Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections

The systematic codon usage bias has an important effect on genetic adaption in native species

Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.

A decision-making framework to maximise the evolutionary potential of populations - Genetic and genomic insights from the common midwife toad (Alytes obstetricans) at its range limits

Anthropogenic habitat modification and climate change are fundamental drivers of biodiversity declines, reducing the evolutionary potential of species, particularly at their distributional limits. Supportive breeding or reintroductions of individuals are often made to replenish declining populations, sometimes informed by genetic analysis. However, most approaches utilised (i.e. single locus markers) do not have the resolution to account for local adaptation to environmental conditions, a crucial aspect to consider when selecting donor and recipient populations. Here, we incorporate genetic (microsatellite) and genome-wide SNP (ddRAD-seq) markers, accounting for both neutral and putative adaptive genetic diversity, to inform the conservation management of the threatened common midwife toad, Alytes obstetricans at the northern and eastern edges of its range in Europe. We find geographically structured populations (n = 4), weak genetic differentiation and fairly consistent levels of genetic diversity across localities (observed heterozygosity and allelic richness). Categorising individuals based on putatively adaptive regions of the genome showed that the majority of localities are not strongly locally adapted. However, several localities present high numbers of private alleles in tandem with local adaptation to warmer conditions and rough topography. Combining genetic diversity and local adaptations with estimates of migration rates, we develop a decision-making framework for selecting donor and recipient populations which maximises the geographic dispersal of neutral and putatively adaptive genetic diversity. Our framework is generally applicable to any species, but especially to amphibians, so armed with this information, conservationists may avoid the reintroduction of unsuitable/maladapted individuals to new sites and increase the evolutionary potential of populations within species.

Unveiling the suitable habitats and future conservation strategies of Tridacna maxima in the Indo-Pacific core area based on species distribution model

Climate change is exerting unprecedented impacts on marine habitats, and many sessile invertebrate species, such as the endangered giant clam Tridacna maxima, are particularly sensitive to climate driven changes in their environment. Understanding its spatial distribution and conservation requirements is of crucial significance in formulating effective protection strategies. However, the species has been extensively harvested and depleted in many regions, leading to its listing as endangered species by the International Union for Conservation of Nature (IUCN). While marine protected areas (MPAs) are considered effective conservation tools, it remains uncertain whether existing MPAs adequately protect these vulnerable giant clams. To enhance the management and conservation of this species, we employed a Species Distribution Models (SDMs) approach, integrating occurrence records of T. maxima with environmental variables, to predict its potential distribution based on habitat suitability and capture spatiotemporal changes. Based on geographical and genetic variations, the T. maxima in the Indo-Pacific core region is primarily divided into two populations: the East Indian Ocean-South China Sea population (EIOS) and the West Pacific-Indonesia population (WPI). We first quantified realized niche to reveal significant differences in ecological niche space among different populations. Subsequently, SDMs were constructed at both species and population levels, demonstrating that population-level SDMs provide more reliable predictions of population distributions due to differential responses to climatic predictor variables. Finally, we conducted an assessment to identify conservation gaps for T. maxima beyond the existing MPAs and proposed recommendations for future establishment of MPAs within the current framework. Based on these findings, appropriate conservation policies have been proposed to effectively protect the habitat of different geographical populations of T. maxima. Additionally, spatiotemporal predictions of habitat suitability provide crucial information for developing adaptive management strategies for T. maxima in response to climate change, including designing new protected areas and adjusting the location and extent of existing protected areas based on their geographical distribution.

Will climate change cause Sargassum beds in temperate waters to expand or contract? Evidence from the range shift pattern of Sargassum

Understanding the range shift patterns of foundation species (e.g., macroalgae) under future climatic conditions is critical for biodiversity conservation in coastal ecosystems. These predictions are typically made using species distribution models (SDMs), and severe habitat loss has been predicted for most brown algal forests. Nevertheless, some models showed that local adaptation within species can reduce range loss projections. In this study, we used the brown algae Sargassum fusiforme and Sargassum thunbergii, which are distributed in the Northwest Pacific, to determine whether climate change will cause the Sargassum beds in Northwest Pacific temperate waters to expand or contract. We divided S. fusiforme and S. thunbergii into northern and southern lineages, considering the temperature gradients and phylogeographic structures. We quantified the realized niches of the two lineages using an n-dimensional hypervolume. Significant niche differentiation was detected between lineages for both species, suggesting the existence of local adaptation. Based on these results, lineage-level SDMs were constructed for both species. The prediction results showed the different responses of different lineages to climate change. The suitable distribution area for both species was predicted to move northward, retaining part of the suitable habitat at low latitudes (along the East China Sea). Unfortunately, this expansion could not compensate for losing middle-low latitude areas. Our results have important implications for the future management and protection of macroalgae and emphasize the importance of incorporating intraspecific variation into species distribution predictions.

Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate

Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate-induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species' vulnerability to climate change. A total of 1514 individuals sampled across 24° latitude were genotyped at high geographic (54 stations) and genetic (14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated with local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to further deterioration in southern regions and an impending vulnerable status in the regions at higher latitudes for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understanding future challenges associated with invertebrates essential to ecosystem functioning.

Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data

AIM

We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines.

LOCATION

Oceania, greater Indonesia, and the Philippines.

TAXON

Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species.

RESULTS

Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples.

MAIN CONCLUSIONS

Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.

Evaluation of genetic consequences of stocking on the southern-margin populations of white-spotted charr

Coldwater-adapted freshwater fishes, especially their populations along warm-range margins, are most vulnerable to the climate oscillations associated with global warming. Stocking is a major strategy for avoiding the extinction of these species. However, while stocking can reverse the decline of isolated populations, it may also result in a loss of genetic diversity in the native local population due to the introgressive replacement of hatchery genes. To plan an adequate strategy for conserving locally adapted populations, the genetic impacts of stocking on native lineages should be evaluated from small river branches to wide-ranging drainage areas. We investigated the population genetic structure of white-spotted charr (Salvelinus leucomaenis) within its southern range (Lake Biwa basin, Japan). By applying genome-wide SNP analysis to the population's genetic structure, we assessed the extent of genetic introgression resulting from stocking. White-spotted charr in the Lake Biwa watershed constitutes a distinctive genetic group, within which apparent genetic differentiation was observed. The hatchery-reared fish line commonly used for supplementation stocking in the catchment was discernable from the native population, enabling us to analyze genetic introgression across the entire drainage area. Admixed individuals resulting from hatchery introgression were observed in most of the stocked sites that showed relatively high heterozygosity and nucleotide diversity. However, their genetic differentiation was much lower than that of native populations. The supplementation history as well as the road availability contributed substantially to the introgression of hatchery genes. Populations with the native genetic structure remained in the upstream regions of the tested rivers. However, their heterozygosity and nucleotide diversity were low when compared with that of the populations with hatchery supplementation. Our results shed light on the genetic impacts of stocking on isolated native populations and suggest that conventional supplementation methods cannot preserve a unique biodiversity in the distribution margin.

Genetic-environment associations explain genetic differentiation and variation between western and eastern North Pacific rhinoceros auklet (Cerorhinca monocerata) breeding colonies

Animals are strongly connected to the environments they live in and may become adapted to local environments. Examining genetic-environment associations of key indicator species, like seabirds, provides greater insights into the forces that drive evolution in marine systems. Here we examined a RADseq dataset of 19,213 SNPs for 99 rhinoceros auklets (Cerorhinca monocerata) from five western Pacific and 10 eastern Pacific breeding colonies. We used partial redundancy analyses to identify candidate adaptive loci and to quantify the effects of environmental variation on population genetic structure. We identified 262 candidate adaptive loci, which accounted for 3.0% of the observed genetic variation among western Pacific and eastern Pacific breeding colonies. Genetic variation was more strongly associated with pH and maximum current velocity, than maximum sea surface temperature. Genetic-environment associations explain genetic differences between western and eastern Pacific populations; however, genetic variation within the western and eastern Pacific Ocean populations appears to follow a pattern of isolation-by-distance. This study represents a first to quantify the relationship between environmental and genetic variation for this widely distributed marine species and provides greater insights into the evolutionary forces that act on marine species.

Forecasting habitat suitability and niche shifts of two global maize pests: Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae)

BACKGROUND

Ostrinia furnacalis (ACB) and Ostrinia nubilalis (ECB) are devastating pests of the agricultural crop maize worldwide. However, little is known about their potential distribution and niche shifts during their global invasion. Since long-term selection to past climate variability has shaped their historical niche breadth, such niche shifts may provide an alternative basis for understanding their responses to present and future climate change. By integrating the niche unfilling, stability, and expansion situations into a single framework, our study quantifies the patterns of niche shift in the spatial distribution of these two pests during the different periods.

RESULTS

Our results show that the overall suitable habitats of ACB and ECB in the future decrease but highly and extremely suitable habitat will become more widespread, suggesting these two insects may occur more frequently in specific regions. Compared with Southeast Asia and Australia, the ACB niche in China exhibited expansion rather than unfilling. For ECB, initial niches have a tendency to be retained in Eurasia despite there also being potential for expansion in North America. The niche equivalency and similarity test results further indicate that niche shifts were common for both ACB and ECB in different survival regions during their colonization of new habitat and their suitable habitat changes during the paleoclimate were associated with climatic changes.

CONCLUSIONS

These findings improve our understanding of the ecological characteristics of ACB and ECB worldwide, and will be useful in the development of prevention and control strategies for two insect pests worldwide. © 2024 Society of Chemical Industry.

Genomic insights into the conservation status of the Idle Crayfish Austropotamobius bihariensis Pârvulescu, 2019: low genetic diversity in the endemic crayfish species of the Apuseni Mountains

BACKGROUND

Biodiversity in freshwater ecosystems is declining due to an increased anthropogenic footprint. Freshwater crayfish are keystone species in freshwater ecosystems and play a crucial role in shaping the structure and function of their habitats. The Idle Crayfish Austropotamobius bihariensis is a native European species with a narrow distribution range, endemic to the Apuseni Mountains (Romania). Although its area is small, the populations are anthropogenically fragmented. In this context, the assessment of its conservation status is timely.

RESULTS

Using a reduced representation sequencing approach, we identified 4875 genomic SNPs from individuals belonging to 13 populations across the species distribution range. Subsequent population genomic analyses highlighted low heterozygosity levels, low number of private alleles and small effective population size. Our structuring analyses revealed that the genomic similarity of the populations is conserved within the river basins.

CONCLUSION

Genomic SNPs represented excellent tools to gain insights into intraspecific genomic diversity and population structure of the Idle Crayfish. Our study highlighted that the analysed populations are at risk due to their limited genetic diversity, which makes them extremely vulnerable to environmental alterations. Thus, our results emphasize the need for conservation measures and can be used as a baseline to establish species management programs.

Future carbon sequestration potential in a widespread transcontinental boreal tree species: Standing genetic variation matters!

Climate change (CC) necessitates reforestation/afforestation programs to mitigate its impacts and maximize carbon sequestration. But comprehending how tree growth, a proxy for fitness and resilience, responds to CC is critical to maximize these programs' effectiveness. Variability in tree response to CC across populations can notably be influenced by the standing genetic variation encompassing both neutral and adaptive genetic diversity. Here, a framework is proposed to assess tree growth potential at the population scale while accounting for standing genetic variation. We applied this framework to black spruce (BS, Picea mariana [Mill] B.S.P.), with the objectives to (1) determine the key climate variables having impacted BS growth response from 1974 to 2019, (2) examine the relative roles of local adaptation and the phylogeographic structure in this response, and (3) project BS growth under two Shared Socioeconomic Pathways while taking standing genetic variation into account. We modeled growth using a machine learning algorithm trained with dendroecological and genetic data obtained from over 2600 trees (62 populations divided in three genetic clusters) in four 48-year-old common gardens, and simulated growth until year 2100 at the common garden locations. Our study revealed that high summer and autumn temperatures negatively impacted BS growth. As a consequence of warming, this species is projected to experience a decline in growth by the end of the century, suggesting maladaptation to anticipated CC and a potential threat to its carbon sequestration capacity. This being said, we observed a clear difference in response to CC within and among genetic clusters, with the western cluster being more impacted than the central and eastern clusters. Our results show that intraspecific genetic variation, notably associated with the phylogeographic structure, must be considered when estimating the response of widespread species to CC.

Genomic and Phenotypic Adaptations of Rattus tanezumi to Cold Limit Its Further Northward Expansion and Range Overlap with R. norvegicus

Global climate change has led to shifts in the distribution ranges of many terrestrial species, promoting their migration from lower altitudes or latitudes to higher ones. Meanwhile, successful invaders have developed genetic adaptations enabling the colonization of new environments. Over the past 40 years, Rattus tanezumi (RT) has expanded into northern China (Northwest and North China) from its southern origins. We studied the cold adaptation of RT and its potential for northward expansion by comparing it with sympatric Rattus norvegicus (RN), which is well adapted to cold regions. Through population genomic analysis, we revealed that the invading RT rats have split into three distinct populations: the North, Northwest, and Tibetan populations. The first two populations exhibited high genetic diversity, while the latter population showed remarkably low genetic diversity. These rats have developed various genetic adaptations to cold, arid, hypoxic, and high-UV conditions. Cold acclimation tests revealed divergent thermoregulation between RT and RN. Specifically, RT exhibited higher brown adipose tissue activity and metabolic rates than did RN. Transcriptome analysis highlighted changes in genes regulating triglyceride catabolic processes in RT, including Apoa1 and Apoa4, which were upregulated, under selection and associated with local adaptation. In contrast, RN showed changes in carbohydrate metabolism genes. Despite the cold adaptation of RT, we observed genotypic and phenotypic constraints that may limit its ability to cope with severe low temperatures farther north. Consequently, it is less likely that RT rats will invade and overlap with RN rats in farther northern regions.

Abiotic Stress Tolerance Boosted by Genetic Diversity in Plants

Plant breeding [...].

Variable intraspecific response to climate change in a medicinally important African tree species, Vachellia sieberiana (DC.) (paperbark thorn)

Climate change is predicted to disproportionately impact sub-Saharan Africa, with potential devastating consequences on plant populations. Climate change may, however, impact intraspecific taxa differently. The aim of the study was to determine the current distribution and impact of climate change on three varieties of Vachellia sieberiana, that is, var. sieberiana, var. villosa and var. woodii. Ensemble species distribution models (SDMs) were built in "biomod2" using 66, 45, and 137 occurrence records for var. sieberiana, var. villosa, and var. woodii, respectively. The ensemble SDMs were projected to 2041-2060 and 2081-2100 under three general circulation models (GCMs) and two shared socioeconomic pathways (SSPs). The three GCMs were the Canadian Earth System Model version 5, the Institut Pierre-Simon Laplace Climate Model version 6A Low Resolution, and the Model for Interdisciplinary Research on Climate version 6. The suitable habitat of var. sieberiana predominantly occurs in the Sudanian and Zambezian phytochoria while that of var. villosa largely occurs in the Sudanian phytochorion. The suitable habitat of var. woodii mainly occurs in the Zambezian phyotochorion. There is coexistence of var. villosa and var. sieberiana in the Sudanian phytochorion while var. sieberiana and var. woodii coexist in the Zambezian phytochorion. Under SSP2-4.5 in 2041-2060 and averaged across the three GCMs, the suitable habitat expanded by 33.8% and 119.7% for var. sieberiana and var. villosa, respectively. In contrast, the suitable habitat of var. woodii contracted by -8.4%. Similar trends were observed in 2041-2060 under SSP5-8.5 [var. sieberiana (38.6%), var. villosa (139.0%), and var. woodii (-10.4%)], in 2081-2100 under SSP2-4.5 [var. sieberiana (4.6%), var. villosa (153.4%), and var. woodii (-14.4%)], and in 2081-2100 under SSP5-8.5 [var. sieberiana (49.3%), var. villosa (233.4%), and var. woodii (-30.7%)]. Different responses to climate change call for unique management and conservation decisions for the varieties.

Leopard subspecies conservation under climate and land-use change

Predicting the effects of global environmental changes on species distribution is a top conservation priority, particularly for large carnivores, that contribute to regulating and maintaining ecosystems. As the most widespread and adaptable large felid, ranging across Africa and Asia, leopards are crucial to many ecosystems as both keystone and umbrella species, yet they are threatened across their ranges. We used intraspecific species distribution models (SDMs) to predict changes in range suitability for leopards under future climate and land-use change and identify conservation gaps and opportunities. We generated intraspecific SDMs for the three western leopard subspecies, the African, Panthera pardus pardus; Arabian, Panthera pardus nimr; and Persian, Panthera pardus tulliana, leopards, and overlapped predictions with protected areas (PAs) coverage. We show that leopard subspecies differ in their environmental associations and vulnerability to future changes. The African and Arabian leopards are predicted to lose ~25% and ~14% of their currently suitable range, respectively, while the Persian leopard is predicted to experience ~12% range gains. We found that most areas predicted to be suitable were not protected, with only 4%-16% of the subspecies' ranges falling inside PAs, and that these proportions will decrease in the future. The highly variable responses we found between leopard subspecies highlight the importance of considering intraspecific variation when modelling vulnerability to climate and land-use changes. The predicted decrease in proportion of suitable ranges falling inside PAs threatens global capacity to effectively conserve leopards because survival rates are substantially lower outside PAs due to persecution. Hence, it is important to work with local communities to address negative human-wildlife interactions and to restore habitats to retain landscape connectivity where PA coverage is low. On the other hand, the predicted increase in range suitability across southern Europe presents opportunities for expansion outside of their contemporary range, capitalising on European rewilding schemes.

Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change

BACKGROUND

Climate change is expected to alter the factors that drive changes in adaptive variation. This is especially true for species with long life spans and limited dispersal capabilities. Rapid climate changes may disrupt the migration of beneficial genetic variations, making it challenging for them to keep up with changing environments. Understanding adaptive genetic variations in tree species is crucial for conservation and effective forest management. Our study used landscape genomic analyses and phenotypic traits from a thorough sampling across the entire range of Quercus longinux, an oak species native to Taiwan, to investigate the signals of adaptation within this species.

RESULTS

Using ecological data, phenotypic traits, and 1,933 single-nucleotide polymorphisms (SNPs) from 205 individuals, we classified three genetic groups, which were also phenotypically and ecologically divergent. Thirty-five genes related to drought and freeze resistance displayed signatures of natural selection. The adaptive variation was driven by diverse environmental pressures such as low spring precipitation, low annual temperature, and soil grid sizes. Using linear-regression-based methods, we identified isolation by environment (IBE) as the optimal model for adaptive SNPs. Redundancy analysis (RDA) further revealed a substantial joint influence of demography, geology, and environments, suggesting a covariation between environmental gradients and colonization history. Lastly, we utilized adaptive signals to estimate the genetic offset for each individual under diverse climate change scenarios. The required genetic changes and migration distance are larger in severe climates. Our prediction also reveals potential threats to edge populations in northern and southeastern Taiwan due to escalating temperatures and precipitation reallocation.

CONCLUSIONS

We demonstrate the intricate influence of ecological heterogeneity on genetic and phenotypic adaptation of an oak species. The adaptation is also driven by some rarely studied environmental factors, including wind speed and soil features. Furthermore, the genetic offset analysis predicted that the edge populations of Q. longinux in lower elevations might face higher risks of local extinctions under climate change.

Bringing traits back into the equation: A roadmap to understand species redistribution

Ecological and evolutionary theories have proposed that species traits should be important in mediating species responses to contemporary climate change; yet, empirical evidence has so far provided mixed evidence for the role of behavioral, life history, or ecological characteristics in facilitating or hindering species range shifts. As such, the utility of trait-based approaches to predict species redistribution under climate change has been called into question. We develop the perspective, supported by evidence, that trait variation, if used carefully can have high potential utility, but that past analyses have in many cases failed to identify an explanatory value for traits by not fully embracing the complexity of species range shifts. First, we discuss the relevant theory linking species traits to range shift processes at the leading (expansion) and trailing (contraction) edges of species distributions and highlight the need to clarify the mechanistic basis of trait-based approaches. Second, we provide a brief overview of range shift-trait studies and identify new opportunities for trait integration that consider range-specific processes and intraspecific variability. Third, we explore the circumstances under which environmental and biotic context dependencies are likely to affect our ability to identify the contribution of species traits to range shift processes. Finally, we propose that revealing the role of traits in shaping species redistribution may likely require accounting for methodological variation arising from the range shift estimation process as well as addressing existing functional, geographical, and phylogenetic biases. We provide a series of considerations for more effectively integrating traits as well as extrinsic and methodological factors into species redistribution research. Together, these analytical approaches promise stronger mechanistic and predictive understanding that can help society mitigate and adapt to the effects of climate change on biodiversity.

Climate change and its effects on body size and shape: the role of endocrine mechanisms

In many organisms, rapidly changing environmental conditions are inducing dramatic shifts in diverse phenotypic traits with consequences for fitness and population viability. However, the mechanisms that underlie these responses remain poorly understood. Endocrine signalling systems often influence suites of traits and are sensitive to changes in environmental conditions; they are thus ideal candidates for uncovering both plastic and evolved consequences of climate change. Here, we use body size and shape, a set of integrated traits predicted to shift in response to rising temperatures with effects on fitness, and insulin-like growth factor-1 as a case study to explore these ideas. We review what is known about changes in body size and shape in response to rising temperatures and then illustrate why endocrine signalling systems are likely to be critical in mediating these effects. Lastly, we discuss research approaches that will advance understanding of the processes that underlie rapid responses to climate change and the role endocrine systems will have. Knowledge of the mechanisms involved in phenotypic responses to climate change will be essential for predicting both the ecological and the long-term evolutionary consequences of a warming climate. This article is part of the theme issue 'Endocrine responses to environmental variation: conceptual approaches and recent developments'.

Rolling with the punches: Organism-environment interactions shape spatial pattern of adaptive differentiation in the widespread mantis shrimp Oratosquilla oratoria

Investigating spatial pattern of adaptive variation and its underlying processes can inform the adaptive potential distributed within species ranges, which is increasingly important in the context of a changing climate. A correct interpretation of adaptive variation pattern requires that population history and the ensuing population genetic structure are taken into account. Here we carried out such a study by integrating population genomic analyses, demographic model testing and species distribution modeling to investigate patterns and causes of adaptive differentiation in a widespread mantis shrimp, Oratosquilla oratoria, along a replicated, broad-scale temperature gradient in the northwestern Pacific (NWP). Our results supported a strong hierarchical ecogeographic structure dominated by habitat-linked divergence among O. oratoria populations accompanied with introgressive hybridization. A combined FST outlier and environmental correlation analyses revealed remarkable temperature-associated clines in allele frequency across paired North-South populations on Chinese and Japanese coasts, and identified a suite of loci associated with temperature adaptation. Further demographic model testing revealed the observed clinal variation derived partly from Pleistocene divergence followed by recent secondary contact. More importantly, the likelihood of hybridization is predicted to increase as climate change progresses, which would break barriers to gene flow and enable the spread of adaptive genetic variation. These results support that not only is temperature-driven adaptive differentiation occurs in O. oratoria but that such pattern is likely attributed to ancient adaptive variation, sustained by contemporary ocean conditions and a semi-permeable barrier to gene flow maintained by selection. They moreover provide genomic insights into the distribution of adaptive potential across O. oratoria' s species range. This work can serve as a case study to characterize adaptive diversity of marine species in the NWP by integrating environmental and genetic data at temporal and spatial scales in a population genomic framework, which would improve management and conservation actions under climate change.

Genomics for monitoring and understanding species responses to global climate change

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.

Finding genes and pathways that underlie coral adaptation

Mass coral bleaching is one of the clearest threats of climate change to the persistence of marine biodiversity. Despite the negative impacts of bleaching on coral health and survival, some corals may be able to rapidly adapt to warming ocean temperatures. Thus, a significant focus in coral research is identifying the genes and pathways underlying coral heat adaptation. Here, we review state-of-the-art methods that may enable the discovery of heat-adaptive loci in corals and identify four main knowledge gaps. To fill these gaps, we describe an experimental approach combining seascape genomics with CRISPR/Cas9 gene editing to discover and validate heat-adaptive loci. Finally, we discuss how information on adaptive genotypes could be used in coral reef conservation and management strategies.

The ecological and evolutionary consequences of tropicalisation

Tropicalisation is a marine phenomenon arising from contemporary climate change, and is characterised by the range expansion of tropical/subtropical species and the retraction of temperate species. Tropicalisation occurs globally and can be detected in both tropical/temperate transition zones and temperate regions. The ecological consequences of tropicalisation range from single-species impacts (e.g., altered behaviour) to whole ecosystem changes (e.g., phase shifts in intertidal and subtidal habitats). Our understanding of the evolutionary consequences of tropicalisation is limited, but emerging evidence suggests that tropicalisation could induce phenotypic change as well as shifts in the genotypic composition of both expanding and retracting species. Given the rapid rate of contemporary climate change, research on tropicalisation focusing on shifts in ecosystem functioning, biodiversity change, and socioeconomic impacts is urgently needed.

Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens

Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments and good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains, and we gathered data on an array of 21 phenotype traits. Population genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selection sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, and SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production traits. These insights not only provide genetic reference for the purification and breeding of Wenchang chickens but also broaden our understanding of the genetic basis of phenotypic diversity in chickens.

Predicting the future of our oceans-Evaluating genomic forecasting approaches in marine species

Climate change is restructuring biodiversity on multiple scales and there is a pressing need to understand the downstream ecological and genomic consequences of this change. Recent advancements in the field of eco-evolutionary genomics have sought to include evolutionary processes in forecasting species' responses to climate change (e.g., genomic offset), but to date, much of this work has focused on terrestrial species. Coastal and offshore species, and the fisheries they support, may be even more vulnerable to climate change than their terrestrial counterparts, warranting a critical appraisal of these approaches in marine systems. First, we synthesize knowledge about the genomic basis of adaptation in marine species, and then we discuss the few examples where genomic forecasting has been applied in marine systems. Next, we identify the key challenges in validating genomic offset estimates in marine species, and we advocate for the inclusion of historical sampling data and hindcasting in the validation phase. Lastly, we describe a workflow to guide marine managers in incorporating these predictions into the decision-making process.

Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming

The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.

Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests

Dipterocarpoideae species form the emergent layer of Asian rainforests. They are the indicator species for Asian rainforest distribution, but they are severely threatened. Here, to understand their adaptation and population decline, we assemble high-quality genomes of seven Dipterocarpoideae species including two autotetraploid species. We estimate the divergence time between Dipterocarpoideae and Malvaceae and within Dipterocarpoideae to be 108.2 (97.8‒118.2) and 88.4 (77.7‒102.9) million years ago, and we identify a whole genome duplication event preceding dipterocarp lineage diversification. We find several genes that showed a signature of selection, likely associated with the adaptation to Asian rainforests. By resequencing of two endangered species, we detect an expansion of effective population size after the last glacial period and a recent sharp decline coinciding with the history of local human activities. Our findings contribute to understanding the diversification and adaptation of dipterocarps and highlight anthropogenic disturbances as a major factor in their endangered status.

Declining salinity and increasing temperature reduce the diversity and resilience of benthic diatoms

Climate change will modify the marine ecosystem in several ways, but the effects of changing climate on benthic diatoms, which are one of the most important photosynthesizing organism groups in benthic habitats, are poorly studied. We conducted a mesocosm experiment to investigate the effects of increasing temperature and decreasing salinity on the taxonomic and functional diversity of benthic diatoms. We showed that decreasing salinity affects the taxonomic and functional composition of communities, and the threshold salinity for community composition is ~5. This indicates that when climate change leads to decreasing salinity in brackish systems, the most pronounced changes in communities occur in areas where salinity decreases from >5 to <5. We also showed that both increasing temperature and decreasing salinity exert stress on communities and, hence, lead to the decrease of the alpha and beta diversity of communities. This indicates that climate change reduces the size of the species pool of diatoms. Our results show that, along with the changing climate, we can expect benthic diatom communities to become less diverse and less resilient.

Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.

Local adaptation with gene flow in a highly dispersive shark

Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.

Projection of current and future distribution of adaptive genetic units in an alpine ungulate

Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate-the Northern chamois (Rupicapra rupicapra)-could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.

Assessing the invasive potential of different source populations of ragweed (Ambrosia artemisiifolia L.) through genomically informed species distribution modelling

The genetic composition of founding populations is likely to play a key role in determining invasion success. Individual genotypes may differ in habitat preference and environmental tolerance, so their ability to colonize novel environments can be highly variable. Despite the importance of genetic variation on invasion success, its influence on the potential distribution of invaders is rarely investigated. Here, we integrate population genomics and ecological niche models (ENMs) into a single framework to predict the distribution of globally invasive common ragweed (Ambrosia artemisiifolia) in Australia. We identified three genetic clusters for ragweed and used these to construct cluster-specific ENMs and characterize within-species niche differentiation. The potential range of ragweed in Australia depended on the genetic composition and continent of origin of the introduced population. Invaders originating from warmer, wetter climates had a broader potential distribution than those from cooler, drier ones. By quantifying this change, we identified source populations most likely to expand the ragweed distribution. As prevention remains the most effective method of invasive species management, our work provides a valuable way of ranking the threat posed by different populations to better inform management decisions.

A cross-sectional study to assess faculty and student knowledge of climate change and health: Readiness for curricular integration

AIMS

To examine the perceived knowledge, attitudes and beliefs regarding climate change and health of academic faculty and students in programmes for health professionals and to identify barriers/facilitators to and resources required for curriculum integration.

DESIGN

Cross-sectional survey eliciting quantitative and open-ended responses.

METHODS

A 22-question survey to assess climate-health knowledge/attitudes/beliefs was distributed to all students and faculty (n = 224) at one academic institution in the United States. Open-ended questions addressed barriers, facilitators and required resources. Descriptive statistics are reported, and thematic analysis was used to identify themes from open-ended responses.

RESULTS

Response rate was 15%. Most respondents (76%) were between 20 and 34 years old. The majority were from nursing (39%), occupational therapy (13%) and communication speech disorders (12.5%). Most respondents perceived climate change as relevant to direct patient care (78%) and believed that it is impacting the health of individuals (86%) and should be integrated into curricula (89%). Yet, most (60%) reported modest to no knowledge about the health impacts. Faculty reported little to no comfort teaching climate change and health concepts (76%). Open-ended responses identified student/faculty receptivity and professional/clinical relevance as important facilitators of successful integration. Barriers included intensity of programmes; time and competing curricular priorities; and a lack of faculty expertise, resources, institutional and professional commitment.

CONCLUSIONS

Most health professions students and faculty indicated that educating future health professionals about climate change and health is important, but existing barriers must be addressed.

IMPACT

This study addressed student and faculty perceptions of integrating climate change and health into health professions curricula. Discipline-specific and interprofessional educational approaches are necessary to optimize future health professionals' efforts to prevent and mitigate climate change impacts for at-risk patients, communities and populations.

Landscape genomics analysis provides insights into future climate change-driven risk in rhesus macaque

Climate change significantly affects the suitability of wildlife habitats. Thus, understanding how animals adapt ecologically and genetically to climate change is important for targeted species protection. Rhesus macaques (Macaca mulatta) are widely distributed and multi-climatically adapted primates. This study explored how rhesus macaques adapt to climate change by integrating ecological and genetic methods and applying species distribution models (SDMs) and a gradient forest (GF) model. The findings suggested that temperature seasonality primarily affects habitat suitability and indicated that climate change will have a dramatic impact on macaque populations in the future. We also applied genotype-environment association (GEA) analyses and selection signature analyses to identify genes associated with climate change and provide possible explanations for the adaptation of rhesus macaques to climatic environments. The population genomics analyses suggested that the Taihang population has the highest genomic vulnerability with inbreeding and low heterozygosity. Combined with the higher ecological vulnerability, additional conservation strategies are required for this population under higher risk of climate change. Our work measured the impact of climate change and enabled the identification of populations that exhibit high vulnerability to severe climate change. Such information is useful for selecting populations of rhesus macaques as subject of long-term monitoring or evolutionary rescue under future climate change.

Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill

Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.

Genomic signals of local adaptation in Picea crassifolia

BACKGROUND

Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere.

RESULTS

Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding.

CONCLUSIONS

Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations.

Accelerating local extinction associated with very recent climate change

Climate change has already caused local extinction in many plants and animals, based on surveys spanning many decades. As climate change accelerates, the pace of these extinctions may also accelerate, potentially leading to large-scale, species-level extinctions. We tested this hypothesis in a montane lizard. We resurveyed 18 mountain ranges in 2021-2022 after only ~7 years. We found rates of local extinction among the fastest ever recorded, which have tripled in the past ~7 years relative to the preceding ~42 years. Further, climate change generated local extinction in ~7 years similar to that seen in other organisms over ~70 years. Yet, contrary to expectations, populations at two of the hottest sites survived. We found that genomic data helped predict which populations survived and which went extinct. Overall, we show the increasing risk to biodiversity posed by accelerating climate change and the opportunity to study its effects over surprisingly brief timescales.

Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivore Lynx lynx (Linnaeus, 1758)

Local adaptations to the environment are an important aspect of the diversity of a species and their discovery, description and quantification has important implications for the fields of taxonomy, evolutionary and conservation biology. In this study, we scan genomes from several populations across the distributional range of the Eurasian lynx, with the objective of finding genomic windows under positive selection which may underlie local adaptations to different environments. A total of 394 genomic windows are found to be associated to local environmental conditions, and they are enriched for genes involved in metabolism, behaviour, synaptic organization and neural development. Adaptive genetic structure, reconstructed from SNPs in candidate windows, is considerably different than the neutral genetic structure of the species. A widespread adaptively homogeneous group is recovered occupying areas of harsher snow and temperature climatic conditions in the north-western, central and eastern parts of the distribution. Adaptively divergent populations are recovered in the westernmost part of the range, especially within the Baltic population, but also predicted for different patches in the western and southern part of the range, associated with different snow and temperature regimes. Adaptive differentiation driven by climate does not correlate much with the subspecies taxonomic delimitations, suggesting that subspecific divergences are mostly driven by neutral processes of genetic drift and gene flow. Our results will aid the selection of source populations for assisted gene flow or genetic rescue programs by identifying what climatic patterns to look for as predictors of pre-adaptation of individuals. Particularly, the Carpathian population is confirmed as the best source of individuals for the genetic rescue of the endangered, isolated and genetically eroded Balkan population. Additionally, reintroductions in central and western Europe, currently based mostly on Carpathian lynxes, could consider the Baltic population as an additional source to increase adaptive variation and likely improve adaptation to their milder climate.

Estimating the Spatial Distribution and Future Conservation Requirements of the Spotted Seal in the North Pacific

Local adaptation has been increasingly involved in the designation of species conservation strategies to response to climate change. Marine mammals, as apex predators, are climatechange sensitive, and their spatial distribution and conservation requirements are critically significant for designing protection strategies. In this study, we focused on an ice-breeding marine mammal, the spotted seal (Phoca largha), which exhibits distinct morphological and genetic variations across its range. Our objectives were to quantify the ecological niches of three spotted seal populations, construct the species-level model and population-level models that represent different regions in the Bering population (BDPS), Okhotsk population (ODPS) and southern population (SDPS), and conduct a conservation gap analysis. Our findings unequivocally demonstrated a clear niche divergence among the three populations. We predicted habitat contraction for the BDPS and ODPS driven by climate change; in particular, the spotted seals inhabiting Liaodong Bay may face breeding habitat loss. However, most spotted seal habitats are not represented in existing marine protected areas. Drawing upon these outcomes, we propose appropriate conservation policies to effectively protect the habitat of the different geographical populations of spotted seals. Our research addresses the importance of incorporating local adaptation into species distribution modeling to inform conservation and management strategies.

Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera

BACKGROUND AND AIMS

Understanding adaptive genetic variation and whether it can keep pace with predicted future climate change is critical in assessing the genetic vulnerability of species and developing conservation management strategies. The lack of information on adaptive genetic variation in relict species carrying abundant genetic resources hinders the assessment of genetic vulnerability. Using a landscape genomics approach, this study aimed to determine how adaptive genetic variation shapes population divergence and to predict the adaptive potential of Pterocarya macroptera (a vulnerable relict species in China) under future climate scenarios.

METHODS

We applied restriction site-associated DNA sequencing (RAD-seq) to obtain 8244 single-nucleotide polymorphisms (SNPs) from 160 individuals across 28 populations. We examined the pattern of genetic diversity and divergence, and then identified outliers by genetic differentiation (FST) and genotype-environment association (GEA) methods. We further dissected the effect of geographical/environmental gradients on genetic variation. Finally, we predicted genetic vulnerability and adaptive risk under future climate scenarios.

KEY RESULTS

We identified three genetic lineages within P. macroptera: the Qinling-Daba-Tianmu Mountains (QDT), Western Sichuan (WS) and Northwest Yunnan (NWY) lineages, which showed significant signals of isolation by distance (IBD) and isolation by environment (IBE). IBD and IBE explained 3.7-5.7 and 8.6-12.8 % of the genetic structure, respectively. The identified GEA SNP-related genes were involved in chemical defence and gene regulation and may exhibit higher genetic variation to adapt to the environment. Gradient forest analysis revealed that the genetic variation was mainly shaped by temperature-related variables, indicating its adaptation to local thermal environments. A limited adaptive potential was suggested by the high levels of genetic vulnerability in marginal populations.

CONCLUSIONS

Environmental gradient mainly shaped the population differentiation of P. macroptera. Marginal populations may be at high risk of extinction, and thus proactive management measures, such as assisted gene flow, are required to ensure the survival of these populations.

Identifying genetic variation associated with environmental gradients and drought-tolerance phenotypes in ponderosa pine

As climate changes, understanding the genetic basis of local adaptation in plants becomes an ever more pressing issue. Combining genotype-environment association (GEA) with genotype-phenotype association (GPA) analysis has an exciting potential to uncover the genetic basis of environmental responses. We use these approaches to identify genetic variants linked to local adaptation to drought in Pinus ponderosa. Over 4 million Single Nucleotide Polymorphisms (SNPs) were identified using 223 individuals from across the Sierra Nevada of California. 927,740 (22.3%) SNPs were retained after filtering for proximity to genes and used in our association analyses. We found 1374 associated with five major climate variables, with the largest number (1151) associated with April 1st snowpack. We also conducted a greenhouse study with various drought-tolerance traits measured in first-year seedlings of a subset of the genotyped trees grown in the greenhouse. 796 SNPs were associated with control-condition trait values, while 1149 were associated with responsiveness of these traits to drought. While no individual SNPs were associated with both the environmental variables and the measured traits, several annotated genes were associated with both, particularly those involved in cell wall formation, biotic and abiotic stress responses, and ubiquitination. However, the functions of many of the associated genes have not yet been determined due to the lack of gene annotation information for conifers. Future studies are needed to assess the developmental roles and ecological significance of these unknown genes.

Accounting for trait variability and coordination in predictions of drought-induced range shifts in woody plants

Functional traits offer a promising avenue to improve predictions of species range shifts under climate change, which will entail warmer and often drier conditions. Although the conceptual foundation linking traits with plant performance and range shifts appears solid, the predictive ability of individual traits remains generally low. In this review, we address this apparent paradox, emphasizing examples of woody plants and traits associated with drought responses at the species' rear edge. Low predictive ability reflects the fact not only that range dynamics tend to be complex and multifactorial, as well as uncertainty in the identification of relevant traits and limited data availability, but also that trait effects are scale- and context-dependent. The latter results from the complex interactions among traits (e.g. compensatory effects) and between them and the environment (e.g. exposure), which ultimately determine persistence and colonization capacity. To confront this complexity, a more balanced coverage of the main functional dimensions involved (stress tolerance, resource use, regeneration and dispersal) is needed, and modelling approaches must be developed that explicitly account for: trait coordination in a hierarchical context; trait variability in space and time and its relationship with exposure; and the effect of biotic interactions in an ecological community context.

Evolutionary dynamics of Euphorbia carniolica suggest a complex Plio-Pleistocene history of understorey species of deciduous forest in southeastern Europe

Deciduous forests form the dominant natural vegetation of Europe today, but were restricted to small refugia during Pleistocene cold stages, implying an evolutionary past shaped by recurrent range contractions and expansions. Cold-stage forest refugia were probably widespread in southern and central Europe, with the northwestern Balkan Peninsula being of particular importance. However, the actual number and location of deciduous forest refugia, as well as the connections between them, remain disputed. Here, we address the evolutionary dynamics of the deciduous forest understorey species Euphorbia carniolica as a proxy for past forest dynamics. To do so, we obtained genomic and morphometric data from populations representing the species' entire range, investigated phylogenetic position and intraspecific genetic variation, tested explicit demographic scenarios and applied species distribution models. Our data support two disjoint groups linked to separate refugia on the northwestern and central Balkan Peninsula. We find that genetic differentiation between groups started in the early Pleistocene via vicariance, suggesting a larger distribution in the past. Both refugia acted as sources for founder events to the southeastern Alps and the Carpathians; the latter were likely colonised before the last cold stage. In line with traditional views on the pre-Pleistocene origin of many southeastern European deciduous forest species, the origin of E. carniolica was dated to the late Pliocene. The fact that E. carniolica evolved at a time when a period of continuous forestation was ending in much of Eurasia provides an interesting biogeographical perspective on the past links between Eurasian deciduous forests and their biota.

Beat the heat: thermal respites and access to food associated with increased bumble bee heat tolerance

Climate change poses a threat to organisms across the world, with cold-adapted species such as bumble bees (Bombus spp.) at particularly high risk. Understanding how organisms respond to extreme heat events associated with climate change as well as the factors that increase resilience or prime organisms for future stress can inform conservation actions. We investigated the effects of heat stress within different contexts (duration, periodicity, with and without access to food, and in the laboratory versus field) on bumble bee (Bombus impatiens) survival and heat tolerance. We found that both prolonged (5 h) heat stress and nutrition limitation were negatively correlated with worker bee survival and thermal tolerance. However, the effects of these acute stressors were not long lasting (no difference in thermal tolerance among treatment groups after 24 h). Additionally, intermittent heat stress, which more closely simulates the forager behavior of leaving and returning to the nest, was not negatively correlated with worker thermal tolerance. Thus, short respites may allow foragers to recover from thermal stress. Moreover, these results suggest there is no priming effect resulting from short- or long-duration exposure to heat - bees remained equally sensitive to heat in subsequent exposures. In field-caught bumble bees, foragers collected during warmer versus cooler conditions exhibited similar thermal tolerance after being allowed to recover in the lab for 16 h. These studies offer insight into the impacts of a key bumble bee stressor and highlight the importance of recovery duration, stressor periodicity and context on bumble bee thermal tolerance outcomes.

Climate change impacts the distribution of Quercus section Cyclobalanopsis (Fagaceae), a keystone lineage in East Asian evergreen broadleaved forests

East Asian evergreen broadleaved forests (EBFLs) harbor high species richness, but these ecosystems are severely impacted by global climate change and deforestation. Conserving and managing EBLFs requires understanding dominant tree distribution dynamics. In this study, we used 29 species in Quercus section Cyclobalanopsis-a keystone lineage in East Asian EBLFs-as proxies to predict EBLF distribution dynamics using species distribution models (SDMs). We examined climatic niche overlap, similarity, and equivalency among seven biogeographical regions' species using 'ecospat'. We also estimated the effectiveness of protected areas in the predicted range to elucidate priority conservation regions. Our results showed that the climatic niches of most geographical groups differ. The western species under the Indian summer monsoon regime were mainly impacted by temperature factors, whereas precipitation impacted the eastern species under the East Asian summer monsoon regime. Our simulation predicted a northward range expansion of section Cyclobalanopsis between 2081 and 2100, except for the ranges of the three Himalayan species analyzed, which might shrink significantly. The greatest shift of highly suitable areas was predicted for the species in the South Pacific, with a centroid shift of over 300 km. Remarkably, only 7.56% of suitable habitat is currently inside protected areas, and the percentage is predicted to continue declining in the future. To better conserve Asian EBLFs, establishing nature reserves in their northern distribution ranges, and transplanting the populations with predicted decreasing numbers and degraded habitats to their future highly suitable areas, should be high-priority objectives.

Niche shifts and range expansions after invasions of two major pests: the Asian longhorned beetle and the citrus longhorned beetle

BACKGROUND

In recent years, the quarantine forestry pests the Asian longhorned beetle (ALB) Anoplophora glabripennis and the citrus longhorned beetle (CLB) Anoplophora chinensis have spread across the Northern Hemisphere, triggering concern about their potential distribution. However, little is known about the niche shifts of the pests during the invasion, making it difficult to assess their potential ranges. We thus employed two distinct approaches (i.e., ordination-based and reciprocal model-based) to compare the native and invaded niches of ALB and CLB after their spread to new continents based on global occurrence records. We further constructed models with pooled occurrences from both the native and invaded ranges to analyze the effects of occurrence partitioning on predicted ranges.

RESULTS

We detected expansions in the invaded niches of both pests, indicating that the niches shifted to varying extents after the invasion. Large shares of the native niches of ALB and CLB remained unfilled, revealing the potential for further invasion in new regions. The models calibrated with pooled occurrences clearly underestimated the potential ranges in invaded regions compared with the projections based on partitioned models considering native and invaded areas separately.

CONCLUSIONS

These results emphasize the importance of elucidating the niche dynamics of invasive species for obtaining accurately predicted ranges, which may help identify risk areas masked by the assumption of niche conservatism. Furthermore, prevention and quarantine measures for ALB and CLB are clearly needed to avoid future serious damage to forest ecosystems. © 2023 Society of Chemical Industry.

Thermophilisation of communities differs between land plant lineages, land use types and elevation

Bryophytes provide key ecosystem services at the global scale such as carbon storage and primary production in resource limited habitats, but compared to vascular plants knowledge on how these organisms face recent climate warming is fragmentary. This is particularly critical because bryophytes differ fundamentally from vascular plants in their ecophysiological and biological characteristics, so that community alterations most likely have different dynamics. In a comparative approach, we analysed thermophilisation of bryophyte and vascular plant communities in 1146 permanent plots distributed along an elevational gradient of nearly 3.000 m in Switzerland (Central Europe) that were visited in 5-years intervals between 2001 and 2021. We estimated thermophilisation from changes in unweighted mean temperature indicator values of species, compared it to expected thermophilisation rates given the shift of isotherms and addressed differences between the two lineages, major land use types (managed grasslands, forests, unmanaged open areas), life strategy types (long- and short-lived species) and in elevation. Thermophilisation of bryophyte communities was on average 2.1 times higher than of vascular plant communities and at high elevations it approximated the expected rate given the shift of isotherms. Thermophilisation of both, bryophyte and vascular plant communities was not driven by a loss of cryophilic species but by an increase in thermophilic and mesophilic species, indicating an in-filling process. Furthermore, our data show that thermophilisation is higher in managed grasslands than in forests. We suggest that the higher responsiveness of bryophytes compared to vascular plants depends on their poikilohydry and dispersal capacity and that lower thermophilisation of forests communities is related to the buffering effect of microclimatic conditions in the interior of forests. Our study emphasises the heterogeneity of climate warming effects on plants because response dynamics differ between taxonomic groups as well as between land use types and along elevational gradients.

Post-glacial range formation of temperate forest understorey herbs - Insights from a spatio-temporally explicit modelling approach

Aim

Our knowledge of Pleistocene refugia and post-glacial recolonization routes of forest understorey plants is still very limited. The geographical ranges of these species are often rather narrow and show highly idiosyncratic, often fragmented patterns indicating either narrow and species-specific ecological tolerances or strong dispersal limitations. However, the relative roles of these factors are inherently difficult to disentangle.

Location

Central and south-eastern Europe.

Time period

17,100 BP - present.

Major taxa studied

Five understorey herbs of European beech forests: Aposeris foetida, Cardamine trifolia, Euphorbia carniolica, Hacquetia epipactis and Helleborus niger.

Methods

We used spatio-temporally explicit modelling to reconstruct the post-glacial range dynamics of the five forest understorey herbs. We varied niche requirements, demographic rates and dispersal abilities across plausible ranges and simulated the spread of species from potential Pleistocene refugia identified by phylogeographical analyses. Then we identified the parameter settings allowing for the most accurate reconstruction of their current geographical ranges.

Results

We found a largely homogenous pattern of optimal parameter settings among species. Broad ecological niches had to be combined with very low but non-zero rates of long-distance dispersal via chance events and low rates of seed dispersal over moderate distances by standard dispersal vectors. However, long-distance dispersal events, although rare, led to high variation among replicated simulation runs.

Main conclusions

Small and fragmented ranges of many forest understorey species are best explained by a combination of broad ecological niches and rare medium- and long-distance dispersal events. Stochasticity is thus an important determinant of current species ranges, explaining the idiosyncratic distribution patterns of the study species despite strong similarities in refugia, ecological tolerances and dispersal abilities.

Changing with the times: Seasonal environmental gradients unveil dynamic bat assemblages and vulnerability

Uncovering the temporal and spatial dynamics of biological communities in response to biotic and abiotic drivers is essential to predict the effects of environmental change on biodiversity. Similarly, estimating species vulnerability in the face of such dynamics is crucial for implementing effective conservation actions. We explored how bat diversity changes over the year across an altitudinal gradient and identified the environmental drivers that shape bat communities. By analysing species' marginality within the biophysical niche space, we evaluated bats' vulnerability to foreseeable environmental changes. Our results suggest that altitude, the proportion of forest cover and shrub cover are the main drivers shaping bat communities year-round. Additionally, while some bat species are restricted to a single ecological assemblage (or ecological preferences group), others show greater plasticity throughout the year. Importantly, we found that although bats associated with highland habitats and forests could be particularly vulnerable to environmental changes (in particular Myotis mystacinus), this vulnerability correlates poorly with their national conservation status. We suggest that species' ecological plasticity is critical for the resilience of biological communities exposed to environmental changes and should be considered when planning tailored conservation strategies.

Climate change, host plant availability, and irrigation shape future region-specific distributions of the Sitobion grain aphid complex

BACKGROUND

Understanding where species occur using species distribution models has become fundamental to ecology. Although much attention has been paid to invasive species, questions about climate change related range shifts of widespread insect pests remain unanswered. Here, we incorporated bioclimatic factors and host plant availability into CLIMEX models to predict distributions under future climate scenarios of major cereal pests of the Sitobion grain aphid complex (Sitobion avenae, S. miscanthi, and S. akebiae). Additionally, we incorporated the application of irrigation in our models to explore the relevance of a frequently used management practice that may interact with effects of climate change of the pest distributions.

RESULTS

Our models predicted that the area potentially at high risk of outbreaks of the Sitobion grain aphid complex would increase from 41.3% to 53.3% of the global land mass. This expansion was underlined by regional shifts in both directions: expansion of risk areas in North America, Europe, most of Asia, and Oceania, and contraction of risk areas in South America, Africa, and Australia. In addition, we found that host plant availability limited the potential distribution of pests, while the application of irrigation expanded it.

CONCLUSION

Our study provides insights into potential risk areas of insect pests and how climate, host plant availability, and irrigation affect the occurrence of the Sitobion grain aphid complex. Our results thereby support agricultural policy makers, farmers, and other stakeholders in their development and application of management practices aimed at maximizing crop yields and minimizing economic losses. © 2023 Society of Chemical Industry.