Adaptation to climate change through genetic accommodation and assimilation of plastic phenotypes

Genome-wide sequencing reveals geographical variations in the thermal adaptation of an aquaculture species with frequent seedling introductions

Climate change and human activity are essential factors affecting marine biodiversity and aquaculture, and understanding the impacts of human activities on the genetic structure to increasing high temperatures is crucial for sustainable aquaculture and marine biodiversity conservation. As a commercially important bivalve, the Manila clam Ruditapes philippinarum is widely distributed along the coast of China, and it has been frequently introduced from Fujian Province, China, to other regions for aquaculture. In this study, we collected four populations of Manila clams from different areas to evaluate their thermal tolerance by measuring cardiac performance and genetic variations using whole-genome resequencing. The upper thermal limits of the clams showed high variations within and among populations. Different populations displayed divergent genetic compositions, and the admixed population was partly derived from the Zhangzhou population in Fujian Province, implying a complex genomic landscape under the influence of local genetic sources and human introductions. Multiple single nucleotide polymorphisms (SNPs) were associated with the cardiac functional traits, and some of these SNPs can affect the codon usage and the structural stability of the resulting protein. This study shed light on the importance of establishing long-term ecological and genetic monitoring programs at the local level to enhance resilience to future climate change.

Dissecting wheat above-ground architecture for enhanced water use efficiency and grain yield in the subtropics

BACKGROUND

Growing wheat under climate change scenarios challenges, scientists to develop drought and heat-tolerant genotypes. The adaptive traits should therefore be explored and engineered for this purpose. Thus, this study aimed to dissect surface traits and optimizing the leaf architecture to enhance water use efficiency (WUE) and grain yield. Twenty-six wheat genotypes were assessed for five novel leaf traits (NLTs: leaf prickle hairs, groove type, rolling, angle and wettability) under normal, drought and heat conditions following triplicated factorial randomized complete block design (RCBD). The data for NLTs, physiological traits (stomatal conductance, WUE, transpiration, and photosynthesis), and standard morphological and yield traits were recorded. Leaves were sampled at the stem elongation stage (Zadoks 34) to measure the leaf water content (%), contact angle, and to obtain pictures through scanning electron microscopy (SEM). The air moisture harvesting efficiency was evaluated for five selected genotypes. The ideotype concept was applied to evaluate the best-performing genotypes.

RESULTS

The correlation analysis indicated that long leaf prickle hairs (> 100 μm), short stomatal aperture and density (40-60 mm- 2), inward to spiral leaf rolling, medium leaf indentation, low contact angle hysteresis (< 10°), and cuticular wax were positively associated with WUE. This, in turn, was significantly correlated to grain yield. Thus, the genotypes (E-1) with these traits and alternate leaf wettability had maximum grain yield (502 g m- 2) and WUE supported with high photosynthesis rate, and relative water content (94 and 75% under normal and stress conditions, respectively). However, the genotype (1-hooded) with dense leaf hairs on edges but droopy leaves, spiral leaf rolling, and lighter groove, also performed better in terms of grain yield (450 g m- 2) under heat stress conditions by maintaining high photosynthesis and WUE with low stomatal conductance and transpiration rate.

CONCLUSION

The SEM analysis verified that the density of hairs on the leaf surface and epicuticular wax contributes towards alternate wettability patterns thereby increasing the water-use efficiency and yield of the wheat plant. This study paves a way towards screening and and developing heat and drought-tolerant cultivars that are water-saving and climate-resilient.

A Long-Lived Alpine Perennial Advances Flowering under Warmer Conditions but Not Enough to Maintain Reproductive Success

AbstractAssessing whether phenological shifts in response to climate change confer a fitness advantage requires investigating the relationships among phenology, fitness, and environmental drivers of selection. Despite widely documented advancements in phenology with warming climate, we lack empirical estimates of how selection on phenology varies in response to continuous climate drivers or how phenological shifts in response to warming conditions affect fitness. We leverage an unusual long-term dataset with repeated, individual measurements of phenology and reproduction in a long-lived alpine plant. We analyze phenotypic plasticity in flowering phenology in relation to two climate drivers, snowmelt timing and growing degree days (GDDs). Plants flower earlier with increased GDDs and earlier snowmelt, and directional selection also favors earlier flowering under these conditions. However, reproduction still declines with warming and early snowmelt, even when flowering is early. Furthermore, the steepness of this reproductive decline increases dramatically with warming conditions, resulting in very little fruit production regardless of flowering time once GDDs exceed approximately 225 degree days or snowmelt occurs before May 15. Even though advancing phenology confers a fitness advantage relative to stasis, these shifts are insufficient to maintain reproduction under warming, highlighting limits to the potential benefits of phenological plasticity under climate change.

Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone

Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.

Warming effects on lizard gut microbiome depend on habitat connectivity

Climate warming and landscape fragmentation are both factors well known to threaten biodiversity and to generate species responses and adaptation. However, the impact of warming and fragmentation interplay on organismal responses remains largely under-explored, especially when it comes to gut symbionts, which may play a key role in essential host functions and traits by extending its functional and genetic repertoire. Here, we experimentally examined the combined effects of climate warming and habitat connectivity on the gut bacterial communities of the common lizard (Zootoca vivipara) over three years. While the strength of effects varied over the years, we found that a 2°C warmer climate decreases lizard gut microbiome diversity in isolated habitats. However, enabling connectivity among habitats with warmer and cooler climates offset or even reversed warming effects. The warming effects and the association between host dispersal behaviour and microbiome diversity appear to be a potential driver of this interplay. This study suggests that preserving habitat connectivity will play a key role in mitigating climate change impacts, including the diversity of the gut microbiome, and calls for more studies combining multiple anthropogenic stressors when predicting the persistence of species and communities through global changes.

Incorporating otolith-isotope inferred field metabolic rate into conservation strategies

Fluctuating ocean conditions are rearranging whole networks of marine communities-from individual-level physiological thresholds to ecosystem function. Physiological studies support predictions from individual-level responses (biochemical, cellular, tissue, respiratory potential) based on laboratory experiments. The otolith-isotope method of recovering field metabolic rate has recently filled a gap for the bony fishes, linking otolith stable isotope composition to in situ oxygen consumption and experienced temperature estimates. Here, we review the otolith-isotope method focusing on the biochemical and physiological processes that yield estimates of field metabolic rate. We identify a multidisciplinary pathway in the application of this method, providing concrete research goals (field, modeling) aimed at linking individual-level physiological data to higher levels of biological organization. We hope that this review will provide researchers with a transdisciplinary 'roadmap', guiding the use of the otolith-isotope method to bridge the gap between individual-level physiology, observational field studies, and modeling efforts, while ensuring that in situ data is central in marine policy-making aimed at mitigating climatic and anthropogenic threats.

Gene expression plasticity facilitates acclimatization of a long-lived Caribbean coral across divergent reef environments

Local adaptation can increase fitness under stable environmental conditions. However, in rapidly changing environments, compensatory mechanisms enabled through plasticity may better promote fitness. Climate change is causing devastating impacts on coral reefs globally and understanding the potential for adaptive and plastic responses is critical for reef management. We conducted a four-year, three-way reciprocal transplant of the Caribbean coral Siderastrea siderea across forereef, backreef, and nearshore populations in Belize to investigate the potential for environmental specialization versus plasticity in this species. Corals maintained high survival within forereef and backreef environments, but transplantation to nearshore environments resulted in high mortality, suggesting that nearshore environments present strong environmental selection. Only forereef-sourced corals demonstrated evidence of environmental specialization, exhibiting the highest growth in the forereef. Gene expression profiling 3.5 years post-transplantation revealed that transplanted coral hosts exhibited profiles more similar to other corals in the same reef environment, regardless of their source location, suggesting that transcriptome plasticity facilitates acclimatization to environmental change in S. siderea. In contrast, algal symbiont (Cladocopium goreaui) gene expression showcased functional variation between source locations that was maintained post-transplantation. Our findings suggest limited acclimatory capacity of some S. siderea populations under strong environmental selection and highlight the potential limits of coral physiological plasticity in reef restoration.

Synergistic response to climate stressors in coral is associated with genotypic variation in baseline expression

As environments are rapidly reshaped due to climate change, phenotypic plasticity plays an important role in the ability of organisms to persist and is considered an especially important acclimatization mechanism for long-lived sessile organisms such as reef-building corals. Often, this ability of a single genotype to display multiple phenotypes depending on the environment is modulated by changes in gene expression, which can vary in response to environmental changes via two mechanisms: baseline expression and expression plasticity. We used transcriptome-wide expression profiling of eleven genotypes of common-gardened Acropora cervicornis to explore genotypic variation in the expression response to thermal and acidification stress, both individually and in combination. We show that the combination of these two stressors elicits a synergistic gene expression response, and that both baseline expression and expression plasticity in response to stress show genotypic variation. Additionally, we demonstrate that frontloading of a large module of coexpressed genes is associated with greater retention of algal symbionts under combined stress. These results illustrate that variation in the gene expression response of individuals to climate change stressors can persist even when individuals have shared environmental histories, affecting their performance under future climate change scenarios.

Endocrine flexibility can facilitate or constrain the ability to cope with global change

Global climate change has increased average environmental temperatures world-wide, simultaneously intensifying temperature variability and extremes. Growing numbers of studies have documented phenological, behavioural and morphological responses to climate change in wild populations. As systemic signals, hormones can contribute to orchestrating many of these phenotypic changes. Yet little is known about whether mechanisms like hormonal flexibility (reversible changes in hormone concentrations) facilitate or limit the ability of individuals, populations and species to cope with a changing climate. In this perspective, we discuss different mechanisms by which hormonal flexibility, primarily in glucocorticoids, could promote versus hinder evolutionary adaptation to changing temperature regimes. We focus on temperature because it is a key gradient influenced by climate change, it is easy to quantify, and its links to hormones are well established. We argue that reaction norm studies that connect individual responses to population-level and species-wide patterns will be critical for making progress in this field. We also develop a case study on urban heat islands, where several key questions regarding hormonal flexibility and adaptation to climate change can be addressed. Understanding the mechanisms that allow animals to cope when conditions become more challenging will help in predicting which populations are vulnerable to ongoing climate change. This article is part of the theme issue 'Endocrine responses to environmental variation: conceptual approaches and recent developments'.

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.

Genetic basis of variation in thermal developmental plasticity for Drosophila melanogaster body pigmentation

Seasonal differences in insect pigmentation are attributed to the influence of ambient temperature on pigmentation development. This thermal plasticity is adaptive and heritable, and thereby capable of evolving. However, the specific genes contributing to the variation in plasticity that can drive its evolution remain largely unknown. To address this, we analysed pigmentation and pigmentation plasticity in Drosophila melanogaster. We measured two components of pigmentation in the thorax and abdomen: overall darkness and the proportion of length covered by darker pattern elements (a trident in the thorax and bands in the abdomen) in females from two developmental temperatures (17 or 28°C) and 191 genotypes. Using a GWAS approach to identify the genetic basis of variation in pigmentation and its response to temperature, we identified numerous dispersed QTLs, including some mapping to melanogenesis genes (yellow, ebony, and tan). Remarkably, we observed limited overlap between QTLs for variation within specific temperatures and those influencing thermal plasticity, as well as minimal overlap between plasticity QTLs across pigmentation components and across body parts. For most traits, consistent with selection favouring the retention of plasticity, we found that lower plasticity alleles were often at lower frequencies. The functional analysis of selected candidate QTLs and pigmentation genes largely confirmed their contributions to variation in pigmentation and/or pigmentation plasticity. Overall, our study reveals the existence and underlying basis of extensive and trait-specific genetic variation for pigmentation and pigmentation plasticity, offering a rich reservoir of raw material for natural selection to shape the evolution of these traits independently.

Identification and genetic diversity analysis of broomrape in Xinjiang, China

BACKGROUND

As a holoparasitic weed, broomrape has seriously threatened the production of economically important crops, such as melon, watermelon, processed tomato, and sunflower, in Xinjiang in recent years. However, the distribution and genetic diversity of broomrape populations in Xinjiang are not clear at present, which hinders their prevention and control. The purpose of this study was to identify the main species and the genetic differentiation structure of the broomrape population in Xinjiang.

METHODS AND RESULTS

In the present study, 93 samples from different geographic regions of Xinjiang were collected to identify the species based on ITS and plastid rps2 regions, and the samples were also used to analyze the genetic diversity based on ISSR markers. The results showed that broomrape is not monophyletic in Xinjiang and consists of two major clades (Orobanche cf. aegyptiaca and O. cernua) and three subclades (O. cf. aegyptiaca var. tch, O. cf. aegyptiaca var. klz, and O. cernua.var. alt) based on phylogenetic analysis. Furthermore, the results of the genetic diversity analysis indicated that the average polymorphic information content and marker index were high values of 0.58 and 7.38, respectively, showing the efficiency of the ISSR markers in detecting polymorphism among the broomrape population studied. Additionally, the 11 selected primers produced 154 repeatable polymorphic bands, of which 150 were polymorphic. The genetic diversity of the samples was 37.19% within populations and 62.81% among the populations, indicating that the main genetic differentiation occurred among the populations. There was less gene exchange between populations, with a gene flow index (Nm) of 0.2961 (< 1). The UPGMA dendrogram indicated that most populations with similar geographical conditions and hosts were clustered first, and then all samples were separated into two major groups and seven subclusters.

CONCLUSION

The broomrapes are mainly O. cf. aegyptiaca and O. cernua in Xinjiang, which were separated into two major groups and seven subclusters based on ISSR markers. Our results provide a theoretical basis for breeding broomrape-resistant varieties.

Plasticity and associated epigenetic mechanisms play a role in thermal evolution during range expansion

Due to global change, many species are shifting their distribution and are thereby confronted with novel thermal conditions at the moving range edges. Especially during the initial phases of exposure to a new environment, it has been hypothesized that plasticity and associated epigenetic mechanisms enable species to cope with environmental change. We tested this idea by capitalizing on the well-documented southward range expansion of the damselfly Ischnura elegans from France into Spain where the species invaded warmer regions in the 1950s in eastern Spain (old edge region) and in the 2010s in central Spain (new edge region). Using a common garden experiment at rearing temperatures matching the ancestral and invaded thermal regimes, we tested for evolutionary changes in (thermal plasticity in) larval life history and heat tolerance in these expansion zones. Through the use of de- and hypermethylating agents, we tested whether epigenetic mechanisms play a role in enabling heat tolerance during expansion. We used the phenotype of the native sister species in Spain, I. graellsii, as proxy for the locally adapted phenotype. New edge populations converged toward the phenotype of the native species through plastic thermal responses in life history and heat tolerance while old edge populations (partly) constitutively evolved a faster life history and higher heat tolerance than the core populations, thereby matching the native species. Only the heat tolerance of new edge populations increased significantly when exposed to the hypermethylating agent. This suggests that the DNA methylation machinery is more amenable to perturbation at the new edge and shows it is able to play a role in achieving a higher heat tolerance. Our results show that both (evolved) plasticity as well as associated epigenetic mechanisms are initially important when facing new thermal regimes but that their importance diminishes with time.

Variation in phenotypic plasticity across age-at-maturity genotypes in wild Atlantic salmon

Evolution of phenotypic plasticity requires genotype-environment interaction. The discovery of two large-effect loci in the vgll3 and six6 genomic regions associated with the number of years the Atlantic salmon spend feeding at sea before maturation (sea age), provides a unique opportunity to study evolutionary potential of phenotypic plasticity. Using data on 1246 Atlantic salmon caught in the River Surna in Norway, we show that variation in mean sea age among years (smolt cohorts 2013-2018) is influenced by genotype frequencies as well as interaction effects between genotype and year. Genotype-year interactions suggest that genotypes may differ in their response to environmental variation across years, implying genetic variation in phenotypic plasticity. Our results also imply that plasticity in sea age will evolve as an indirect response to selection on mean sea age due to a shared genetic basis. Furthermore, we demonstrate differences between years in the additive and dominance functional genetic effects of vgll3 and six6 on sea age, suggesting that evolutionary responses will vary across environments. Considering the importance of age at maturity for survival and reproduction, genotype-environment interactions likely play an important role in local adaptation and population demography in Atlantic salmon.

Assessing the global vulnerability of dryland birds to heatwaves

As global average surface temperature increases, extreme climatic events such as heatwaves are becoming more frequent and intense, which can drive biodiversity responses such as rapid population declines and/or shifts in species distributions and even local extirpations. However, the impacts of extreme climatic events are largely ignored in conservation plans. Birds are known to be susceptible to heatwaves, especially in dryland ecosystems. Understanding which birds are most vulnerable to heatwaves, and where these birds occur, can offer a scientific basis for adaptive management and conservation. We assessed the relative vulnerability of 1196 dryland bird species to heatwaves using a trait-based approach. Among them, 888 bird species are estimated to be vulnerable to heatwaves (170 highly vulnerable, eight extremely vulnerable), of which ~91% are currently considered non-threatened by the IUCN, which suggests that many species will likely become newly threatened with intensifying climate change. We identified the top three hotspot areas of heatwave-vulnerable species in Australia (208 species), Southern Africa (125 species) and Eastern Africa (99 species). Populations of vulnerable species recorded in the Living Planet Database were found to be declining significantly faster than those of non-vulnerable species (p = .048) after heatwaves occurred. In contrast, no significant difference in population trends between vulnerable and non-vulnerable species was detected when no heatwave occurred (p = .34). This suggests that our vulnerability framework correctly identified vulnerable species and that heatwaves are already impacting the population trends of these species. Our findings will help prioritize heatwave-vulnerable birds in dryland ecosystems in risk mitigation and adaptation management as the frequency of heatwaves accelerates in the coming decades.

Got milkweed? Genetic assimilation as potential source for the evolution of nonmigratory monarch butterfly wing shape

Monarch butterflies (Danaus plexippus) are well studied for their annual long-distance migration from as far north as Canada to their overwintering grounds in Central Mexico. At the end of the cold season, monarchs start to repopulate North America through short-distance migration over the course of multiple generations. Interestingly, some populations in various tropical and subtropical islands do not migrate and exhibit heritable differences in wing shape and size, most likely an adaptation to island life. Less is known about forewing differences between long- and short-distance migrants in relation to island populations. Given their different migratory behaviors, we hypothesized that these differences would be reflected in wing morphology. To test this, we analyzed forewing shape and size of three different groups: nonmigratory, lesser migratory (migrate short-distances), and migratory (migrate long-distances) individuals. Significant differences in shape appear in all groups using geometric morphometrics. As variation found between migratory and lesser migrants has been shown to be caused by phenotypic plasticity, and lesser migrants develop intermediate forewing shapes between migratory and nonmigratory individuals, we suggest that genetic assimilation might be an important mechanism to explain the heritable variation found between migratory and nonmigratory populations. Additionally, our research confirms previous studies which show that forewing size is significantly smaller in nonmigratory populations when compared to both migratory phenotypes. Finally, we found sexual dimorphism in forewing shape in all three groups, but for size in nonmigratory populations only. This might have been caused by reduced constraints on forewing size in nonmigratory populations.

A continuum of selection on life-history traits under differential environmental heterogeneity. A commentary on 'Chasing the fitness optimum: temporal variation in genetic and environmental expression of life-history traits for a perennial plant'

This article comments on:

Mason W. Kulbaba, Zebadiah Yoko and Jill A. Hamilton. Chasing the fitness optimum: temporal variation in the genetic and environmental expression of life-history traits for a perennial plant, Annals of Botany, Volume 132, Issue 7, 1 December 2023, Pages 1191–1204 https://doi.org/10.1093/aob/mcad100

Consistent traffic noise impacts few fitness-related traits in a field cricket

BACKGROUND

Anthropogenic habitat change is occurring rapidly, and organisms can respond through within-generation responses that improve the match between their phenotype and the novel conditions they encounter. But, plastic responses can be adaptive or maladaptive and are most likely to be adaptive only when contemporary conditions reasonably mimic something experienced historically to which a response has already evolved. Noise pollution is a ubiquitous anthropogenic stressor that accompanies expanding urbanization. We tested whether the amplitude of traffic noise influences a suite of fitness-related traits (e.g. survival, life history, reproductive investment, immunity) and whether that depends on the life stage at which the noise is experienced (juvenile or adult). Our treatments mimic the conditions experienced by animals living in urban roadside environments with variable vehicle types, but continuous movement of traffic. We used the Pacific field cricket, an acoustically communicating insect that was previously shown to experience some negative behavioral and life history responses to very loud, variable traffic noise, as a model system.

RESULTS

After exposing crickets to one of four traffic noise levels (silence, 50dBA, 60dBA, and 70dBA which are commonly experienced in their natural environment) during development, at adulthood, or both, we measured a comprehensive suite of fifteen fitness-related traits. We found that survival to adulthood was lower under some noise treatments than under silence, and that the number of live offspring hatched depended on the interaction between a female's juvenile and adult exposure to traffic noise. Both of these suggest that our noise treatments were indeed a stressor. However, we found no evidence of negative or positive fitness effects of noise on the other thirteen measured traits.

CONCLUSIONS

Our results suggest that, in contrast to previous work with loud, variable traffic noise, when noise exposure is relatively constant, plasticity may be sufficient to buffer many negative fitness effects and/or animals may be able to habituate to these conditions, regardless of amplitude. Our work highlights the importance of understanding how the particular characteristics of noise experienced by animals influence their biological responses and provides insight into how commensal animals thrive in human-dominated habitats.

The impacts of thermal heterogeneity across microhabitats on post-settlement selection of intertidal mussels

Rapid genetic selection is critical for allowing natural populations to adapt to different thermal environments such as those that occur across intertidal microhabitats with high degrees of thermal heterogeneity. To address the question of how thermal regimes influence selection and adaptation in the intertidal black mussel Mytilisepta virgata, we continuously recorded environmental temperatures in both tidal pools and emergent rock microhabitats and then assessed genetic differentiation, gene expression patterns, RNA editing level, and cardiac performance. Our results showed that the subpopulations in the tidal pool and on emergent rocks had different genetic structures and exhibited different physiological and molecular responses to high-temperature stress. These results indicate that environmental heterogeneity across microhabitats is important for driving genetic differentiation and shed light on the importance of post-settlement selection for adaptively modifying the genetic composition and thermal responses of these intertidal mussels.

Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis

Regulatory variants in gene expression serve as bridges linking genetic variation and phenotypic plasticity. Environmental conditions typically influence the effects of regulatory variants on phenotypic plasticity; however, such genotype-by-environment interactions (G × E) are poorly understood. This study aimed to investigate the genetic basis of G × E in estuarine oyster (Crassostrea ariakensis), which is an important model animal for studying environmental adaption owing to its high plasticity and large intraspecific divergence. Genome-wide mapping of expression quantitative trait loci (eQTLs) for 23 environmental adaptive genes was performed for 256 estuarine oysters. We identified 1194 eQTL single nucleotide polymorphisms (eSNPs), including 433 cis-eSNPs in four genes and 722 trans-eSNPs in eight genes. The expression variation explanation of cis-eSNPs (9.95%) was significantly higher than that of trans-eSNPs (9.15%). We specifically showed cis- and trans-eSNPs with high linkage disequilibrium (LD) for Traf7, Slc6a5, Ggt, and Dap3. For example, we identified a cis-regulatory LD block containing 68 cis-eSNP and a trans-regulatory LD block, including 20 trans-eSNPs in Traf7. A high proportion (85%) of 40 vital eSNPs exhibited significant G × E effects. We identified crossing and nonparallel interactions of G × E, with the tag cis-eSNPs of Baat and Slc6a5 as representatives. Our results indicated that cis-eQTLs are highly conserved. This study provides insights into the understanding of adaptive evolutionary mechanisms and phenotypic response prediction to variable environments, as well as the genetic improvement for superior adaptive traits for genetic resource conservation and aquaculture.

Role of phenotypic and transcriptomic plasticity in alpine adaptation of Arabidopsis arenosa

Plasticity is an important component of the response of organism to environmental changes, but whether plasticity facilitates adaptation is still largely debated. Using transcriptomic and phenotypic data, we explored the evolution of ancestral plasticity during alpine colonization in Arabidopsis arenosa. We leveraged naturally replicated adaptation in four distinct mountain regions in Central Europe. We sampled seeds from ancestral foothill and independently formed alpine populations in each region and raised them in growth chambers under conditions approximating their natural environments. We gathered RNA-seq and genetic data of 48 and 63 plants and scored vegetative and flowering traits in 203 and 272 plants respectively. Then, we compared gene expression and trait values over two treatments differing in temperature and irradiance and elevations of origin and quantified the extent of ancestral and derived plasticity. At the transcriptomic level, initial plastic changes tended to be more reinforced than reversed in adapted alpine populations. Genes showing reinforcement were involved in the stress response, developmental processes and morphogenesis and those undergoing reversion were related to the stress response (light and biotic stress). At the phenotypic level, initial plastic changes in all but one trait were also reinforced supporting a facilitating role of phenotypic plasticity during colonization of an alpine environment. Our results contrasted with previous studies that showed generally higher reversion than reinforcement and supported the idea that ancestral plasticity tends to be reinforced in the context of alpine adaptation. However, plasticity may also be the source of potential maladaptation, especially at the transcriptomic level.

Linking temperature dependence of fitness effects of mutations to thermal niche adaptation

Fitness effects of mutations may generally depend on temperature that influences all rate-limiting biophysical and biochemical processes. Earlier studies suggested that high temperatures may increase the availability of beneficial mutations ('more beneficial mutations'), or allow beneficial mutations to show stronger fitness effects ('stronger beneficial mutation effects'). The 'more beneficial mutations' scenario would inevitably be associated with increased proportion of conditionally beneficial mutations at higher temperatures. This in turn predicts that populations in warm environments show faster evolutionary adaptation but suffer fitness loss when faced with cold conditions, and those evolving in cold environments become thermal-niche generalists ('hotter is narrower'). Under the 'stronger beneficial mutation effects' scenario, populations evolving in warm environments would show faster adaptation without fitness costs in cold environments, leading to a 'hotter is (universally) better' pattern in thermal niche adaptation. We tested predictions of the two competing hypotheses using an experimental evolution study in which populations of two model bacterial species, Escherichia coli and Pseudomonas fluorescens, evolved for 2400 generations at three experimental temperatures. Results of reciprocal transplant experiments with our P. fluorescens populations were largely consistent with the 'hotter is narrower' prediction. Results from the E. coli populations clearly suggested stronger beneficial mutation effects at higher assay temperatures, but failed to detect faster adaptation in populations evolving in warmer experimental environments (presumably because of limitation in the supply of genetic variation). Our results suggest that the influence of temperature on mutational effects may provide insight into the patterns of thermal niche adaptation and population diversification across thermal conditions.

Simultaneous warming and acidification limit population fitness and reveal phenotype costs for a marine copepod

Phenotypic plasticity and evolutionary adaptation allow populations to cope with global change, but limits and costs to adaptation under multiple stressors are insufficiently understood. We reared a foundational copepod species, Acartia hudsonica, under ambient (AM), ocean warming (OW), ocean acidification (OA), and combined ocean warming and acidification (OWA) conditions for 11 generations (approx. 1 year) and measured population fitness (net reproductive rate) derived from six life-history traits (egg production, hatching success, survival, development time, body size and sex ratio). Copepods under OW and OWA exhibited an initial approximately 40% fitness decline relative to AM, but fully recovered within four generations, consistent with an adaptive response and demonstrating synergy between stressors. At generation 11, however, fitness was approximately 24% lower for OWA compared with the AM lineage, consistent with the cost of producing OWA-adapted phenotypes. Fitness of the OWA lineage was not affected by reversal to AM or low food environments, indicating sustained phenotypic plasticity. These results mimic those of a congener, Acartia tonsa, while additionally suggesting that synergistic effects of simultaneous stressors exert costs that limit fitness recovery but can sustain plasticity. Thus, even when closely related species experience similar stressors, species-specific costs shape their unique adaptive responses.

Evolution of butterfly seasonal plasticity driven by climate change varies across life stages

Photoperiod is a common cue for seasonal plasticity and phenology, but climate change can create cue-environment mismatches for organisms that rely on it. Evolution could potentially correct these mismatches, but phenology often depends on multiple plastic decisions made during different life stages and seasons that may evolve separately. For example, Pararge aegeria (Speckled wood butterfly) has photoperiod-cued seasonal life history plasticity in two different life stages: larval development time and pupal diapause. We tested for climate change-associated evolution of this plasticity by replicating common garden experiments conducted on two Swedish populations 30 years ago. We found evidence for evolutionary change in the contemporary larval reaction norm-although these changes differed between populations-but no evidence for evolution of the pupal reaction norm. This variation in evolution across life stages demonstrates the need to consider how climate change affects the whole life cycle to understand its impacts on phenology.

Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

BACKGROUND

Individual functional modifications shape the ability of wildlife populations to cope with anthropogenic environmental changes. But instead of adaptive response, human-altered environments can generate a succession of deleterious functional changes leading to the extinction of the population. To study how persistent anthropogenic changes impacted local species' population status, we characterised population structure, genetic diversity and individual response of gene expression in the tree frog Hyla orientalis along a gradient of radioactive contamination around the Chernobyl nuclear power plant.

RESULTS

We detected lower effective population size in populations most exposed to ionizing radiation in the Chernobyl Exclusion Zone that is not compensated by migrations from surrounding areas. We also highlighted a decreased body condition of frogs living in the most contaminated area, a distinctive transcriptomics signature and stop-gained mutations in genes involved in energy metabolism. While the association with dose will remain correlational until further experiments, a body of evidence suggests the direct or indirect involvement of radiation exposure in these changes.

CONCLUSIONS

Despite ongoing migration and lower total dose rates absorbed than at the time of the accident, our results demonstrate that Hyla orientalis specimens living in the Chernobyl Exclusion Zone are still undergoing deleterious changes, emphasizing the long-term impacts of the nuclear disaster.

Behavioural plasticity in activity and sexual interactions in a social lizard at high environmental temperatures

Sexual selection often shapes social behavioural activities, such as movement in the environment to find possible partners, performance of displays to signal dominance and courtship behaviours. Such activities may be negatively influenced by increasing temperatures, especially in ectotherms, because individuals either have to withstand the unfavourable condition or are forced to allocate more time to thermoregulation by increasing shelter seeking behaviour. Thus, they "miss" opportunities for social and reproductive interactions. Moreover, behavioural displays of ectotherms closely depend on temperature; consequently, mate choice behaviours may be disrupted, ultimately modifying sexual selection patterns. Therefore, it would be interesting to elucidate how increasing temperatures associated with global warming may influence activity and social interactions in the species' natural habitat and, specifically how high temperatures may modify intersexual interactions. Consequently, our aim was to explore differences in the daily pattern of social interactions in an ectotherm model, Tropidurus spinulosus, in two thermally different habitats and to determine how high temperatures modify mate choice. High environmental temperatures were found to be associated with a bimodal pattern in daily activity, which was closely linked to the daily variations in the thermal quality of the habitat; whereas the pattern and frequency of social displays showed less plasticity. The time allocated to mate choice generally decreased with increasing temperature since individuals increased the use of thermal refuges; this result supports the hypothesis of "missed opportunities". Moreover, at high temperatures, both sexes showed changes in mate selection dynamics, with females possibly "rushing" mate choice and males showing an increase in intermale variability of reproductive displays. In our ectotherm model, plastic adjustments in the behavioural activity pattern induced by high temperatures, plus the modification of the displays during courtship may ultimately modify mate choice patterns and sexual selection dynamics.

Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication

Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.

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.

Trade-offs between baseline thermal tolerance and thermal tolerance plasticity are much less common than it appears

Thermal tolerance plasticity is a core mechanism by which organisms can mitigate the effects of climate change. As a result, there is a need to understand how variation in tolerance plasticity arises. The baseline tolerance/plasticity trade-off hypothesis (hereafter referred to as the trade-off hypothesis, TOH) has recently emerged as a potentially powerful explanation. The TOH posits that organisms with high baseline thermal tolerance have reduced thermal tolerance plasticity relative to those with low baseline tolerance. Many studies have found support for the TOH. However, this support must be regarded cautiously because the most common means of testing the TOH can yield spurious "trade-offs" due to regression to the mean. I acquired data for 25 previously published analyses that supported the TOH at the intraspecific level and reanalyzed them after applying a method that adjusts plasticity estimates for regression to the mean. Only six of the 25 analyses remained statistically significant after adjustment, and effect size and variance explained decreased in all cases. The few data sets in which support for the TOH was maintained after adjustment point to areas of future study, but are too few to make generalizations at this point. In sum, regression to the mean has led to a substantial overestimation of support for the TOH and must be accounted for in future tests of the hypothesis.

Plastic responses to warmer climates: a semi-natural experiment on lizard populations

Facing warming environments, species can exhibit plastic or microevolutionary changes in their thermal physiology to adapt to novel climates. Here, using semi-natural mesocosms, we experimentally investigated over two successive years whether a 2°C-warmer climate produces selective and inter- and intragenerational plastic changes in the thermal traits (preferred temperature and dorsal coloration) of the lizard Zootoca vivipara. In a warmer climate, the dorsal darkness, dorsal contrast, and preferred temperature of adults plastically decreased and covariances between these traits were disrupted. While selection gradients were overall weak, selection gradients for darkness were slightly different between climates and in the opposite direction to plastic changes. Contrary to adults, male juveniles were darker in warmer climates either through plasticity or selection and this effect was strengthened by intergenerational plasticity when juveniles' mothers also experienced warmer climates. While the plastic changes in adult thermal traits alleviate the immediate overheating costs of warming, its opposite direction to selective gradients and to juveniles' phenotypic responses may slow down evolutionary shifts toward phenotypes that are better adapted to future climates. Our study demonstrates the importance of considering inter- and intragenerational plasticity along with selective processes to better understand adaptation and population dynamics in light of climate change.

Modeling plant diseases under climate change: evolutionary perspectives

Infectious plant diseases are a major threat to global agricultural productivity, economic development, and ecological integrity. There is widespread concern that these social and natural disasters caused by infectious plant diseases may escalate with climate change and computer modeling offers a unique opportunity to address this concern. Here, we analyze the intrinsic problems associated with current modeling strategies and highlight the need to integrate evolutionary principles into polytrophic, eco-evolutionary frameworks to improve predictions. We particularly discuss how evolutionary shifts in functional trade-offs, relative adaptability between plants and pathogens, ecosystems, and climate preferences induced by climate change may feedback to future plant disease epidemics and how technological advances can facilitate the generation and integration of this relevant knowledge for better modeling predictions.

Frank Beach Award Winner: The centrality of the hypothalamic-pituitary-adrenal axis in dealing with environmental change across temporal scales

Understanding if and how individuals and populations cope with environmental change is an enduring question in evolutionary ecology that has renewed importance given the pace of change in the Anthropocene. Two evolutionary strategies of coping with environmental change may be particularly important in rapidly changing environments: adaptive phenotypic plasticity and/or bet hedging. Adaptive plasticity could enable individuals to match their phenotypes to the expected environment if there is an accurate cue predicting the selective environment. Diversifying bet hedging involves the production of seemingly random phenotypes in an unpredictable environment, some of which may be adaptive. Here, I review the central role of the hypothalamic-pituitary-adrenal (HPA) axis and glucocorticoids (GCs) in enabling vertebrates to cope with environmental change through adaptive plasticity and bet hedging. I first describe how the HPA axis mediates three types of adaptive plasticity to cope with environmental change (evasion, tolerance, recovery) over short timescales (e.g., 1-3 generations) before discussing how the implications of GCs on phenotype integration may depend upon the timescale under consideration. GCs can promote adaptive phenotypic integration, but their effects on phenotypic co-variation could also limit the dimensions of phenotypic space explored by animals over longer timescales. Finally, I discuss how organismal responses to environmental stressors can act as a bet hedging mechanism and therefore enhance evolvability by increasing genetic or phenotypic variability or reducing patterns of genetic and phenotypic co-variance. Together, this emphasizes the crucial role of the HPA axis in understanding fundamental questions in evolutionary ecology.

Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes' Selective Footprints in the Genes Network Regulating Flowering Time

Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.

Weak gene-gene interaction facilitates the evolution of gene expression plasticity

BACKGROUND

Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation. However, we know little about what determines the evolution of phenotypic plasticity, including gene expression plasticity. Recent laboratory-based studies suggest dominance of reversing gene expression plasticity-plastic responses that move the levels of gene expression away from the new optima. Nevertheless, evidence from natural populations is still limited.

RESULTS

Here, we studied gene expression plasticity and its evolution in the montane and lowland populations of an elevationally widespread songbird-the Rufous-capped Babbler (Cyanoderma ruficeps)-with reciprocal transplant experiments and transcriptomic analyses; we set common gardens at altitudes close to these populations' native ranges. We confirmed the prevalence of reversing plasticity in genes associated with altitudinal adaptation. Interestingly, we found a positive relationship between magnitude and degree of evolution in gene expression plasticity, which was pertinent to not only adaptation-associated genes but also the whole transcriptomes from multiple tissues. Furthermore, we revealed that genes with weaker expressional interactions with other genes tended to exhibit stronger plasticity and higher degree of plasticity evolution, which explains the positive magnitude-evolution relationship.

CONCLUSIONS

Our experimental evidence demonstrates that species may initiate their adaptation to new habitats with genes exhibiting strong expression plasticity. We also highlight the role of expression interdependence among genes in regulating the magnitude and evolution of expression plasticity. This study illuminates how the evolution of phenotypic plasticity in gene expression facilitates the adaptation of species to challenging environments in nature.

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.

The blowfly Chrysomya latifrons inhabits fragmented rainforests, but shows no population structure

Climate change and deforestation are causing rainforests to become increasingly fragmented, placing them at heightened risk of biodiversity loss. Invertebrates constitute the greatest proportion of this biodiversity, yet we lack basic knowledge of their population structure and ecology. There is a compelling need to develop our understanding of the population dynamics of a wide range of rainforest invertebrates so that we can begin to understand how rainforest fragments are connected, and how they will cope with future habitat fragmentation and climate change. Blowflies are an ideal candidate for such research because they are widespread, abundant, and can be easily collected within rainforests. We genotyped 188 blowflies (Chrysomya latifrons) from 15 isolated rainforests and found high levels of gene flow, a lack of genetic structure between rainforests, and low genetic diversity - suggesting the presence of a single large genetically depauperate population. This highlights that: (1) the blowfly Ch. latifrons inhabits a ~ 1000 km stretch of Australian rainforests, where it plays an important role as a nutrient recycler; (2) strongly dispersing flies can migrate between and connect isolated rainforests, likely carrying pollen, parasites, phoronts, and pathogens along with them; and (3) widely dispersing and abundant insects can nevertheless be genetically depauperate. There is an urgent need to better understand the relationships between habitat fragmentation, genetic diversity, and adaptive potential-especially for poorly dispersing rainforest-restricted insects, as many of these may be particularly fragmented and at highest risk of local extinction.

Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora

Phenotypic plasticity in ancestral populations is hypothesized to facilitate adaptation, but evidence is piecemeal and often contradictory. Further, whether ancestral plasticity increases the probability of parallel adaptive changes has not been explored. The most general finding is that ancestral responses to a new environment are reversed following adaptation (known as reversion). We investigated the contribution of ancestral plasticity to adaptive evolution of gene expression in two independently evolved lineages of zinc-tolerant Silene uniflora. We found that the general pattern of reversion is driven by the absence of a widespread stress response in zinc-adapted plants compared with zinc-sensitive plants. We show that ancestral plasticity that moves expression closer to the optimum value in the new environment influences the evolution of gene expression among genes that are likely to be involved in adaptation and increases the chance that genes are recruited repeatedly during adaptation. However, despite convergence in gene expression levels between independently adapted lineages, ancestral plasticity does not influence how similar expression values of adaptive genes become. Surprisingly, we also observed that ancestral plasticity that increases fitness often becomes genetically determined and fixed, that is, genetically assimilated. These results emphasize the important role of ancestral plasticity in parallel adaptation.

Jack pine of all trades: Deciphering intraspecific variability of a key adaptive trait at the rear edge of a widespread fire-embracing North American conifer

PREMISE

Understanding mechanisms fostering long-term persistence of marginal populations should provide key insights about species resilience facing climate change. Cone serotiny is a key adaptive trait in Pinus banksiana (jack pine), which shows phenotypic variation according to the fire regime. Compared to range-core populations within the fire-prone boreal forest, low and variable serotiny in rear-edge populations suggest local adaptation to uncommon and unpredictable wildfire regime. We assessed environmental/physiological factors that might modulate intraspecific variation in cone serotiny.

METHODS

We experimentally subjected closed cones to incrementing temperatures, then tested seed germination to determine whether and how various ecological factors (cone age, branch height, tree size, tree age) are related to cone dehiscence and seed viability in jack pines from rear-edge and range-core populations in eastern Canada.

RESULTS

Cones from rear-edge populations dehisce at a lower opening temperature, which increases with cone age. Cones from range-core stands open at a more constant, yet higher temperature. Cones from rear-edge stands take between 13 and 27 years to reach the level of serotiny achieved at the range core. At the rear edge, seed viability is steady (51%), whereas it decreases from 70% to 30% in 20 years at the range core.

CONCLUSIONS

We inferred the mechanisms of a bet-hedging strategy in rear-edge populations, which ensures steady recruitment during fire-free intervals and successful postfire regeneration. This capacity to cope with infrequent and unpredictable fire regime should increase the resilience of jack pine populations as global changes alter fire dynamics of the boreal forest.

Cis- and Trans-variations of Stearoyl-CoA Desaturase Provide New Insights into the Mechanisms of Diverged Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species

The evolution of phenotypic plasticity plays an essential role in adaptive responses to climate change; however, its regulatory mechanisms in marine organisms which exhibit high phenotypic plasticity still remain poorly understood. The temperature-responsive trait oleic acid content and its major gene stearoyl-CoA desaturase (Scd) expression have diverged in two allopatric congeneric oyster species, cold-adapted Crassostrea gigas and warm-adapted Crassostrea angulata. In this study, genetic and molecular methods were used to characterize fatty acid desaturation and membrane fluidity regulated by oyster Scd. Sixteen causative single-nucleotide polymorphisms (SNPs) were identified in the promoter/cis-region of the Scd between wild C. gigas and C. angulata. Further functional experiments showed that an SNP (g.-333C [C. gigas allele] >T [C. angulata allele]) may influence Scd transcription by creating/disrupting the binding motif of the positive trans-factor Y-box factor in C. gigas/C. angulata, which mediates the higher/lower constitutive expression of Scd in C. gigas/C. angulata. Additionally, the positive trans-factor sterol-regulatory element-binding proteins (Srebp) were identified to specifically bind to the promoter of Scd in both species, and were downregulated during cold stress in C. gigas compared to upregulated in C. angulata. This partly explains the relatively lower environmental sensitivity (plasticity) of Scd in C. gigas. This study serves as an experimental case to reveal that both cis- and trans-variations shape the diverged pattern of phenotypic plasticity, which provides new insights into the formation of adaptive traits and the prediction of the adaptive potential of marine organisms to future climate change.

ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactrocera dorsalis

Introduction: While it has been suggested that histone modifications can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome histone modification patterns in invasive species, leaving the regulatory landscape of histone modifications in invasive species unclear. Methods: Here, we screen genome-wide patterns of two important histone modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and trimethylated Histone H3 Lysine 27 (H3K27me3), in adult thorax muscles of a notorious invasive pest, the Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). Results: We identified promoters featured by the occupancy of H3K4me3, H3K27me3 or bivalent histone modifications that were respectively annotated with unique genes key to muscle development and structure maintenance. In addition, we found H3K27me3 occupied the entire body of genes, where the average enrichment was almost constant. Transcriptomic analysis indicated that H3K4me3 is associated with active gene transcription, and H3K27me3 is mostly associated with transcriptional repression. Importantly, we identified genes and putative motifs modified by distinct histone modification patterns that may possibly regulate flight activity. Discussion: These findings provide the first evidence of histone modification signature in B. dorsalis, and will be useful for future studies of epigenetic signature in other invasive insect species.

The role of plastic and evolved DNA methylation in parallel adaptation of threespine stickleback (Gasterosteus aculeatus)

Repeated phenotypic patterns among populations undergoing parallel evolution in similar environments provide support for the deterministic role of natural selection. Epigenetic modifications can mediate plastic and evolved phenotypic responses to environmental change and might make important contributions to parallel adaptation. While many studies have explored the genetic basis of repeated phenotypic divergence, the role of epigenetic processes during parallel adaptation remains unclear. The parallel evolution of freshwater ecotypes of threespine stickleback fish (Gasterosteus aculeatus) following colonization of thousands of lakes and streams from the ocean is a classic example of parallel phenotypic and genotypic adaptation. To investigate epigenetic modifications during parallel adaptation of threespine stickleback, we reanalysed three independent data sets that investigated DNA methylation variation between marine and freshwater ecotypes. Although we found widespread methylation differentiation between ecotypes, there was no significant tendency for CpG sites associated with repeated methylation differentiation across studies to be parallel versus nonparallel. To next investigate the role of plastic versus evolved changes in methylation during freshwater adaptation, we explored if CpG sites exhibiting methylation plasticity during salinity change were more likely to also show evolutionary divergence in methylation between ecotypes. The directions of divergence between ecotypes were generally in the opposite direction to those observed for plasticity when ecotypes were challenged with non-native salinity conditions, suggesting that most plastic responses are likely to be maladaptive during colonization of new environments. Finally, we found a greater number of CpG sites showing evolved changes when ancestral marine ecotypes are acclimated to freshwater environments, whereas plastic changes predominate when derived freshwater ecotypes transition back to their ancestral marine environments. These findings provide evidence for an epigenetic contribution to parallel adaptation and demonstrate the contrasting roles of plastic and evolved methylation differences during adaptation to new environments.

Evidence for adaptive morphological plasticity in the Caribbean coral, Acropora cervicornis

Genotype-by-environment interactions (GxE) indicate that variation in organismal traits cannot be explained by fixed effects of genetics or site-specific plastic responses alone. For tropical coral reefs experiencing dramatic environmental change, identifying the contributions of genotype, environment, and GxE on coral performance will be vital for both predicting persistence and developing restoration strategies. We quantified the impacts of G, E, and GxE on the morphology and survival of the endangered coral, Acropora cervicornis, through an in situ transplant experiment exposing common garden (nursery)-raised clones of ten genotypes to nine reef sites in the Florida Keys. By fate-tracking outplants over one year with colony-level 3D photogrammetry, we uncovered significant GxE on coral size, shape, and survivorship, indicating that no universal winner exists in terms of colony performance. Rather than differences in mean trait values, we found that individual-level morphological plasticity is adaptive in that the most plastic individuals also exhibited the fastest growth and highest survival. This indicates that adaptive morphological plasticity may continue to evolve, influencing the success of A. cervicornis and resulting reef communities in a changing climate. As focal reefs are active restoration sites, the knowledge that variation in phenotype is an important predictor of performance can be directly applied to restoration planning. Taken together, these results establish A. cervicornis as a system for studying the ecoevolutionary dynamics of phenotypic plasticity that also can inform genetic- and environment-based strategies for coral restoration.

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.

On the hidden temporal dynamics of plant adaptation

Adaptation to a wide range of environments is a major driver of plant diversity. It is now possible to catalog millions of potential adaptive genomic differences segregating between environments within a plant species in a single experiment. Understanding which of these changes contributes to adaptive phenotypic divergence between plant populations is a major goal of evolutionary biologists and crop breeders. In this review, we briefly highlight the approaches frequently used to understand the genetic basis of adaptive phenotypes in plants, and we discuss some of the limitations of these methods. We propose that direct observation of the process of adaptation using multigenerational studies and whole genome sequencing is a crucial missing component of recent studies of plant adaptation because it complements several shortcomings of sampling-based techniques.

Experimental Evolution Shows Body Size Decrease in Response to Hypoxia, with a Complex Effect on Plastic Size Response to Temperature

AbstractThere is a scientific debate whether oxygen concentration may be a factor driving the pattern of size decrease at higher temperature. Central to this debate is the fact that oxygen availability relative to demand for living organisms decreases with increasing temperature. We examined whether rotifers Lecane inermis exposed to hypoxic conditions would evolve smaller sizes than rotifers exposed to normoxic conditions, using experimental evolution with the same fluctuating temperature but differentiated by three regimes of oxygen availability: normoxia, hypoxia throughout the whole thermal range, and hypoxia only at the highest temperature. Immediately after the six-month experiment (more than 90 generations), we tested the plasticity of size responses to temperature in three post-evolution groups, and we related these responses to fitness. The results show that normoxic rotifers had evolved significantly larger sizes than two hypoxic rotifer groups, which were similar in size. All three groups displayed similar plastic body size reductions in response to warming over the range of temperatures they were exposed to during the period of experimental evolution, but they showed different and complex responses at two temperatures below this range. Any type of plastic response to different temperatures resulted in a similar fitness pattern across post-evolution groups. We conclude that (i) these rotifers showed a genetic basis for the pattern of size decrease following evolution under both temperature-dependent and temperature-independent hypoxia; and (ii) plastic body size responds consistently to temperatures that are within the thermal range that the rotifers experienced during their evolutionary history, but responses become more noisy at novel temperatures, suggesting the importance of evolutionary responses to reliable environmental cues.

Evolved reductions in body temperature and the metabolic costs of thermoregulation in deer mice native to high altitude

The evolution of endothermy was instrumental to the diversification of birds and mammals, but the energetic demands of maintaining high body temperature could offset the advantages of endothermy in some environments. We hypothesized that reductions in body temperature help high-altitude natives overcome the metabolic challenges of cold and hypoxia in their native environment. Deer mice (Peromyscus maniculatus) from high-altitude and low-altitude populations were bred in captivity to the second generation and were acclimated as adults to warm normoxia or cold hypoxia. Subcutaneous temperature (Tsub, used as a proxy for body temperature) and cardiovascular function were then measured throughout the diel cycle using biotelemetry. Cold hypoxia increased metabolic demands, as reflected by increased food consumption and heart rate (associated with reduced vagal tone). These increased metabolic demands were offset by plastic reductions in Tsub (approx. 2°C) in response to cold hypoxia, and highlanders had lower Tsub (approx. 1°C) than lowlanders in both environmental treatments. Empirical and theoretical evidence suggested that these reductions could together reduce metabolic demands by approximately 10-30%. Therefore, plastic and evolved reductions in body temperature can help mammals overcome the metabolic challenges at high altitude and may be a valuable energy-saving strategy in some non-hibernating endotherms in extreme environments.

Individual variation, personality, and the ability of animals to cope with climate change

The Sixth Assessment of the Intergovernmental Panel on Climate Change describes negative effects of climate change on animals occurring on a larger scale than previously appreciated. Animal species are increasingly experiencing more frequent and extreme weather in comparison with conditions in which the species evolved. Individual variation in behavioural and physiological responses of animals to stimuli from the environment is ubiquitous across all species. Populations with relatively high levels of individual variation are more likely to be able to survive in a range of environmental conditions and cope with climate change than populations with low levels of variation. Behavioural and physiological responses are linked in animals, and personality can be defined as consistent individual behavioural and physiological responses of animals to changes in their immediate environment. Glucocorticoids (cortisol and corticosterone) are hormones that, in addition to metabolic roles, are released when the neuroendocrine stress system is activated in response to stimuli from the environment perceived to be threatening. The size of a glucocorticoid response of an animal is an indication of the animal’s personality. Animals with reactive personalities have relatively high glucocorticoid responses, are relatively slow and thorough to explore new situations, and are more flexible and able to cope with changing or unpredictable conditions than animals with proactive personalities. Animals with reactive personalities are likely to be better able to cope with environmental changes due to climate change than animals with proactive personalities. A reaction norm shows the relationship between phenotype and environmental conditions, with the slope of a reaction norm for an individual animal a measure of phenotypic plasticity. If reaction norm slopes are not parallel, there is individual variation in plasticity. Populations with relatively high individual variation in plasticity of reaction norms will have more animals that can adjust to a new situation than populations with little variation in plasticity, so are more likely to persist as environments change due to climate change. Future studies of individual variation in plasticity of responses to changing environments will help understanding of how populations of animals may be able to cope with climate change.