreme world.

Combating ecosystem collapse from the tropics to the Antarctic.

Globally, collapse of ecosystems-potentially irreversible change to ecosystem structure, composition and function-imperils biodiversity, human health and well-being. We examine the current state and recent trajectories of 19 ecosystems, spanning 58° of latitude across 7.7 M km2 , from Australia's coral reefs to terrestrial Antarctica. Pressures from global climate change and regional human impacts, occurring as chronic 'presses' and/or acute 'pulses', drive ecosystem collapse. Ecosystem responses to 5-17 pressures were categorised as four collapse profiles-abrupt, smooth, stepped and fluctuating. The manifestation of widespread ecosystem collapse is a stark warning of the necessity to take action. We present a three-step assessment and management framework (3As Pathway Awareness, Anticipation and Action) to aid strategic and effective mitigation to alleviate further degradation to help secure our future.

In search of a general theory of species' range evolution.

Despite the pervasiveness of the world's biodiversity, no single species has a truly global distribution. In fact, most species have very restricted distributions. What limits species from expanding beyond their current geographic ranges? This has been classically treated by ecologists as an ecological problem and by evolutionary biologists as an evolutionary problem. Such a dichotomy is false-the problem of species' ranges sits firmly within the realm of evolutionary ecology. In support of this view, Polechová presents new theory that explains species' range limits with reference to two key factors central to both ecological and evolutionary theory-migration and population size. This new model sets the scene for empirical tests of range limit theory and builds the case for assisted gene flow as a key management tool for threatened species.

Temperature and pathogen exposure act independently to drive host phenotypic trajectories.

Natural populations are experiencing an increase in the occurrence of both thermal stress and disease outbreaks. How these two common stressors interact to determine host phenotypic shifts will be important for population persistence, yet a myriad of different traits and pathways are a target of both stressors, making generalizable predictions difficult to obtain. Here, using the host Daphnia magna and its bacterial pathogen Pasteuria ramosa, we tested how temperature and pathogen exposure interact to drive shifts in multivariate host phenotypes. We found that these two stressors acted mostly independently to shape host phenotypic trajectories, with temperature driving a faster pace of life by favouring early development and increased intrinsic population growth rates, while pathogen exposure impacted reproductive potential through reductions in lifetime fecundity. Studies focussed on extreme thermal stress are increasingly showing how pathogen exposure can severely hamper the thermal tolerance of a host. However, our results suggest that under milder thermal stress, and in terms of life-history traits, increases in temperature might not exacerbate the impact of pathogen exposure on host performance, and vice versa.

Basal resistance enhances warming tolerance of alien over indigenous species across latitude.

Soil systems are being increasingly exposed to the interactive effects of biological invasions and climate change, with rising temperatures expected to benefit alien over indigenous species. We assessed this expectation for an important soil-dwelling group, the springtails, by determining whether alien species show broader thermal tolerance limits and greater tolerance to climate warming than their indigenous counterparts. We found that, from the tropics to the sub-Antarctic, alien species have the broadest thermal tolerances and greatest tolerance to environmental warming. Both groups of species show little phenotypic plasticity or potential for evolutionary change in tolerance to high temperature. These trait differences between alien and indigenous species suggest that biological invasions will exacerbate the impacts of climate change on soil systems, with profound implications for terrestrial ecosystem functioning.

Temporal specific coevolution of Hsp70 and co-chaperone stv expression in Drosophila melanogaster under selection for heat tolerance.

Heat shock proteins (Hsps) have long been candidates for ecological adaptation given their unequivocal role in mitigating cell damage from heat stress, but linking Hsps to heat tolerance has proven difficult given the complexity of thermal adaptation. Experimental evolution has been utilized to examine direct and correlated responses to selection for increased heat tolerance in Drosophila, often focusing on the major Hsp family Hsp70 and/or the master regulator HSF as a selection response, but rarely on other aspects of the heat shock complex. We examined Hsp70 and co-chaperone stv isoform transcript expression in Australian D. melanogaster lines selected for static heat tolerance, and observed a temporal and stv isoform specific, coordinated transcriptional selection response with Hsp70, suggesting that increased chaperone output accompanied increased heat tolerance. We hypothesize that the coordinated evolutionary response of Hsp70 and stv may have arisen as a correlated response resulting from a shared regulatory hierarchy. Our work highlights the complexity and specificity of the heat shock response in D. melanogaster. The selected lines examined also showed correlated responses for other measures of heat tolerance, and the coevolution of Hsp70 and stv provide new avenues to examine the common mechanisms underpinning direct and correlated phenotypic responses to selection for heat tolerance.

Phenotypic Plasticity for Desiccation Resistance, Climate Change, and Future Species Distributions: Will Plasticity Have Much Impact?

AbstractWhile species distribution models (SDMs) are widely used to predict the vulnerability of species to climate change, they do not explicitly indicate the extent to which plastic responses ameliorate climate change impacts. Here we use data on plastic responses of 32 species of Drosophila to desiccation stress to suggest that basal resistance, rather than adult hardening, is relatively more important in determining species differences in desiccation resistance and sensitivity to climate change. We go on to show, using the semimechanistic SDM CLIMEX, that the inclusion of plasticity has some impact on current species distributions and future vulnerability for widespread species but has little impact on the distribution of arguably more vulnerable tropically restricted species.

The influence of immune activation on thermal tolerance along a latitudinal cline.

Global change is shifting both temperature patterns and the geographic distribution of pathogens, and infection has already been shown to substantially reduce host thermal performance, potentially placing populations at greater risk that previously thought. But what about individuals that are able to successfully clear an infection? Whilst the direct damage a pathogen causes will likely lead to reductions in host's thermal tolerance, the response to infection often shares many underlying pathways with the general stress response, potentially acting as a buffer against subsequent thermal stress. Here, by exposing Drosophila melanogaster to heat-killed bacterial pathogens, we investigate how activation of a host's immune system can modify any response to both heat and cold temperature stress. In a single focal population, we find that immune activation can improve a host's knockdown times during heat shock, potentially offsetting some of the damage that would subsequently arise as an infection progresses. Conversely, immune activation had a detrimental effect on CTmax and did not influence lower thermal tolerance as measured by chill-coma recovery time. However, we also find that the influence of immune activation on heat knockdown times is not generalizable across an entire cline of locally adapted populations. Instead, immune activation led to signals of local adaptation to temperature being lost, erasing the previous advantage that populations in warmer regions had when challenged with heat stress. Our results suggest that activation of the immune system may help buffer individuals against the detrimental impact of infection on thermal tolerance; however, any response will be population specific and potentially not easily predicted across larger geographic scales, and dependent on the form of thermal stress faced by a host.

Thermal performance curves reveal shifts in optima, limits and breadth in early life.

Understanding thermal performance at life stages that limit persistence is necessary to predict responses to climate change, especially for ectotherms whose fitness (survival and reproduction) depends on environmental temperature. Ectotherms often undergo stage-specific changes in size, complexity and duration that are predicted to modify thermal performance. Yet performance is mostly explored for adults, while performance at earlier stages that typically limit persistence remains poorly understood. Here, we experimentally isolate thermal performance curves at fertilization, embryo development and larval development stages in an aquatic ectotherm whose early planktonic stages (gametes, embryos and larvae) govern adult abundances and dynamics. Unlike previous studies based on short-term exposures, responses with unclear links to fitness or proxies in lieu of explicit curve descriptors (thermal optima, limits and breadth), we measured performance as successful completion of each stage after exposure throughout, and at temperatures that explicitly capture curve descriptors at all stages. Formal comparisons of descriptors using a combination of generalized linear mixed modelling and parametric bootstrapping reveal important differences among life stages. Thermal performance differs significantly from fertilization to embryo development (with thermal optimum declining by ∼2°C, thermal limits shifting inwards by ∼8-10°C and thermal breadth narrowing by ∼10°C), while performance declines independently of temperature thereafter. Our comparisons show that thermal performance at one life stage can misrepresent performance at others, and point to gains in complexity during embryogenesis, rather than subsequent gains in size or duration of exposure, as a key driver of thermal sensitivity in early life.

Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species.

BACKGROUND: Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adaptations in the past. Here we investigate the genetic changes associated with adaptation to arid environments, specifically climatic extremes and new cactus hosts, through such an analysis of five repleta group Drosophila species. RESULTS: We find disproportionately high rates of gene gains in internal branches in the species' phylogeny where cactus use and subsequently cactus specialisation and high heat and desiccation tolerance evolved. The terminal branch leading to the most heat and desiccation resistant species, Drosophila aldrichi, also shows disproportionately high rates of both gene gains and positive selection. Several Gene Ontology terms related to metabolism were enriched in gene gain events in lineages where cactus use was evolving, while some regulatory and developmental genes were strongly selected in the Drosophila aldrichi branch. Transcriptomic analysis of flies subjected to sublethal heat shocks showed many more downregulation responses to the stress in a heat sensitive versus heat resistant species, confirming the existence of widespread regulatory as well as structural changes in the species' differing adaptations. Gene Ontology terms related to metabolism were enriched in the differentially expressed genes in the resistant species while terms related to stress response were over-represented in the sensitive one. CONCLUSION: Adaptations to new cactus hosts and hot desiccating environments were associated with periods of accelerated evolutionary change in diverse biochemistries. The hundreds of genes involved suggest adaptations of this sort would be difficult to achieve in the timeframes projected for anthropogenic climate change.

Pathogen exposure disrupts an organism's ability to cope with thermal stress.

As a result of global climate change, species are experiencing an escalation in the severity and regularity of extreme thermal events. With patterns of disease distribution and transmission predicted to undergo considerable shifts in the coming years, the interplay between temperature and pathogen exposure will likely determine the capacity of a population to persist under the dual threat of global change and infectious disease. In this study, we investigated how exposure to a pathogen affects an individual's ability to cope with extreme temperatures. Using experimental infections of Daphnia magna with its obligate bacterial pathogen Pasteuria ramosa, we measured upper thermal limits of multiple host and pathogen genotype combinations across the dynamic process of infection and under various forms (static and ramping) of thermal stress. We find that pathogens substantially limit the thermal tolerance of their host, with the reduction in upper thermal limits on par with the breadth of variation seen across similar species entire geographical ranges. The precise magnitude of any reduction, however, was specific to the host and pathogen genotype combination. In addition, as thermal ramping rate slowed, upper thermal limits of both healthy and infected individuals were reduced. Our results suggest that the capacity of a population to evolve new thermal limits, when also faced with the threat of infection, will depend not only on a host's genetic variability in warmer environments, but also on the frequency of host and pathogen genotypes. We suggest that pathogen-induced alterations of host thermal performance should be taken into account when assessing the resilience of any population and its potential for adaptation to global change.

Comparing thermal performance curves across traits: how consistent are they?

Thermal performance curves (TPCs) are intended to approximate the relationship between temperature and fitness, and are commonly integrated into species distributional models for understanding climate change responses. However, TPCs may vary across traits because selection and environmental sensitivity (plasticity) differ across traits or because the timing and duration of the temperature exposure, here termed time scale, may alter trait variation. Yet, the extent to which TPCs vary temporally and across traits is rarely considered in assessments of climate change responses. Using a common garden approach, we estimated TPCs for standard metabolic rate (SMR), and activity in Drosophila melanogaster at three test temperatures (16, 25 and 30°C), using flies from each of six developmental temperatures (16, 18, 20, 25, 28 and 30°C). We examined the effects of time scale of temperature exposure (minutes/hours versus days/weeks) in altering TPC shape and position, and commonly used descriptors of the TPC: thermal optimum (Topt), thermal limits (Tmin and Tmax) and thermal breadth (Tbr). In addition, we collated previously published estimates of TPCs for fecundity and egg-to-adult viability in D. melanogaster We found that the descriptors of the TPCs varied across traits (egg-to-adult viability, SMR, activity and fecundity), but variation in TPCs within these traits was small across studies when measured at the same time scales. The time scale at which traits were measured contributed to greater variation in TPCs than the observed variance across traits, although the relative importance of time scale differed depending on the trait (activity versus fecundity). Variation in the TPC across traits and time scales suggests that TPCs using single traits may not be an accurate predictor of fitness and thermal adaptation across environments.