Strong phenotypic plasticity limits potential for evolutionary responses to climate change

Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication

The domestication of crops, coupled with agroecosystem development, is associated with major environmental changes and provides an ideal model of phenotypic plasticity. Here, we examined 32 genotypes of three tetraploid wheat (Triticum turgidum L.) subspecies, wild emmer, emmer, and durum wheat, which are representative of the key stages in the domestication of tetraploid wheat. We developed a pipeline that integrates RNA-Seq data and population genomics to assess gene expression plasticity and identify selection signatures under diverse nitrogen availability conditions. Our analysis revealed differing gene expression responses to nitrogen availability across primary (wild emmer to emmer) and secondary (emmer to durum wheat) domestication. Notably, nitrogen triggered the expression of twice as many genes in durum wheat compared to that in emmer and wild emmer. Unique selection signatures were identified at each stage: primary domestication mainly influenced genes related to biotic interactions, whereas secondary domestication affected genes related to amino acid metabolism, in particular lysine. Selection signatures were found in differentially expressed genes (DEGs), notably those associated with nitrogen metabolism, such as the gene encoding glutamate dehydrogenase (GDH). Overall, our study highlights the pivotal role of nitrogen availability in the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.

Selection on genome-wide gene expression plasticity of rice in wet and dry field environments

Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment. Gene expression plasticity was neutral for most gradually plastic transcripts, but transcripts with discrete patterns of expression showed stronger selection on expression plasticity. Whether plasticity was adaptive and co-gradient or maladaptive and counter-gradient varied among varietal groups. No transcripts that experienced selection for plasticity across environments showed selection against plasticity within environments, indicating a lack of evidence for costs of adaptive plasticity that may constrain its evolution. Selection on expression plasticity was influenced by degree of plasticity, transcript length and gene body methylation. We observed positive selection on plasticity of co-expression modules containing transcripts involved in photosynthesis, translation and responsiveness to abiotic stress. Taken together, these results indicate that patterns of selection on expression plasticity were context-dependent and likely associated with environmental conditions of varietal groups, but that the evolution of adaptive plasticity would likely not be constrained by opposing patterns of selection on plasticity within compared to across environments. These results offer a genome-wide view of patterns of selection and ecological constraints on gene expression plasticity and provide insights into the interplay between plastic and evolutionary responses to drought at the molecular level.

Alternative splicing in parallel evolution and the evolutionary potential in sticklebacks

Repeatability of adaptation to similar environments provides opportunity to evaluate the predictability of natural selection. While many studies have investigated gene expression differences between populations adapted to contrasting environments, the role of post-transcriptional processes such as alternative splicing has rarely been evaluated in the context of parallel adaptation. To address the aforementioned knowledge gap, we reanalysed transcriptomic data from three pairs of threespine stickleback (Gasterosteus aculeatus) ecotypes adapted to marine or freshwater environment. First, we identified genes with repeated expression or splicing divergence across ecotype pairs, and compared the genetic architecture and biological processes between parallelly expressed and parallelly spliced loci. Second, we analysed the extent to which parallel adaptation was reflected at gene expression and alternative splicing levels. Finally, we tested how the two axes of transcriptional variation differed in their potential for evolutionary change. Although both repeated differential splicing and differential expression across ecotype pairs showed tendency for parallel divergence, the degree of parallelism was lower for splicing than expression. Furthermore, parallel divergences in splicing and expression were likely to be associated with distinct cis-regulatory genetic variants and functionally unique set of genes. Finally, we found that parallelly spliced genes showed higher nucleotide diversity than parallelly expressed genes, indicating splicing is less susceptible to genetic variation erosion during parallel adaptation. Our results provide novel insight into the role of splicing in parallel adaptation, and underscore the contribution of splicing to the evolutionary potential of wild populations under environmental change.

Higher thermal plasticity in flowering phenology increases flowering output

Ongoing climate change poses an increasing threat to biodiversity. To avoid decline or extinction, species need to either adjust or adapt to new environmental conditions or track their climatic niches across space. In sessile organisms such as plants, phenotypic plasticity can help maintain fitness in variable and even novel environmental conditions and is therefore likely to play an important role in allowing them to survive climate change, particularly in the short term. Understanding a species' response to rising temperature is crucial for planning well-targeted and cost-effective conservation measures. We sampled seeds of three Hypericum species (H. maculatum, H. montanum, and H. perforatum), from a total of 23 populations originating from different parts of their native distribution areas in Europe. We grew them under four different temperature regimes in a greenhouse to simulate current and predicted future climatic conditions in the distribution areas. We measured flowering start, flower count, and subsequent seed weight, allowing us to study variations in the thermal plasticity of flowering phenology and its relation to fitness. Our results show that individuals flowered earlier with increasing temperature, while the degree of phenological plasticity varied among species. More specifically, the plasticity of H. maculatum varied depending on population origin, with individuals from the leading range edge being less plastic. Importantly, we show a positive relationship between higher plasticity and increased flower production, indicating adaptive phenological plasticity. The observed connection between plasticity and fitness supports the idea that plasticity may be adaptive. This study underlines the need for information on plasticity for predicting species' potential to thrive under global change and the need for studies on whether higher phenotypic plasticity is currently being selected as natural populations experience a rapidly changing climate.

Transcriptomics of differences in thermal plasticity associated with selection for an exaggerated male sexual trait

The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperature. Temperature decrease to 18 °C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28 °C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection of males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has a potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.

Maternal investment and early thermal conditions affect performance and antipredator responses

Exposure to increased temperatures during early development can lead to phenotypic plasticity in morphology, physiology, and behavior across a range of ectothermic animals. In addition, maternal effects are known to be important contributors to phenotypic variation in offspring. Whether the 2 factors interact to shape offspring morphology and behavior is rarely explored. This is critical because climate change is expected to impact both incubation temperature and maternal stress and resource allocation. Using a fully factorial design, and Bayesian multivariate mixed models, we explored how the manipulation of early thermal environment and yolk-quantity in eggs affected the morphology, performance, and antipredator behavior of 2 sympatric Australian skink species (Lampropholis delicata and L. guichenoti). We found that juveniles from the hot treatment were larger than those on the cold treatment in L. guichenoti but not L. delicata. Using repeated behavioral measures for individual lizards, we found an interaction between incubation temperature and maternal investment in performance, with running speed being affected in a species-specific way by the treatment. We predicted that changes in performance should influence antipredator responses. In support of this prediction, we found that maternal investment impacted antipredator behavior, with animals from the yolk-reduced and cold treatment resuming activity faster after a simulated predatory attack in L. delicata. However, the prediction was not supported in L. guichenoti. Our results highlight the importance of exploring the multifaceted role that environments play across generations to understand how different anthropogenic factors will impact wildlife in the future.

Environmental effects on genetic variance are likely to constrain adaptation in novel environments

Adaptive plasticity allows populations to cope with environmental variation but is expected to fail as conditions become unfamiliar. In novel conditions, populations may instead rely on rapid adaptation to increase fitness and avoid extinction. Adaptation should be fastest when both plasticity and selection occur in directions of the multivariate phenotype that contain abundant genetic variation. However, tests of this prediction from field experiments are rare. Here, we quantify how additive genetic variance in a multivariate phenotype changes across an elevational gradient, and test whether plasticity and selection align with genetic variation. We do so using two closely related, but ecologically distinct, sister species of Sicilian daisy (Senecio, Asteraceae) adapted to high and low elevations on Mt. Etna. Using a quantitative genetic breeding design, we generated and then reciprocally planted c. 19,000 seeds of both species, across an elevational gradient spanning each species' native elevation, and then quantified mortality and five leaf traits of emergent seedlings. We found that genetic variance in leaf traits changed more across elevations than between species. The high-elevation species at novel lower elevations showed changes in the distribution of genetic variance among the leaf traits, which reduced the amount of genetic variance in the directions of selection and the native phenotype. By contrast, the low-elevation species mainly showed changes in the amount of genetic variance at the novel high elevation, and genetic variance was concentrated in the direction of the native phenotype. For both species, leaf trait plasticity across elevations was in a direction of the multivariate phenotype that contained a moderate amount of genetic variance. Together, these data suggest that where plasticity is adaptive, selection on genetic variance for an initially plastic response could promote adaptation. However, large environmental effects on genetic variance are likely to reduce adaptive potential in novel environments.

Incorporating plant phenological responses into species distribution models reduces estimates of future species loss and turnover

Anthropogenetic climate change has caused range shifts among many species. Species distribution models (SDMs) are used to predict how species ranges may change in the future. However, most SDMs rarely consider how climate-sensitive traits, such as phenology, which affect individuals' demography and fitness, may influence species' ranges. Using > 120 000 herbarium specimens representing 360 plant species distributed across the eastern United States, we developed a novel 'phenology-informed' SDM that integrates phenological responses to changing climates. We compared the ranges of each species forecast by the phenology-informed SDM with those from conventional SDMs. We further validated the modeling approach using hindcasting. When examining the range changes of all species, our phenology-informed SDMs forecast less species loss and turnover under climate change than conventional SDMs. These results suggest that dynamic phenological responses of species may help them adjust their ecological niches and persist in their habitats as the climate changes. Plant phenology can modulate species' responses to climate change, mitigating its negative effects on species persistence. Further application of our framework will contribute to a generalized understanding of how traits affect species distributions along environmental gradients and facilitate the use of trait-based SDMs across spatial and taxonomic scales.

Gene expression plasticity followed by genetic change during colonization in a high-elevation environment

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called 'plasticity first.' Herein, we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimentally implemented hypoxia acclimation (plastic stage), and colonized highland (colonized stage). Using a group of co-expressed genes from the cardiac and flight muscles, respectively, we demonstrate that gene expression plasticity to hypoxia tolerance is more often reversed than reinforced at the colonized stage. By correlating gene expression change with muscle phenotypes, we show that colonized tree sparrows reduce maladaptive plasticity that largely associated with decreased hypoxia tolerance. Conversely, adaptive plasticity that is congruent with increased hypoxia tolerance is often reinforced in the colonized tree sparrows. Genes displaying large levels of reinforcement or reversion plasticity (i.e. 200% of original level) show greater genetic divergence between ancestral and colonized populations. Overall, our work demonstrates that gene expression plasticity at the initial stage of high-elevation colonization can be reversed or reinforced through selection-driven adaptive modification.

Plasticity of Gene Expression and Thermal Tolerance: Implications for Climate Change Vulnerability in a Tropical Forest Lizard

AbstractTropical ectotherms are thought to be especially vulnerable to climate change because they have evolved in temporally stable thermal environments and therefore have decreased tolerance for thermal variability. Thus, they are expected to have narrow thermal tolerance ranges, live close to their upper thermal tolerance limits, and have decreased thermal acclimation capacity. Although models often predict that tropical forest ectotherms are especially vulnerable to rapid environmental shifts, these models rarely include the potential for plasticity of relevant traits. We measured phenotypic plasticity of thermal tolerance and thermal preference as well as multitissue transcriptome plasticity in response to warmer temperatures in a species that previous work has suggested is highly vulnerable to climate warming, the Panamanian slender anole lizard (Anolis apletophallus). We found that many genes, including heat shock proteins, were differentially expressed across tissues in response to short-term warming. Under long-term warming, the voluntary thermal maxima of lizards also increased, although thermal preference exhibited only limited plasticity. Using these data, we modeled changes in the activity time of slender anoles through the end of the century under climate change and found that plasticity should delay declines in activity time by at least two decades. Our results suggest that slender anoles, and possibly other tropical ectotherms, can alter the expression of genes and phenotypes when responding to shifting environmental temperatures and that plasticity should be considered when predicting the future of organisms under a changing climate.

Chasing the fitness optimum: temporal variation in the genetic and environmental expression of life-history traits for a perennial plant

BACKGROUND AND AIMS

The ability of plants to track shifting fitness optima is crucial within the context of global change, where increasing environmental extremes may have dramatic consequences for life history, fitness, and ultimately population persistence. However, tracking changing conditions relies on the relationship between genetic and environmental variance, where selection may favour plasticity, the evolution of genetic differences, or both depending on the spatial and temporal scale of environmental heterogeneity.

METHODS

Over three years, we compared the genetic and environmental components of phenological and life-history variation in a common environment for the spring perennial Geum triflorum. Populations were sourced from alvar habitats that exhibit extreme but predictable annual flood-desiccation cycles and prairie habitats that exhibit similar but less predictable variation in water availability.

KEY RESULTS

Heritability was generally higher for early life-history (emergence probability) relative to later life-history traits (total seed mass), indicating that traits associated with establishment are under stronger genetic control relative to later life-history fitness expressions, where plasticity may play a larger role. This pattern was particularly notable in seeds sourced from environmentally extreme but predictable alvar habitats relative to less predictable prairie environments. Fitness landscapes based on seed source origin, largely characterized by varying water availability and flower production, described selection as the degree of maladaptation of seed source environment relative to the prairie common garden environment. Plants from alvar populations were consistently closer to the fitness optimum across all years. Annually, the breadth of the fitness optimum expanded primarily along a moisture gradient, with inclusion of more populations onto the expanding optimum.

CONCLUSIONS

These results highlight the importance of temporally and spatially varying selection in life-history evolution, indicating plasticity may become a primary mechanism needed to track fitness for later life-history events within perennial systems.

Does the definition of a novel environment affect the ability to detect cryptic genetic variation?

Anthropogenic change exposes populations to environments that have been rare or entirely absent from their evolutionary past. Such novel environments are hypothesized to release cryptic genetic variation, a hidden store of variance that can fuel evolution. However, support for this hypothesis is mixed. One possible reason is a lack of clarity in what is meant by 'novel environment', an umbrella term encompassing conditions with potentially contrasting effects on the exposure or concealment of cryptic variation. Here, we use a meta-analysis approach to investigate changes in the total genetic variance of multivariate traits in ancestral versus novel environments. To determine whether the definition of a novel environment could explain the mixed support for a release of cryptic genetic variation, we compared absolute novel environments, those not represented in a population's evolutionary past, to extreme novel environments, those involving frequency or magnitude changes to environments present in a population's ancestry. Despite sufficient statistical power, we detected no broad-scale pattern of increased genetic variance in novel environments, and finding the type of novel environment did not explain any significant variation in effect sizes. When effect sizes were partitioned by experimental design, we found increased genetic variation in studies based on broad-sense measures of variance, and decreased variation in narrow-sense studies, in support of previous research. Therefore, the source of genetic variance, not the definition of a novel environment, was key to understanding environment-dependant genetic variation, highlighting non-additive genetic variance as an important component of cryptic genetic variation and avenue for future research.

Whole-Genome Sequencing Reveals That Regulatory and Low Pleiotropy Variants Underlie Local Adaptation to Environmental Variability in Purple Sea Urchins

AbstractOrganisms experience environments that vary across both space and time. Such environmental heterogeneity shapes standing genetic variation and may influence species' capacity to adapt to rapid environmental change. However, we know little about the kind of genetic variation that is involved in local adaptation to environmental variability. To address this gap, we sequenced the whole genomes of 140 purple sea urchins (Strongylocentrotus purpuratus) from seven populations that vary in their degree of pH variability. Despite no evidence of global population structure, we found a suite of single-nucleotide polymorphisms (SNPs) tightly correlated with local pH variability (outlier SNPs), which were overrepresented in regions putatively involved in gene regulation (long noncoding RNA and enhancers), supporting the idea that variation in regulatory regions is important for local adaptation to variability. In addition, outliers in genes were found to be (i) enriched for biomineralization and ion homeostasis functions related to low pH response, (ii) less central to the protein-protein interaction network, and (iii) underrepresented among genes highly expressed during early development. Taken together, these results suggest that loci that underlie local adaptation to pH variability in purple sea urchins fall in regions with potentially low pleiotropic effects (based on analyses involving regulatory regions, network centrality, and expression time) involved in low pH response (based on functional enrichment).

Differential effects of parental and developmental temperatures on larval thermal adaptation in oviparous and viviparous model fish species

Phenotypic plasticity has been identified as a major mechanism of response to changing temperatures. Parental effects are potentially important drivers of ecological and evolutionary dynamics, while developmental plasticity also plays a key role in generating phenotypic variation. However, little is known of the interaction between parental effects and developmental plasticity on the thermal phenotypes of fishes with different reproductive modes (i.e. oviparous vs. viviparous). To understand the contributions of inter- and intra-generational plasticity of thermal phenotypes (preferred temperature, avoidance temperatures, critical thermal thresholds) in fishes with different reproductive modes, we carried out a factorial experiment in which both breeding parents and offspring were exposed to lower (22 °C) or higher (28 °C) temperatures, using zebrafish (Danio rerio) and guppies (Poecilia reticulata) as representative oviparous and viviparous species. We found that offspring thermal preference and avoidance of both species were significantly influenced by parental effects and developmental plasticity, with higher thermal preference and avoidance consistent with higher background (parental) temperature treatments. However, parental effects were only found to impose significant effect on the thermal tolerances of guppies. The findings suggest that phenotypic plasticity, both within and across generations, may be an important mechanism to adapt to rapid climate changes, and that future temperature fluctuations may impose more profound effects on viviparous fish species in general.

Differential Morpho-Physiological and Biochemical Responses of Duckweed Clones from Saudi Arabia to Salinity

Salinity affects the morphological, physiological, and biochemical characteristics of several plant species. The current study was conducted to investigate differential salt tolerance potentials among ten duckweed clones under different salt-stress conditions. Morphological and physiological parameters, including fronds length, fronds number, root length, root number, Na+/K+, chlorophyll, proline contents, and fresh harvest weight, were recorded for each of the ten duckweed clones collected from different Saudi Arabia regions. Additionally, the expression patterns of seven salt-related genes were monitored in a salt-tolerant duckweed genotype. The results show that the Madinah-2 (Spirodela polyryiza) and Al-Qassim (Landoltia punctata) clones presented higher performances for all the tested morphological and physiological parameters compared to other genotypes under salt-stress conditions. At concentrations greater than 150 mM NaCl, these aforementioned traits were affected for all the genotypes tested, except Madinah-2 (S. polyryiza) and Al-Qassim (L. punctata) clones, both of which exhibited high tolerance behavior under high salt conditions (200 mM and 250 mM NaCl). The principal component analysis (PCA) showed that the first five principal components accounted for 94.8% of the total variance among the studied traits. Morphological and physiological traits are the major portions of PC1. Moreover, the expression pattern analysis of NHX, BZIP, ST, and KTrans transcript revealed their upregulation in the Al-Qassim clone under salt-stress conditions, suggesting that these genes play a role in this clone's tolerance to salt-induced stress. Overall, this study indicates that the Al-Qassim clone could be used in a brackish-water duckweed-based treatment program with a simultaneous provision of valuable plant biomass.

Responses to predation pressure involve similar sets of genes in two divergent species of Daphnia

Species that are not closely related can express similar inducible traits, but molecular mechanisms underlying the observed responses are often unknown, nor is it known if these mechanisms are shared between such species. Here, we compared transcriptional profiles of two Daphnia species (D. mitsukuri and D. sinensis) from different subgenera, at both juvenile and adult developmental stages. Both species were exposed to the same predation threat (fish kairomones), and both showed similar induced morphological changes (reduced body length). At the early developmental stage, response to predation risk resulted in similar changes in expression levels of 23 orthologues in both species. These orthologues, involved in 107 GO categories, changed in the same direction in both species (over- or underexpressed), in comparison to non-exposed controls. Several of these orthologues were associated with DNA replication, structural constituents of cuticle or innate immune response. In both species, the differentially expressed (DE) genes on average had higher ω (dN /dS ) values than non-DE genes, suggesting that these genes had experienced greater positive selection or lower purifying selection than non-DE genes. Overall, our results suggest that similar suites of genes, responding in similar ways to predation pressure, have been retained in Daphnia for many millions of years.

Understanding and applying biological resilience, from genes to ecosystems

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand 'biological resilience', or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience.

Variation in nest-building behaviour in birds: a multi-species approach

Researchers have long suggested that animals with greater behavioural flexibility will be more likely to survive in face of environmental changes. However, it is unknown how this varies across species. Nest building is a behaviour directly related to the reproduction and survival of species by conferring protection from external environmental conditions. The study of nests offers a window into the behaviour of birds, and variation in nest morphology is necessarily linked to variation in building behaviours. We test whether variation in nest morphology is phylogenetically conserved by using data on nest morphology from 55 passerine species (>700 specimens) and measuring intraspecific variability in nest structure. We found that species mean and within-species variation in nest morphology are phylogenetically conserved, and that species with domed nests presented higher levels of nest morphology variation than cup nest species. We also revealed that the capacity of species to present innovative behaviours is not linked with how they vary nest morphology. Moreover, we revealed that nests from species with larger variation in clutch size and that are built by single parents are more variable. Our results help in the understanding of how behaviour and extended phenotypes evolve, and highlight the importance of exploring the phylogenetic history of behavioural flexibility when trying to predict the capacity of species to respond to novel challenges. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Genome architecture and selective signals compensatorily shape plastic response to a new environment

Transcriptional plasticity interacts with natural selection in complex ways and is crucial for the survival of species under rapid climate change. How 3D genome architecture affects transcriptional plasticity and its interaction with genetic adaptation are unclear. We transplanted estuarine oysters to a new environment and found that genes located in active chromatin regions exhibited greater transcriptional plasticity, and changes in these regions were negatively correlated with selective signals. This indicates a trade-off between 3D active regions and selective signals in shaping plastic responses to a new environment. Specifically, a mutation, lincRNA, and changes in the accessibility of a distal enhancer potentially affect its interaction with the ManⅡa gene, which regulates the muscle function and survival of oysters. Our findings reveal that 3D genome architecture compensates for the role of genetic adaptation in environmental response to new environments and provide insights into synergetic genetic and epigenetic interactions critical for fitness-related trait and survival in a model marine species.

Hidden genetic variation in plasticity provides the potential for rapid adaptation to novel environments

Rapid environmental change is forcing populations into environments where plasticity will no longer maintain fitness. When populations are exposed to novel environments, evolutionary theory predicts that genetic variation in fitness will increase and should be associated with genetic differences in plasticity. If true, then genetic variation in plasticity can increase adaptive potential in novel environments, and population persistence via evolutionary rescue is more likely. To test whether genetic variation in fitness increases in novel environments and is associated with plasticity, we transplanted 8149 clones of 314 genotypes of a Sicilian daisy (Senecio chrysanthemifolius) within and outside its native range, and quantified genetic variation in fitness, and plasticity in leaf traits and gene expression. Although mean fitness declined by 87% in the novel environment, genetic variance in fitness increased threefold and was correlated with plasticity in leaf traits. High fitness genotypes showed greater plasticity in gene expression, but lower plasticity in most leaf traits. Interestingly, genotypes with the highest fitness in the novel environment had the lowest fitness at the native site. These results suggest that standing genetic variation in plasticity could help populations to persist and adapt to novel environments, despite remaining hidden in native environments.

The genome sequence of the Squinting Bush Brown, Bicyclus anynana (Butler, 1879)

We present a genome assembly from an individual female Bicyclus anynana (the Squinting Bush Brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 457.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length.

Effects of Amazonian flying rivers on frog biodiversity and populations in the Atlantic rainforest

Given the speed at which humans are changing the climate, species with high degrees of endemism may not have time to avoid extinction through adaptation. We investigated through teleconnection analysis the origin of rainfall that determines the phylogenetic diversity of rainforest frogs and the effects of microclimate differences in shaping the morphological traits of isolated populations (which contribute to greater phylogenetic diversity and speciation). We also investigated through teleconnection analysis how deforestation in Amazonia can affect ecosystem services that are fundamental to maintaining the climate of the Atlantic rainforest biodiversity hotspot. Seasonal winds known as flying rivers carry water vapor from Amazonia to the Atlantic Forest, and the breaking of this ecosystem service could lead Atlantic Forest species to population decline and extinction in the short term. Our results suggest that the selection of morphological traits that shape Atlantic Forest frog diversity and their population dynamics are influenced by the Amazonian flying rivers. Our results also suggest that the increases of temperature anomalies in the Atlantic Ocean due to global warming and in the Amazon forest due to deforestation are already breaking this cycle and threaten the biodiversity of the Atlantic Forest hotspot.

Acute cold stress and supercooling capacity of Mediterranean fruit fly populations across the Northern Hemisphere (Middle East and Europe)

The Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae), holds an impressive record of successful invasion events promoted by globalization in fruit trade and human mobility. In addition, C. capitata is gradually expanding its geographic distribution to cooler temperate areas of the Northern Hemisphere. Cold tolerance of C. capitata seems to be a crucial feature that promotes population establishment and hence invasion success. To elucidate the interplay between the invasion process in the northern hemisphere and cold tolerance of geographically isolated populations of C. capitata, we determined (a) the response to acute cold stress survival of adults, and (b) the supercooling capacity (SCP) of immature stages and adults. To assess the phenotypic plasticity in these populations, the effect of acclimation to low temperatures on acute cold stress survival in adults was also examined. The results revealed that survival after acute cold stress was positively related to low temperature acclimation, except for females originating from Thessaloniki (northern Greece). Adults from the warmer environment of South Arava (Israel) were less tolerant after acute cold stress compared with those from Heraklion (Crete, Greece) and Thessaloniki. Plastic responses to cold acclimation were population specific, with the South Arava population being more plastic compared to the two Greek populations. For SCP, the results revealed that there is little to no correlation between SCP and climate variables of the areas where C. capitata populations originated. SCP was much lower than the lowest temperature individuals are likely to experience in their respective habitats. These results set the stage for asking questions regarding the evolutionary adaptive processes that facilitate range expansions of C. capitata into cooler temperate areas of Europe.

The lack of genetic variation underlying thermal transcriptomic plasticity suggests limited adaptability of the Northern shrimp, Pandalus borealis

Introduction

Genetic variation underlies the populations’ potential to adapt to and persist in a changing environment, while phenotypic plasticity can play a key role in buffering the negative impacts of such change at the individual level.

Methods

We investigated the role of genetic variation in the thermal response of the northern shrimp Pandalus borealis, an ectotherm species distributed in the Arctic and North Atlantic Oceans. More specifically, we estimated the proportion transcriptomic responses explained by genetic variance of female shrimp from three origins after 30 days of exposure to three temperature treatments.

Results

We characterized the P. borealis transcriptome (170,377 transcripts, of which 27.48% were functionally annotated) and then detected a total of 1,607 and 907 differentially expressed transcripts between temperatures and origins, respectively. Shrimp from different origins displayed high but similar level of transcriptomic plasticity in response to elevated temperatures. Differences in transcript expression among origins were not correlated to population genetic differentiation or diversity but to environmental conditions at origin during sampling.

Discussion

The lack of genetic variation explaining thermal plasticity suggests limited adaptability in this species’ response to future environmental changes. These results together with higher mortality observed at the highest temperature indicate that the thermal niche of P. borealis will likely be restricted to higher latitudes in the future. This prediction concurs with current decreases in abundance observed at the southern edge of this species geographical distribution, as it is for other cold-adapted crustaceans.

Adaptive divergence and underlying mechanisms in response to salinity gradients between two Crassostrea oysters revealed by phenotypic and transcriptomic analyses

Comparing the responses of closely related species to environmental changes is an efficient method to explore adaptive divergence, for a better understanding of the adaptive evolution of marine species under rapidly changing climates. Oysters are keystone species thrive in intertidal and estuarine areas where frequent environmental disturbance occurs including fluctuant salinity. The evolutionary divergence of two sister species of sympatric estuarine oysters, Crassostrea hongkongensis and Crassostrea ariakensis, in response to euryhaline habitats on phenotypes and gene expression, and the relative contribution of species effect, environment effect, and their interaction to the divergence were explored. After a 2-month outplanting at high- and low-salinity locations in the same estuary, the high growth rate, percent survival, and high tolerance indicated by physiological parameters suggested that the fitness of C. ariakensis was higher under high-salinity conditions and that of C. hongkongensis was higher under low-salinity conditions. Moreover, a transcriptomic analysis showed the two species exhibited differentiated transcriptional expression in high- and low-salinity habitats, largely caused by the species effect. Several of the important pathways enriched in divergent genes between species were also salinity-responsive pathways. Specifically, the pyruvate and taurine metabolism pathway and several solute carriers may contribute to the hyperosmotic adaptation of C. ariakensis, and some solute carriers may contribute to the hypoosmotic adaptation of C. hongkongensis. Our findings provide insights into the phenotypic and molecular mechanisms underlying salinity adaptation in marine mollusks, which will facilitate the assessment of the adaptive capacity of marine species in the context of climate change and will also provide practical information for marine resource conservation and aquaculture.

Threatened species could be more vulnerable to climate change in tropical countries

Climate change is a major threat impacting insects globally, yet the impact on tropical insects is largely unknown. Here, I assessed the climatic vulnerability of Bangladeshi butterflies (242 species). About 42 % of species could experience range contraction, and the impact could be significantly more severe among threatened species. Depending on Socio-Economic Pathways (ssps), the future climatic condition could be unsuitable for 2 (ssp126) - 34 % (ssp585) species. The mean elevation of the suitable habitat could increase by 238 %, and the situation could be more severe for the threatened butterflies. Further, 54 % of the realised niche of butterflies could be altered. Although there might be no significant association between the shift in habitat suitability along the elevational gradient, migratory species could experience a more significant shift than non-migrants. Overall, climate change could have a severe impact on Bangladeshi butterflies. To mitigate insect decline globally and meet the Post 2020 Biodiversity Framework targets, immediate detection of climate change impact on tropical insects and developing effective conservation strategies is essential.

Phenotypic evolution as an Ornstein-Uhlenbeck process: The effect of environmental variation and phenotypic plasticity

Here we investigate phenotypic evolution from the perspective of the Ornstein-Uhlenbeck (OU) process. Evolutionarily speaking, the model assumes the existence of stabilizing selection toward a phenotypic optimum. The standard (OU) model is modified to include environmental variation by taking a moving phenotypic optimum and endowing organisms with phenotypic plasticity. These two processes lead to an effective fitness landscape, which deforms the original. We observe that the simultaneous occurrence of environmental variation and phenotypic plasticity leads to skewed phenotypic distributions. The skewness of the resulting phenotypic distributions strongly depends on the rate of environmental variation and strength of selection. When generalized to more than one trait, the phenotypic distributions are not only affected by the magnitude of the rate of environmental variation but also by its direction. A remarkable feature of our predictions is the existence of an upper bound for the critical rate of environmental variation to allow population persistence, even if there is no cost associated with phenotypic plasticity.

The social evolution of individual differences: Future directions for a comparative science of personality in social behavior

Personality is essential for understanding the evolution of cooperation and conflict in behavior. However, personality science remains disconnected from the field of social evolution, limiting our ability to explain how personality and plasticity shape phenotypic adaptation in social behavior. Researchers also lack an integrative framework for comparing personality in the contextualized and multifaceted behaviors central to social interactions among humans and other animals. Here we address these challenges by developing a social evolutionary approach to personality, synthesizing theory, methods, and organizing questions in the study of individuality and sociality in behavior. We critically review current measurement practices and introduce social reaction norm models for comparative research on the evolution of personality in social environments. These models demonstrate that social plasticity affects the heritable variance of personality, and that individual differences in social plasticity can further modify the rate and direction of adaptive social evolution. Future empirical studies of frequency- and density-dependent social selection on personality are crucial for further developing this framework and testing adaptive theory of social niche specialization.

Of telomeres and temperature: Measuring thermal effects on telomeres in ectothermic animals

Ectotherms are classic models for understanding life-history tradeoffs, including the reproduction-somatic maintenance tradeoffs that may be reflected in telomere length and their dynamics. Importantly, life-history traits of ectotherms are tightly linked to their thermal environment, with diverse or synergistic mechanistic explanations underpinning the variation. Telomere dynamics potentially provide a mechanistic link that can be used to monitor thermal effects on individuals in response to climatic perturbations. Growth rate, age and developmental stage are all affected by temperature, which interacts with telomere dynamics in complex and intriguing ways. The physiological processes underpinning telomere dynamics can be visualized and understood using thermal performance curves (TPCs). TPCs reflect the evolutionary history and the thermal environment during an individual's ontogeny. Telomere maintenance should be enhanced at or near the thermal performance optimum of a species, population and individual. The thermal sensitivity of telomere dynamics should reflect the interacting TPCs of the processes underlying them. The key processes directly underpinning telomere dynamics are mitochondrial function (reactive oxygen production), antioxidant activity, telomerase activity and telomere endcap protein status. We argue that identifying TPCs for these processes will significantly help design robust, repeatable experiments and field studies of telomere dynamics in ectotherms. Conceptually, TPCs are a valuable framework to predict and interpret taxon- and population-specific telomere dynamics across thermal regimes. The literature of thermal effects on telomeres in ectotherms is sparse and mostly limited to vertebrates, but our conclusions and recommendations are relevant across ectothermic animals.

Rate of environmental variation impacts the predictability in evolution

In the two last decades, we have improved our understanding of the adaptive evolution of natural populations under constant and stable environments. For instance, experimental methods from evolutionary biology have allowed us to explore the structure of fitness landscapes and survey how the landscape properties can constrain the adaptation process. However, understanding how environmental changes can affect adaptation remains challenging. Very little progress has been made with respect to time-varying fitness landscapes. Using the adaptive-walk approximation, we survey the evolutionary process of populations under a scenario of environmental variation. In particular, we investigate how the rate of environmental variation influences the predictability in evolution. We observe that the rate of environmental variation not only changes the duration of adaptive walks towards fitness peaks of the fitness landscape, but also affects the degree of repeatability of both outcomes and evolutionary paths. In general, slower environmental variation increases the predictability in evolution. The accessibility of endpoints is greatly influenced by the ecological dynamics. The dependence of these quantities on the genome size and number of traits is also addressed. To our knowledge, this contribution is the first to use the predictive approach to quantify and understand the impact of the speed of environmental variation on the degree of parallelism of the evolutionary process.

Partitioning variance in immune traits in a zooplankton host-Fungal parasite system

Host immune traits arise from both genetic and environmental sources of variation. When immune traits have a strong genetic basis, the presence and severity of disease in a population may influence the distribution of those traits. Our study addressed how two immune-related traits (gut penetrability and the hemocyte response) are shaped by genetic and environmental sources of variation, and how the presence of a virulent disease altered the relative frequency of these traits in natural populations. Daphnia dentifera hosts were sampled from five Indiana lakes between June and December 2017 before and during epidemics of their fungal pathogen, Metschnikowia bicuspidata. Collected Daphnia were experimentally exposed to Metschnikowia and assayed for their gut penetrability, hemocyte response, and multi-locus genotype. Mixed-effects models were constructed to partition variance in immune traits between genetic and environmental sources. We then isolated the genetic sources to produce genotype-specific estimates of immune traits for each multi-locus genotype. Finally, we assessed the relative frequency and dynamics of genotypes during epidemics and asked whether genotypes with more robust immune responses increased in frequency during epidemics. Although genotype was an important source of variation for both gut penetrability and the hemocyte response, environmental factors (e.g., resource availability, Metschnikowia prevalence, and co-infection) still explained a large portion of observed variation, suggesting a high degree of flexibility in Daphnia immune traits. Additionally, no significant associations were detected between a genotype's immune traits and its frequency in a population. Our study highlights the power of variance partitioning in understanding the factors driving variation in Daphnia traits and motivates further research on immunological flexibility and the ecological drivers of immune variation.

Transcriptomic stability or lability explains sensitivity to climate stressors in coralline algae

BACKGROUND

Crustose coralline algae (CCA) are calcifying red macroalgae that play important ecological roles including stabilisation of reef frameworks and provision of settlement cues for a range of marine invertebrates. Previous research into the responses of CCA to ocean warming (OW) and ocean acidification (OA) have found magnitude of effect to be species-specific. Response to OW and OA could be linked to divergent underlying molecular processes across species.

RESULTS

Here we show Sporolithon durum, a species that exhibits low sensitivity to climate stressors, had little change in metabolic performance and did not significantly alter the expression of any genes when exposed to temperature and pH perturbations. In contrast, Porolithon onkodes, a major coral reef builder, reduced photosynthetic rates and had a labile transcriptomic response with over 400 significantly differentially expressed genes, with differential regulation of genes relating to physiological processes such as carbon acquisition and metabolism. The differential gene expression detected in P. onkodes implicates possible key metabolic pathways, including the pentose phosphate pathway, in the stress response of this species.

CONCLUSIONS

We suggest S. durum is more resistant to OW and OA than P. onkodes, which demonstrated a high sensitivity to climate stressors and may have limited ability for acclimatisation. Understanding changes in gene expression in relation to physiological processes of CCA could help us understand and predict how different species will respond to, and persist in, future ocean conditions predicted for 2100.

Meta-analysis reveals weak but pervasive plasticity in insect thermal limits

Extreme temperature events are increasing in frequency and intensity due to climate change. Such events threaten insects, including pollinators, pests and disease vectors. Insect critical thermal limits can be enhanced through acclimation, yet evidence that plasticity aids survival at extreme temperatures is limited. Here, using meta-analyses across 1374 effect sizes, 74 studies and 102 species, we show that thermal limit plasticity is pervasive but generally weak: per 1 °C rise in acclimation temperature, critical thermal maximum increases by 0.09 °C; and per 1 °C decline, critical thermal minimum decreases by 0.15 °C. Moreover, small but significant publication bias suggests that the magnitude of plasticity is marginally overestimated. We find juvenile insects are more plastic than adults, highlighting that physiological responses of insects vary through ontogeny. Overall, we show critical thermal limit plasticity is likely of limited benefit to insects during extreme climatic events, yet we need more studies in under-represented taxa and geographic regions.

The ability of organisms to acclimate to high temperatures is increasingly put to test by climate change. This global meta-analysis shows that plasticity of thermal limits in insects is widespread but unlikely to keep pace with climate change.

The immediate costs and long-term benefits of assisted gene flow in large populations

With the genetic health of many plant and animal populations deteriorating due to climate change outpacing adaptation, interventions, such as assisted gene flow (AGF), may provide genetic variation necessary for populations to adapt to climate change. We ran genetic simulations to mimic different AGF scenarios in large populations and measured their outcomes on population-level fitness to determine circumstances in which it is worthwhile to perform AGF. In the absence of inbreeding depression, AGF was beneficial within a few generations only when introduced genotypes had much higher fitness than local individuals and traits affecting fitness were controlled by a few genes of large effect. AGF was harmful over short periods (e.g., first ∼10-20 generations) if there was strong outbreeding depression or introduced deleterious genetic variation. When the adaptive trait was controlled by many loci of small effect, the benefits of AGF took over 10 generations to realize-potentially too long for most climate-related management scenarios. The genomic integrity of the recipient population typically remained intact following AGF; the amount of genetic material from the donor population usually constituted no more of the recipient population's genome than the fraction of the population introduced. Significant genomic turnover (e.g., >50% replacement) only occurred when the selective advantage of the adaptive trait and translocation fraction were extremely high. Our results will be useful when adaptive management is used to maintain the genetic health and productivity of large populations under climate change.

The evolution of neurosensation provides opportunities and constraints for phenotypic plasticity

Phenotypic plasticity is widely regarded as important for enabling species resilience to environmental change and for species evolution. However, insight into the complex mechanisms by which phenotypic plasticity evolves in nature is limited by our ability to reconstruct evolutionary histories of plasticity. By using part of the molecular mechanism, we were able to trace the evolution of pre-feeding phenotypic plasticity across the class Echinoidea and identify the origin of plasticity at the base of the regular urchins. The neurosensory foundation for plasticity was ancestral within the echinoids. However, coincident development of the plastic trait and the neurosensory system was not achieved until the regular urchins, likely due to pleiotropic effects and linkages between the two colocalized systems. Plasticity continues to evolve within the urchins with numerous instances of losses associated with loss of sensory abilities and neurons, consistent with a cost of maintaining these capabilities. Thus, evidence was found for the neurosensory system providing opportunities and constraints to the evolution of phenotypic plasticity.

Evolution in response to climate in the native and introduced ranges of a globally distributed plant

The extent to which species can adapt to spatiotemporal climatic variation in their native and introduced ranges remains unresolved. To address this, we examined how clines in cyanogenesis (hydrogen cyanide [HCN] production-an antiherbivore defense associated with decreased tolerance to freezing) have shifted in response to climatic variation in space and time over a 60-year period in both the native and introduced ranges of Trifolium repens. HCN production is a polymorphic trait controlled by variation at two Mendelian loci (Ac and Li). Using phenotypic assays, we estimated within-population frequencies of HCN production and dominant alleles at both loci (i.e., Ac and Li) from 10,575 plants sampled from 131 populations on five continents, and then compared these frequencies to those from historical data collected in the 1950s. There were no clear relationships between changes in the frequency of HCN production, Ac, or Li and changes in temperature between contemporary and historical samples. We did detect evidence of continued evolution to temperature gradients in the introduced range, whereby the slope of contemporary clines for HCN and Ac in relation to winter temperature became steeper than historical clines and more similar to native clines. These results suggest that cyanogenesis clines show no clear changes through time in response to global warming, but introduced populations continue to adapt to their contemporary environments.

Consistent heat tolerance under starvation across seasonal morphs in Mycalesis mineus (Lepidoptera: Nymphalidae)

Heat tolerance is a key trait for understanding insect responses to extreme heat events, but tolerance may be modulated by changes in food availability and seasonal variability in temperature. Differences in sensitivity and resistance across life stages are also important determinants of species responses. Using a full-factorial experimental design, we here investigated the effects of larval starvation, adult starvation, and seasonal morph (developmental temperature) on heat tolerance of a seasonally polyphenic butterfly, Mycalesis mineus, in both larval and adult stages. While starvation and rearing temperature profoundly influenced various life history traits in the insect, none of the treatments affected adult heat tolerance. There was also no evidence of reduced heat tolerance in larvae under starvation stress, though larval thermal tolerance was higher by ~1 °C at the higher developmental temperature. The lack of a starvation effect was unexpected given the general physiological cost of heat tolerance mechanisms. This might be attributed to the ability to tolerate heat being preserved under resource-based trade-offs due to its critical role in ensuring insect survival. Invariant heat tolerance in M. mineus shows that some insects may have thermal capacity to cope with extreme heat under short-term starvation and seasonality disruptions, though more prolonged changes may have greater consequences. The capacity to maintain key physiological function under multiple stressors will be crucial for species resilience in future novel environments.

Adaptive divergence generates distinct plastic responses in two closely related Senecio species

The evolution of plastic responses to external cues allows species to maintain fitness in response to the environmental variations they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity are associated with adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (Senecio, Asteraceae). We sampled 40 representative genotypes of each species from their native range on Mt. Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient that included the native elevational range of each species, and two intermediate elevations. At each elevation, we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content, and gene expression. Traits and differentially expressed genes that changed with elevation in one species often showed little changes in the other species, or changed in the opposite direction. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Adaptive divergence is, therefore, associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.

Do Freshwater Turtles Use Rainfall to Increase Nest Success?

Rainfall following turtle nest construction has long been believed to increase nest survival by its effects on reducing the location cues used by nest predators. However, it is unclear if this is generally the case and if nesting turtles actively use this mechanism to increase their reproductive fitness by deliberately timing nesting to occur before or during rainfall. To address this question, we reviewed studies that examined freshwater turtle nesting behavior and nest predation rates in relation to rainfall. We supplemented our review with data on rainfall and nesting patterns from a 12-year study of two nesting populations of Ouachita Map Turtles (Graptemys ouachitensis). Our review revealed a diversity of responses in rainfall effects on predation and in the propensity for turtles to nest in association with rain. Our mixed findings could reflect a diversity of species- or population-specific responses, local adaptations, species composition of predator community, confounding abiotic factors (e.g., temperature decreases after rainfall) or methodology (e.g., most studies did not quantify rainfall amounts). Our case study on map turtles found very high yearly predation rates (75–100%), precluding our ability to rigorously analyze the association between nest predation and rainfall. However, close examination of the exact timing of both rainfall and predation revealed significantly lower predation rates when rain fell within 24 h after nesting, indicating that rainfall during or after nesting may reduce nest predation. Despite this effect, the best fitted model explaining the propensity to nest found that map turtles were more likely to nest after dry days than after days with rainfall, suggesting that rainfall was not a major factor driving turtles to nest in our populations. In both our review and in our map turtle populations there was little evidence that turtles can anticipate rainfall and nest prior to it occurring (e.g., in response to falling barometric pressure).

Impacts of seasonality on gene expression in the Chinese horseshoe bat

Seasonality can cause changes in many environmental factors which potentially affects gene expression. Here, we used a bat species (Rhinolophus sinicus) from eastern China as a model to explore the molecular mechanisms of seasonal effects, in particular during phenological shifts in the spring and autumn. Based on the analysis of 45 RNA-seq samples, we found strong seasonal effects on gene expression, with a large number of genes identified as either specific or biased to each season. Weighted gene co-expression network analysis also identified multiple modules significantly associated with each season. These seasonal genes were further enriched into different functional categories. Consistent with effects of phenological shifts on bats, we found that genes related to promoting food intake were highly expressed in both autumn and spring. In addition, immunity genes were also highly expressed in both seasons although this seasonal immune response had tissue specificity in different seasons. In female bats, genes related to the delay of ovulation (e.g., NPPC, natriuretic peptide precursor type C) were highly expressed in October, while genes associated with the promotion of reproduction (e.g., DIO2, iodothyronine deiodinase 2) were biasedly expressed in April. Lastly, we found multiple known core clock genes in both October-biased and April-biased expressed genes, which may be involved in regulating the start and end of hibernation, respectively. Overall, together with studies in other land and aquatic animals, our work supports that seasonal gene expression variations may be a general evolutionary response to environmental changes in wild animals.

Niche expansion and adaptive divergence in the global radiation of crows and ravens

The processes that allow some lineages to diversify rapidly at a global scale remain poorly understood. Although earlier studies emphasized the importance of dispersal, global expansions expose populations to novel environments and may also require adaptation and diversification across new niches. In this study, we investigated the contributions of these processes to the global radiation of crows and ravens (genus Corvus). Combining a new phylogeny with comprehensive phenotypic and climatic data, we show that Corvus experienced a massive expansion of the climatic niche that was coupled with a substantial increase in the rates of species and phenotypic diversification. The initiation of these processes coincided with the evolution of traits that promoted dispersal and niche expansion. Our findings suggest that rapid global radiations may be better understood as processes in which high dispersal abilities synergise with traits that, like cognition, facilitate persistence in new environments.

Traits that facilitate adaptive responses to novel environments may facilitate global radiations. Here, the authors describe diversification dynamics of crows, finding that their global radiation coincides with high rates of phenotypic and climatic niche evolution.

Genetics and Plasticity Are Responsible for Ecogeographical Patterns in a Recent Invasion

Patterns of covariation between phenotype and environment are presumed to be reflective of local adaptation, and therefore translate to a meaningful influence on an individual's overall fitness within that specific environment. However, these environmentally driven patterns may be the result of numerous and interacting processes, such as genetic variation, epigenetic variation, or plastic non-heritable variation. Understanding the relative importance of different environmental variables on underlying genetic patterns and resulting phenotypes is fundamental to understanding adaptation. Invasive systems are excellent models for such investigations, given their propensity for rapid evolution. This study uses reduced representation sequencing data paired with phenotypic data to examine whether important phenotypic traits in invasive starlings (Sturnus vulgaris) within Australia appear to be highly heritable (presumably genetic) or appear to vary with environmental gradients despite underlying genetics (presumably non-heritable plasticity). We also sought to determine which environmental variables, if any, play the strongest role shaping genetic and phenotypic patterns. We determined that environmental variables-particularly elevation-play an important role in shaping allelic trends in Australian starlings and may also reinforce neutral genetic patterns resulting from historic introduction regime. We examined a range of phenotypic traits that appear to be heritable (body mass and spleen mass) or negligibly heritable (e.g. beak surface area and wing length) across the starlings' Australian range. Using SNP variants associated with each of these phenotypes, we identify key environmental variables that correlate with genetic patterns, specifically that temperature and precipitation putatively play important roles shaping phenotype in this species. Finally, we determine that overall phenotypic variation is correlated with underlying genetic variation, and that these interact positively with the level of vegetation variation within a region, suggesting that ground cover plays an important role in shaping selection and plasticity of phenotypic traits within the starlings of Australia.

Epigenomics as a paradigm to understand the nuances of phenotypes

Quantifying the relative importance of genomic and epigenomic modulators of phenotype is a focal challenge in comparative physiology, but progress is constrained by availability of data and analytic methods. Previous studies have linked physiological features to coding DNA sequence, regulatory DNA sequence, and epigenetic state, but few have disentangled their relative contributions or unambiguously distinguished causative effects ('drivers') from correlations. Progress has been limited by several factors, including the classical approach of treating continuous and fluid phenotypes as discrete and static across time and environment, and difficulty in considering the full diversity of mechanisms that can modulate phenotype, such as gene accessibility, transcription, mRNA processing and translation. We argue that attention to phenotype nuance, progressing to association with epigenetic marks and then causal analyses of the epigenetic mechanism, will enable clearer evaluation of the evolutionary path. This would underlie an essential paradigm shift, and power the search for links between genomic and epigenomic features and physiology. Here, we review the growing knowledge base of gene-regulatory mechanisms and describe their links to phenotype, proposing strategies to address widely recognized challenges.

Weaving place‐based knowledge for culturally significant species in the age of genomics: Looking to the past to navigate the future

Relationships with place provide critical context for characterizing biocultural diversity. Yet, genetic and genomic studies are rarely informed by Indigenous or local knowledge, processes, and practices, including the movement of culturally significant species. Here, we show how place‐based knowledge can better reveal the biocultural complexities of genetic or genomic data derived from culturally significant species. As a case study, we focus on culturally significant southern freshwater kōura (crayfish) in Aotearoa me Te Waipounamu (New Zealand, herein Aotearoa NZ). Our results, based on genotyping‐by‐sequencing markers, reveal strong population genetic structure along with signatures of population admixture in 19 genetically depauperate populations across the east coast of Te Waipounamu. Environment association and differentiation analyses for local adaptation also indicate a role for hydroclimatic variables—including temperature, precipitation, and water flow regimes—in shaping local adaptation in kōura. Through trusted partnerships between community and researchers, weaving genomic markers with place‐based knowledge has both provided invaluable context for the interpretation of data and created opportunities to reconnect people and place. We envisage such trusted partnerships guiding future genomic research for culturally significant species in Aotearoa NZ and beyond.

Alternative splicing in seasonal plasticity and the potential for adaptation to environmental change

Seasonal plasticity is accomplished via tightly regulated developmental cascades that translate environmental cues into trait changes. Little is known about how alternative splicing and other posttranscriptional molecular mechanisms contribute to plasticity or how these mechanisms impact how plasticity evolves. Here, we use transcriptomic and genomic data from the butterfly Bicyclus anynana, a model system for seasonal plasticity, to compare the extent of differential expression and splicing and test how these axes of transcriptional plasticity differ in their potential for evolutionary change. Between seasonal morphs, we find that differential splicing affects a smaller but functionally unique set of genes compared to differential expression. Further, we find strong support for the novel hypothesis that spliced genes are more susceptible than differentially expressed genes to erosion of genetic variation due to selection on seasonal plasticity. Our results suggest that splicing plasticity is especially likely to experience genetic constraints that could affect the potential of wild populations to respond to rapidly changing environments.

Spatial variation in high temperature-regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower

A major way that organisms can adapt to changing environmental conditions is by evolving increased or decreased phenotypic plasticity. In the face of current global warming, more attention is being paid to the role of plasticity in maintaining fitness as abiotic conditions change over time. However, given that temporal data can be challenging to acquire, a major question is whether evolution in plasticity across space can predict adaptive plasticity across time. In growth chambers simulating two thermal regimes, we generated transcriptome data for western North American scarlet monkeyflowers (Mimulus cardinalis) collected from different latitudes and years (2010 and 2017) to test hypotheses about how plasticity in gene expression is responding to increases in temperature, and if this pattern is consistent across time and space. Supporting the genetic compensation hypothesis, individuals whose progenitors were collected from the warmer-origin northern 2017 descendant cohort showed lower thermal plasticity in gene expression than their cooler-origin northern 2010 ancestors. This was largely due to a change in response at the warmer (40°C) rather than cooler (20°C) treatment. A similar pattern of reduced plasticity, largely due to a change in response at 40°C, was also found for the cooler-origin northern versus the warmer-origin southern population from 2017. Our results demonstrate that reduced phenotypic plasticity can evolve with warming and that spatial and temporal changes in plasticity predict one another.

Profiling Cultivars Development in Kersting's Groundnut [Macrotyloma geocarpum (Harms) Maréchal and Baudet] for Improved Yield, Higher Nutrient Content, and Adaptation to Current and Future Climates

Kersting's groundnut [Macrotyloma geocarpum (Harms.) Maréchal and Baudet], Fabaceae, is an important source of protein and essential amino acids. As a grain legume species, it also contributes to improving soil fertility through symbiotic nitrogen fixation. However, the crop is characterized by a relatively low yield (≤500 kg/ha), and limited progress has been made so far, toward the development of high-yielding cultivars that can enhance and sustain its productivity. Recently, there was an increased interest in alleviating the burdens related to Kersting's groundnut (KG) cultivation through the development of improved varieties. Preliminary investigations assembled germplasms from various producing countries. In-depth ethnobotanical studies and insightful investigation on the reproductive biology of the species were undertaken alongside morphological, biochemical, and molecular characterizations. Those studies revealed a narrow genetic base for KG. In addition, the self-pollinating nature of its flowers prevents cross-hybridization and represents a major barrier limiting the broadening of the genetic basis. Therefore, the development of a research pipeline to address the bottlenecks specific to KG is a prerequisite for the successful expansion of the crop. In this paper, we offer an overview of the current state of research on KG and pinpoint the knowledge gaps; we defined and discussed the main steps of breeding for KG' cultivars development; this included (i) developing an integrated genebank, inclusive germplasm, and seed system management; (ii) assessing end-users preferences and possibility for industrial exploitation of the crop; (iii) identifying biotic and abiotic stressors and the genetic control of responsive traits to those factors; (iv) overcoming the cross-pollination challenges in KG to propel the development of hybrids; (v) developing new approaches to create variability and setting adequate cultivars and breeding approaches; (vi) karyotyping and draft genome analysis to accelerate cultivars development and increase genetic gains; and (vii) evaluating the adaptability and stability of cultivars across various ecological regions.