Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants

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

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

Breeding and Selecting Corals Resilient to Global Warming

Selective breeding of resilient organisms is an emerging topic in marine conservation. It can help us predict how species will adapt in the future and how we can help restore struggling populations effectively in the present. Scleractinian corals represent a potential tractable model system given their widescale phenotypic plasticity across fitness-related traits and a reproductive life history based on mass synchronized spawning. Here, I explore the justification for breeding in corals, identify underutilized pathways of acclimation, and highlight avenues for quantitative targeted breeding from the coral host and symbiont perspective. Specifically, the facilitation of enhanced heat tolerance by targeted breeding of plasticity mechanisms is underutilized. Evidence from theoretical genetics identifies potential pitfalls, including inattention to physical and genetic characteristics of the receiving environment. Three criteria for breeding emerge from this synthesis: selection from warm, variable reefs that have survived disturbance. This information will be essential to protect what we have and restore what we can.

Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica)

Ocean acidification (OA) is a major stressor threatening marine calcifiers, including the eastern oyster (Crassostrea virginica). In this paper, we provide insight into the molecular mechanisms associated with resilience to OA, with the dual intentions of probing both acclimation and adaptation potential in this species. C. virginica were spawned, and larvae were reared in control or acidified conditions immediately after fertilization. RNA samples were collected from larvae and juveniles, and DNA samples were collected from juveniles after undergoing OA-induced mortality and used to contrast gene expression (RNAseq) and SNP (ddRADseq) profiles from animals reared under both conditions. Results showed convergence of evidence from both approaches, particularly in genes involved in biomineralization that displayed significant changes in variant frequencies and gene expression levels among juveniles that survived acidification as compared to controls. Downregulated genes were related to immune processes, supporting previous studies demonstrating a reduction in immunity from exposure to OA. Acclimation to OA via regulation of gene expression might confer short-term resilience to immediate threats; however, the costs may not be sustainable, underscoring the importance of selection of resilient genotypes. Here, we identified SNPs associated with survival under OA conditions, suggesting that this commercially and ecologically important species might have the genetic variation needed for adaptation to future acidification. The identification of genetic features associated with OA resilience is a highly-needed step for the development of marker-assisted selection of oyster stocks for aquaculture and restoration activities.

Microbial community changes correlate with impaired host fitness of Aurelia aurita after environmental challenge

Climate change globally endangers certain marine species, but at the same time, such changes may promote species that can tolerate and adapt to varying environmental conditions. Such acclimatization can be accompanied or possibly even be enabled by a host's microbiome; however, few studies have so far directly addressed this process. Here we show that acute, individual rises in seawater temperature and salinity to sub-lethal levels diminished host fitness of the benthic Aurelia aurita polyp, demonstrated by up to 34% reduced survival rate, shrinking of the animals, and almost halted asexual reproduction. Changes in the fitness of the polyps to environmental stressors coincided with microbiome changes, mainly within the phyla Proteobacteria and Bacteroidota. The absence of bacteria amplified these effects, pointing to the benefit of a balanced microbiota to cope with a changing environment. In a future ocean scenario, mimicked by a combined but milder rise of temperature and salinity, the fitness of polyps was severely less impaired, together with condition-specific changes in the microbiome composition. Our results show that the effects on host fitness correlate with the strength of environmental stress, while salt-conveyed thermotolerance might be involved. Further, a specific, balanced microbiome of A. aurita polyps supports the host's acclimatization. Microbiomes may provide a means for acclimatization, and microbiome flexibility can be a fundamental strategy for marine animals to adapt to future ocean scenarios and maintain biodiversity and ecosystem functioning.

Whole-genome resequencing reveals genetic diversity and selection signals in warm temperate and subtropical Sillago sinica populations

BACKGROUND

Genetic diversity and heterogeneous genomic signatures in marine fish populations may result from selection pressures driven by the strong effects of environmental change. Nearshore fishes are often exposed to complex environments and human activities, especially those with small ranges. However, studies on genetic diversity and population selection signals in these species have mostly been based on a relatively small number of genetic markers. As a newly recorded species of Sillaginidae, the population genetics and genomic selection signals of Sillago sinica are fragmented or even absent.

RESULTS

To address this theoretical gap, we performed whole-genome resequencing of 43 S. sinica individuals from Dongying (DY), Qingdao (QD) and Wenzhou (WZ) populations and obtained 4,878,771 high-quality SNPs. Population genetic analysis showed that the genetic diversity of S. sinica populations was low, but the genetic diversity of the WZ population was higher than that of the other two populations. Interestingly, the three populations were not strictly clustered within the group defined by their sampling location but showed an obvious geographic structure signal from the warm temperate to the subtropics. With further analysis, warm-temperate populations exhibited strong selection signals in genomic regions related to nervous system development, sensory function and immune function. However, subtropical populations showed more selective signalling for environmental tolerance and stress signal transduction.

CONCLUSIONS

Genome-wide SNPs provide high-quality data to support genetic studies and localization of selection signals in S. sinica populations. The reduction in genetic diversity may be related to the bottleneck effect. Considering that low genetic diversity leads to reduced environmental adaptability, conservation efforts and genetic diversity monitoring of this species should be increased in the future. Differences in genomic selection signals between warm temperate and subtropical populations may be related to human activities and changes in environmental complexity. This study deepened the understanding of population genetics and genomic selection signatures in nearshore fishes and provided a theoretical basis for exploring the potential mechanisms of genomic variation in marine fishes driven by environmental selection pressures.

The evolution of plasticity at geographic range edges

Phenotypic plasticity enables rapid responses to environmental change, and could facilitate range shifts in response to climate change. What drives the evolution of plasticity at range edges, and the capacity of range-edge individuals to be plastic, remain unclear. Here, we propose that accurately predicting when plasticity itself evolves or mediates adaptive evolution at expanding range edges requires integrating knowledge on the demography and evolution of edge populations. Our synthesis shows that: (i) the demography of edge populations can amplify or attenuate responses to selection for plasticity through diverse pathways, and (ii) demographic effects on plasticity are modified by the stability of range edges. Our spatially explicit synthesis for plasticity has the potential to improve predictions for range shifts with climate change.

Reconciling the variability in the biological response of marine invertebrates to climate change

As climate change increases the rate of environmental change and the frequency and intensity of disturbance events, selective forces intensify. However, given the complicated interplay between plasticity and selection for ecological - and thus evolutionary - outcomes, understanding the proximate signals, molecular mechanisms and the role of environmental history becomes increasingly critical for eco-evolutionary forecasting. To enhance the accuracy of our forecasting, we must characterize environmental signals at a level of resolution that is relevant to the organism, such as the microhabitat it inhabits and its intracellular conditions, while also quantifying the biological responses to these signals in the appropriate cells and tissues. In this Commentary, we provide historical context to some of the long-standing challenges in global change biology that constrain our capacity for eco-evolutionary forecasting using reef-building corals as a focal model. We then describe examples of mismatches between the scales of external signals relative to the sensors and signal transduction cascades that initiate and maintain cellular responses. Studying cellular responses at this scale is crucial because these responses are the basis of acclimation to changing environmental conditions and the potential for environmental 'memory' of prior or historical conditions through molecular mechanisms. To challenge the field, we outline some unresolved questions and suggest approaches to align experimental work with an organism's perception of the environment; these aspects are discussed with respect to human interventions.

Phenotypic Plasticity Drives Seasonal Thermal Tolerance in a Baltic Copepod

Seasonal changes in environmental conditions require substantial physiological responses for population persistence. Phenotypic plasticity is a common mechanism to tolerate these changes, but for organisms with short generation times rapid adaptation may also be a contributing factor. Here, we aimed to disentangle the impacts of adaptation from phenotypic plasticity on thermal tolerance of the calanoid copepod Acartia hudsonica collected throughout spring and summer of a single year. We used a common garden (11 °C and 18 °C) design to determine the relative impacts of plasticity versus adaptation. Acartia hudsonica were collected from five time points across the season and thermal tolerance was determined using critical thermal maximum (CTmax) followed by additional measurements after one generation of common garden. As sea surface temperature increased through the season, field collected individuals showed corresponding increases in thermal tolerance but decreases in body size. Despite different thermal tolerances of wild collections, common garden animals did not differ in CTmax within thermal treatments. Instead, there was evidence of phenotypic plasticity where higher temperatures were tolerated by the 18 °C versus the 11 °C treatment animals across all collections. Acclimation also had significant effects on body size, with higher temperatures resulting in smaller individuals, consistent with the temperature size rule. Therefore, the differences in thermal tolerance and body size observed in field collected A. hudsonica were likely driven by plasticity rather than adaptation. However, the observed decrease in body size suggests that nutrient availability and ecosystem functioning could be impacted if temperatures consistently increase with no change in copepod abundance. This is the first record of A. hudsonica in the Baltic Sea known to the authors.

Different mechanisms underpin the decline in growth of anchovies and sardines of the Bay of Biscay

Declines in individuals' growth in exploited fish species are generally attributed to evolutionary consequences of size-selective fishing or to plastic responses due to constraints set by changing environmental conditions dampening individuals' growth. However, other processes such as growth compensation and non-directional selection can occur and their importance on the overall phenotypic response of exploited populations has largely been ignored. Using otolith growth data collected in European anchovy and sardine of the Bay of Biscay (18 cohorts from 2000 to 2018), we parameterized the breeder's equation to determine whether declines in size-at-age in these species were due to an adaptive response (i.e. related to directional or non-directional selection differentials within parental cohorts) or a plastic response (i.e. related to changes in environmental). We found that growth at age-0 in anchovy declined between parents and their offspring when biomass increased and the selective disappearance of large individuals was high in parents. Therefore, an adaptive response probably occurred in years with high fishing effort and the large increase in biomass after the collapse of this stock maintained this adaptive response subsequently. In sardine offspring, higher growth at age-0 was associated with increasing biomass between parents and offspring, suggesting a plastic response to a bottom-up process (i.e. a change in food quantity or quality). Parental cohorts in which selection favoured individuals with high growth compensation produced offspring high catch up growth rates, which may explain the smaller decline in growth in sardine relative to anchovy. Finally, on non-directional selection differentials were not significantly related to the changes in growth at age-0 and growth compensation at age-1 in both species. Although anchovy and sardine have similar ecologies, the mechanisms underlying the declines in their growth are clearly different. The consequences of the exploitation of natural populations could be long lasting if density-dependent processes follow adaptive changes.

Ocean acidification stunts molluscan growth at CO2 seeps

Ocean acidification can severely affect bivalve molluscs, especially their shell calcification. Assessing the fate of this vulnerable group in a rapidly acidifying ocean is therefore a pressing challenge. Volcanic CO₂ seeps are natural analogues of future ocean conditions that offer unique insights into the scope of marine bivalves to cope with acidification. Here, we used a 2-month reciprocal transplantation of the coastal mussel Septifer bilocularis collected from reference and elevated pCO₂ habitats to explore how they calcify and grow at CO₂ seeps on the Pacific coast of Japan. We found significant decreases in condition index (an indication of tissue energy reserves) and shell growth of mussels living under elevated pCO₂ conditions. These negative responses in their physiological performance under acidified conditions were closely associated with changes in their food sources (shown by changes to the soft tissue δ¹³C and δ¹⁵N ratios) and changes in their calcifying fluid carbonate chemistry (based on shell carbonate isotopic and elemental signatures). The reduced shell growth rate during the transplantation experiment was further supported by shell δ¹³C records along their incremental growth layers, as well as their smaller shell size despite being of comparable ontogenetic ages (5-7 years old, based on shell δ¹⁸O records). Taken together, these findings demonstrate how ocean acidification at CO₂ seeps affects mussel growth and reveal that lowered shell growth helps them survive stressful conditions.

Microplastic occurrence in finfish and shellfish from the mangroves of the northern Gulf of Oman

This study was conducted to assess microplastic (MP) pollution in some aquatic animals inhabiting planted and natural mangrove swamps in the northern Gulf of Oman. The KOH-NaI solution was used to retrieve MPs from the gastrointestinal tracts of animals. The highest MP prevalence was recorded in crabs (41.65 %) followed by fish (33.89 %) and oysters (20.8 %). The abundance of MPs in examined animals varied from zero in Sphyraena putnamae to 11 particles in a Rhinoptera javanica specimen. When polluted-only animals were considered, the mean abundance of MPs significantly varied among species and between locations. The mean density of ingested MPs was higher in the planted mangrove animals (1.79 ± 2.89 vs. 1.21 ± 2.25 n/individual; mean ± SD). Among the examined fish species, R. javanica ingested the highest number of MPs (3.83 ± 3.93 n/individual; mean ± SD). The polyethylene/ polypropylene fragments or fibers of average 1900 μm size were recorded as predominant (>50 % occurrence) MP particles.

Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms

Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals' response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies nonzero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments in silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral, or no plasticity, without any additional knowledge of the traits assessed and species' biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod Idotea balthica sampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments or correlated to fitness.

Populations of western North American monkeyflowers accrue niche breadth primarily via genotypic divergence in environmental optima

Niche breadth, the range of environments that individuals, populations, and species can tolerate, is a fundamental ecological and evolutionary property, yet few studies have examined how niche breadth is partitioned across biological scales. We use a published dataset of thermal performance for a single population from each of 10 closely related species of western North American monkeyflowers (genus Mimulus) to investigate whether populations achieve broad thermal niches through general purpose genotypes, specialized genotypes with divergent environmental optima, and/or variation among genotypes in the degree of generalization. We found the strongest relative support for the hypothesis that populations with greater genetic variation for thermal optimum had broader thermal niches, and for every unit increase in among‐family variance in thermal optimum, population‐level thermal breadth increased by 0.508°C. While the niche breadth of a single genotype represented up to 86% of population‐level niche breadth, genotype‐level niche breadth had a weaker positive effect on population‐level breadth, with every 1°C increase in genotypic thermal breadth resulting in a 0.062°C increase in population breadth. Genetic variation for thermal breadth was not predictive of population‐level thermal breadth. These findings suggest that populations of Mimulus species have achieved broad thermal niches primarily through genotypes with divergent thermal optima and to a lesser extent via general‐purpose genotypes. Future work examining additional biological hierarchies would provide a more comprehensive understanding of how niche breadth partitioning impacts the vulnerabilities of individuals, populations, and species to environmental change.

Is #SDG13 Trending Online? Insights from Climate Change Discussions on Twitter

Anthropogenic activities over the past few decades have led to increased vulnerability of environmental and ecological stability on this planet. Accelerated climate change is one such subset of the environmental problems that threatens the very existence of humankind in twenty first century. Governments, United Nations (UN) and other humanitarian agencies across the globe have developed and devised strategies for climate action that requires grater public awareness and actions. Social media has played a vital role in information dissemination and raising public awareness of climate change in the digital era. To this aid, an upsurge has been documented in recent times regarding discussions over climate change with #SDG13 (Sustainable Development Goals) at its epicenter. Following the principles of Actor Network Theory (ANT) we analyzed a large volume of Twitter data to understand general citizens' perception and attitude towards climate change. Our findings unveil people's opinion on causes and concerns related to barriers of adopting a more sustainable consumption and lifestyle practice. There is also a growing apathy towards sluggish government actions that makes little difference. People were also found to exchange innovative concepts and measures towards mitigating the effects of climate change.

Effects of thermal acclimation on the proteome of the planarian Crenobia alpina from an alpine freshwater spring

Species' acclimation capacity and their ability to maintain molecular homeostasis outside ideal temperature ranges will partly predict their success following climate change-induced thermal regime shifts. Theory predicts that ectothermic organisms from thermally stable environments have muted plasticity, and that these species may be particularly vulnerable to temperature increases. Whether such species retained or lost acclimation capacity remains largely unknown. We studied proteome changes in the planarian Crenobia alpina, a prominent member of cold-stable alpine habitats that is considered to be a cold-adapted stenotherm. We found that the species' critical thermal maximum (CT_max) is above its experienced habitat temperatures and that different populations exhibit differential CT_max acclimation capacity, whereby an alpine population showed reduced plasticity. In a separate experiment, we acclimated C. alpina individuals from the alpine population to 8, 11, 14 or 17°C over the course of 168 h and compared their comprehensively annotated proteomes. Network analyses of 3399 proteins and protein set enrichment showed that while the species' proteome is overall stable across these temperatures, protein sets functioning in oxidative stress response, mitochondria, protein synthesis and turnover are lower in abundance following warm acclimation. Proteins associated with an unfolded protein response, ciliogenesis, tissue damage repair, development and the innate immune system were higher in abundance following warm acclimation. Our findings suggest that this species has not suffered DNA decay (e.g. loss of heat-shock proteins) during evolution in a cold-stable environment and has retained plasticity in response to elevated temperatures, challenging the notion that stable environments necessarily result in muted plasticity.

Summary: The proteome of an alpine Crenobia alpina population shows plasticity in response to acclimation to warmer temperatures.

Fitness homeostasis across an experimental water gradient predicts species' geographic range and climatic breadth

Species range sizes and realized niche breadths vary tremendously. Understanding the source of this variation has been a long-term aim in evolutionary ecology and is a major tool in efforts to ameliorate the impacts of changing climates on species distributions. Species ranges that span a large climatic envelope can be achieved by a collection of specialized genotypes locally adapted to a small range of conditions, by genotypes with stable fitness across variable environments, or a combination of these factors. We asked whether fitness expressed along a key niche axis, water availability, could explain a species' realized niche breadth--its geographic range and climate breadth-- in 11 species from a clade of jewelflowers whose range sizes vary by two orders of magnitude. Specifically, we explored whether the range size of a species was related to the ability of genotypes (maternal families) to maintain fitness across a range of experimental water availabilities based on 30-year historical field precipitation regimes. We operationally characterized fitness homeostasis through the coefficient of variation (CV) in fitness of a genotype (family) across the experimental water gradient. We found that species with genotypes that had high fitness homeostasis -- low variation in fitness over our treatments --had larger climatic niche breadth and geographic range in their field distributions. The result was robust to alternate measures of fitness homeostasis. Our results show that the fitness homeostasis of genotypes can be a major factor contributing to niche breadth and range size in this clade. Fitness homeostasis can buffer species from loss of genetic diversity and under changing climates, provides time for adaptation to future conditions.

Parents exposed to warming produce offspring lower in weight and condition

The parental environment can alter offspring phenotypes via the transfer of non‐genetic information. Parental effects may be viewed as an extension of (within‐generation) phenotypic plasticity. Smaller size, poorer physical condition, and skewed sex ratios are common responses of organisms to global warming, yet whether parental effects alleviate, exacerbate, or have no impact on these responses has not been widely tested. Further, the relative non‐genetic influence of mothers and fathers and ontogenetic timing of parental exposure to warming on offspring phenotypes is poorly understood. Here, we tested how maternal, paternal, and biparental exposure of a coral reef fish (Acanthochromis polyacanthus) to elevated temperature (+1.5°C) at different ontogenetic stages (development vs reproduction) influences offspring length, weight, condition, and sex. Fish were reared across two generations in present‐day and projected ocean warming in a full factorial design. As expected, offspring of parents exposed to present‐day control temperature that were reared in warmer water were shorter than their siblings reared in control temperature; however, within‐generation plasticity allowed maintenance of weight, resulting in a higher body condition. Parental exposure to warming, irrespective of ontogenetic timing and sex, resulted in decreased weight and condition in all offspring rearing temperatures. By contrast, offspring sex ratios were not strongly influenced by their rearing temperature or that of their parents. Together, our results reveal that phenotypic plasticity may help coral reef fishes maintain performance in a warm ocean within a generation, but could exacerbate the negative effects of warming between generations, regardless of when mothers and fathers are exposed to warming. Alternatively, the multigenerational impact on offspring weight and condition may be a necessary cost to adapt metabolism to increasing temperatures. This research highlights the importance of examining phenotypic plasticity within and between generations across a range of traits to accurately predict how organisms will respond to climate change.

2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation

Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.

A viewpoint on ecological and evolutionary study of plant thermal performance curves in a warming world

We can understand the ecology and evolution of plant thermal niches through thermal performance curves (TPCs), which are unimodal, continuous reaction norms of performance across a temperature gradient. Though there are numerous plant TPC studies, plants remain under-represented in syntheses of TPCs. Further, few studies quantify plant TPCs from fitness-based measurements (i.e. growth, survival and reproduction at the individual level and above), limiting our ability to draw conclusions from the existing literature about plant thermal adaptation. We describe recent plant studies that use a fitness-based TPC approach to test fundamental ecological and evolutionary hypotheses, some of which have uncovered key drivers of climate change responses. Then, we outline three conceptual questions in ecology and evolutionary biology for future plant TPC studies: (i) Do populations and species harbour genetic variation for TPCs? (ii) Do plant TPCs exhibit plastic responses to abiotic and biotic factors? (iii) Do fitness-based TPCs scale up to population-level thermal niches? Moving forward, plant ecologists and evolutionary biologists can capitalize on TPCs to understand how plasticity and adaptation will influence plant responses to climate change.

Transcriptome analysis reveals fluid shear stress (FSS) and atherosclerosis pathway as a candidate molecular mechanism of short-term low salinity stress tolerance in abalone

Background

Transcriptome sequencing is an effective tool to reveal the essential genes and pathways underlying countless biotic and abiotic stress adaptation mechanisms. Although severely challenged by diverse environmental conditions, the Pacific abalone Haliotis discus hannai remains a high-value aquaculture mollusk and a Chinese predominantly cultured abalone species. Salinity is one of such environmental factors whose fluctuation could significantly affect the abalone’s cellular and molecular immune responses and result in high mortality and reduced growth rate during prolonged exposure. Meanwhile, hybrids have shown superiority in tolerating diverse environmental stresses over their purebred counterparts and have gained admiration in the Chinese abalone aquaculture industry.

The objective of this study was to investigate the molecular and cellular mechanisms of low salinity adaptation in abalone. Therefore, this study used transcriptome analysis of the gill tissues and flow cytometric analysis of hemolymph of H. discus hannai (DD) and interspecific hybrid H. discus hannai ♀ x H. fulgens ♂ (DF) during low salinity exposure. Also, the survival and growth rate of the species under various salinities were assessed.

Results

The transcriptome data revealed that the differentially expressed genes (DEGs) were significantly enriched on the fluid shear stress and atherosclerosis (FSS) pathway. Meanwhile, the expression profiles of some essential genes involved in this pathway suggest that abalone significantly up-regulated calmodulin-4 (CaM-4) and heat-shock protein90 (HSP90), and significantly down-regulated tumor necrosis factor (TNF), bone morphogenetic protein-4 (BMP-4), and nuclear factor kappa B (NF-kB).

Also, the hybrid DF showed significantly higher and sustained expression of CaM and HSP90, significantly higher phagocytosis, significantly lower hemocyte mortality, and significantly higher survival at low salinity, suggesting a more active molecular and hemocyte-mediated immune response and a more efficient capacity to tolerate low salinity than DD.

Conclusions

Our study argues that the abalone CaM gene might be necessary to maintain ion equilibrium while HSP90 can offset the adverse changes caused by low salinity, thereby preventing damage to gill epithelial cells (ECs).

The data reveal a potential molecular mechanism by which abalone responds to low salinity and confirms that hybridization could be a method for breeding more stress-resilient aquatic species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08611-8.

Modelling the acclimation capacity of coral reefs to a warming ocean

The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12% to 55%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming.

Tropical coral reefs are among the most productive and diverse ecosystems on Earth. The success of these ecosystems depends on a symbiotic relationship between corals and unicellular algae. This relationship breaks down when water temperature increases above certain levels causing massive coral deaths. Therefore, the future of coral reef ecosystems depends on the capacity of corals to acclimate to current warming rates. Despite many studies have tried to predict the future of coral reefs, these predictions are impaired by uncertainties related to the speed with which corals can acclimate. We developed a model in which corals can acclimate to changing temperature. By comparing model results with observations of coral cover, we estimated the speed of coral acclimation at the community level in different regions of the tropics. Using this information, we quantified the future changes in coral abundances under different warming scenarios. We found that corals of the Great Barrier Reef have higher acclimation capacities than those of other regions. Our results showed substantial coral declines in South East Asia and Caribbean, especially under the highest warming scenarios. Thus, we provide evidence that natural acclimation alone may not be sufficient to offset the decline of corals caused by the expected warming trends.

A reduction in metabolism explains the tradeoffs associated with the long-term adaptation of phytoplankton to high CO2 concentrations

Phytoplankton are responsible for nearly half of global primary productivity and play crucial roles in the Earth's biogeochemical cycles. However, the long-term adaptive responses of phytoplankton to rising CO₂ remains unknown. Here we examine the physiological and proteomics responses of a marine diatom, Phaeodactylum tricornutum, following long-term (c. 900 generations) selection to high CO₂ conditions. Our results show that this diatom responds to long-term high CO₂ selection by downregulating proteins involved in energy production (Calvin cycle, tricarboxylic acid cycle, glycolysis, oxidative pentose phosphate pathway), with a subsequent decrease in photosynthesis and respiration. Nearly similar extents of downregulation of photosynthesis and respiration allow the high CO₂ -adapted populations to allocate the same fraction of carbon to growth, thereby maintaining their fitness during the long-term high CO₂ selection. These results indicate an important role of metabolism reduction under high CO₂ and shed new light on the adaptive mechanisms of phytoplankton in response to climate change.

Individual-based eco-evolutionary models for understanding adaptation in changing seas

As climate change threatens species' persistence, predicting the potential for species to adapt to rapidly changing environments is imperative for the development of effective conservation strategies. Eco-evolutionary individual-based models (IBMs) can be useful tools for achieving this objective. We performed a literature review to identify studies that apply these tools in marine systems. Our survey suggested that this is an emerging area of research fuelled in part by developments in modelling frameworks that allow simulation of increasingly complex ecological, genetic and demographic processes. The studies we identified illustrate the promise of this approach and advance our understanding of the capacity for adaptation to outpace climate change. These studies also identify limitations of current models and opportunities for further development. We discuss three main topics that emerged across studies: (i) effects of genetic architecture and non-genetic responses on adaptive potential; (ii) capacity for gene flow to facilitate rapid adaptation; and (iii) impacts of multiple stressors on persistence. Finally, we demonstrate the approach using simple simulations and provide a framework for users to explore eco-evolutionary IBMs as tools for understanding adaptation in changing seas.

Evolution of Thermal Sensitivity in Changing and Variable Climates

Evolutionary adaptation to temperature and climate depends on both the extent to which organisms experience spatial and temporal environmental variation (exposure) and how responsive they are to the environmental variation (sensitivity). Theoretical models and experiments suggesting substantial potential for thermal adaptation have largely omitted realistic environmental variation. Environmental variation can drive fluctuations in selection that slow adaptive evolution. We review how carefully filtering environmental conditions based on how organisms experience their environment and further considering organismal sensitivity can improve predictions of thermal adaptation. We contrast taxa differing in exposure and sensitivity. Plasticity can increase the rate of evolutionary adaptation in taxa exposed to pronounced environmental variation. However, forms of plasticity that severely limit exposure, such as behavioral thermoregulation and phenological shifts, can hinder thermal adaptation. Despite examples of rapid thermal adaptation, experimental studies often reveal evolutionary constraints. Further investigating these constraints and issues of timescale and thermal history are needed to predict evolutionary adaptation and, consequently, population persistence in changing and variable environments.

Impacts of global warming on marine microbial communities

Global warming in ocean ecosystems alters temperature, acidification, oxygen content, circulation, stratification, and nutrient inputs. Microorganisms play a dominant role in global biogeochemical cycles crucial for a planet's sustainability. Since microbial communities are highly dependent on the temperature factor, fluctuations in the same will lead to adverse effects on the microbial community organization. Throughout the Ocean, increase in evaporation rates causes the surface mixed layer to become shallower. This intensified stratification inhibits vertical transport of nutrient supplies. Such density driven processes will decrease oxygen solubility in surface waters leading to significant decrease of oxygen from future Ocean. Metabolism and diversity of microbes along with ocean biogeochemistry will be at great risk due to global warming and its related effects. As a response to the changes in temperature, alteration in the distribution of phytoplankta communities is observed all over the planet, creating changes in the primary production of the ocean causing massive impact on the biosphere. Marine microbial communities try to adapt to the changing ocean environmental conditions by responding with biogeographic range shifts, community structure modifications, and adaptive evolution. Persistence of this climate change on ocean ecosystems, in future, will pose serious threat to the metabolism and distribution of marine microbes leading to fluctuations in the biogeochemical cycles thereby affecting the overall ecosystem functioning. Genomics plays an important role in marine microbial research by providing tools to study the association between environment and organisms. The ecological and genomic perspectives of marine microbes are being investigated to design effective models to understand their physiology and evolution in a changing ocean. Mesocosm/microcosm experimental studies and field studies are in the need of the hour to evaluate the impact of climate shifts on microbial genesis.

Effects of global warming on species with temperature-dependent sex determination: Bridging the gap between empirical research and management

Global warming could threaten over 400 species with temperature-dependent sex determination (TSD) worldwide, including all species of sea turtle. During embryonic development, rising temperatures might lead to the overproduction of one sex and, in turn, could bias populations' sex ratios to an extent that threatens their persistence. If climate change predictions are correct, and biased sex ratios reduce population viability, species with TSD may go rapidly extinct unless adaptive mechanisms, whether behavioural, physiological or molecular, exist to buffer these temperature-driven effects. Here, we summarize the discovery of the TSD phenomenon and its still elusive evolutionary significance. We then review the molecular pathways underpinning TSD in model species, along with the hormonal mechanisms that interact with temperatures to determine an individual's sex. To illustrate evolutionary mechanisms that can affect sex determination, we focus on sea turtle biology, discussing both the adaptive potential of this threatened TSD taxon, and the risks associated with conservation mismanagement.

Distinct interspecific and intraspecific vulnerability of coastal species to global change

Characterising and predicting species responses to anthropogenic global change is one of the key challenges in contemporary ecology and conservation. The sensitivity of marine species to climate change is increasingly being described with forecasted species distributions, yet these rarely account for population level processes such as genomic variation and local adaptation. This study compares inter- and intraspecific patterns of biological composition to determine how vulnerability to climate change, and its environmental drivers, vary across species and populations. We compare species trajectories for three ecologically important southern African marine invertebrates at two time points in the future, both at the species level, with correlative species distribution models, and at the population level, with gradient forest models. Reported range shifts are species-specific and include both predicted range gains and losses. Forecasted species responses to climate change are strongly influenced by changes in a suite of environmental variables, from sea surface salinity and sea surface temperature, to minimum air temperature. Our results further suggest a mismatch between future habitat suitability (where species can remain in their ecological niche) and genomic vulnerability (where populations retain their genomic composition), highlighting the inter- and intraspecific variability in species' sensitivity to global change. Overall, this study demonstrates the importance of considering species and population level climatic vulnerability when proactively managing coastal marine ecosystems in the Anthropocene.

Differential Tolerance and Seasonal Adaptation to Temperature and Salinity Stress at a Dynamic Range Boundary Between Estuarine Gastropods

AbstractInsight into how coastal organisms will respond to changing temperature and salinity regimes may be derived from studies of adaptation to fluctuating estuarine environments, especially under stressful range-edge conditions. We characterized a dynamic range boundary between two estuarine sea slugs, Alderia modesta (distributed across the North Pacific and North Atlantic) and Alderia willowi, known from southern and central California. The species overlap from Bodega Bay to San Francisco Bay, where populations are dominated by A. modesta after winter rains but by A. willowi after peak summer temperatures. Laboratory assays confirmed superior tolerance to low salinity for the northern species, A. modesta: encapsulated embryos developed at 8 ppt, larvae survived at 4-6 ppt, and adults survived repeated exposure to 2 ppt, salinities that reduced development or survival for the same stages of A. willowi. Adults did not appreciably differ in their high-temperature threshold, however. Each species showed increased tolerance to either temperature or salinity stress at its range margin, indicating plasticity or local adaptation, but at the cost of reduced tolerance to the other stressor. At its northern limit, A. willowi became more tolerant of low salinity during the winter rainy season, but also less heat tolerant. Conversely, A. modesta became more heat resistant from spring to summer at its southern limit, but less tolerant of low salinity. Trade-offs in stress tolerance may generally constrain adaptation and limit biotic response to a rapidly changing environment, as well as differentiating species niches.

Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress

The role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpGO/E ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation. We also observed a correlation between gbM and gene expression flexibility: genes with low DNA methylation tend to show flexible gene expression and plasticity under changing conditions. Furthermore, the empirical determination of global DNA methylation (5-mC) showed patterns of intra and inter-specific divergence that suggests a link between methylation level and the plants' latitude of origin and life history. Although we cannot discern whether gbM regulates gene expression or vice versa, or if other molecular mechanisms play a role in facilitating transcriptome responsiveness, our findings point to the existence of a relationship between gene responsiveness and gbM patterns in marine plants.

Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies

Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to-one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directional climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to-one genotype-phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation-compared to linear reaction norms and genetic determinism-even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations producing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.

Phenotypic stability in scalar calcium of freshwater fish across a wide range of aqueous calcium availability in nature

Spatial environmental gradients can promote adaptive differences among conspecific populations as a result of local adaptation or phenotypic plasticity. Such divergence can be opposed by various constraints, including gene flow, limited genetic variation, temporal fluctuations, or developmental constraints. We focus on the constraint that can be imposed when some populations are found in locations characterized by low levels of an essential nutrient. We use scales of wild fish to investigate phenotypic effects of spatial variation in a potentially limiting nutrient-calcium. If scale calcium (we use "scalar" calcium for consistency with the physiology literature) simply reflects environmental calcium availability, we expect higher levels of scalar calcium in fish from calcium-rich water, compared to fish from calcium-poor water. To consider this "passive response" scenario, we analyzed scalar calcium concentrations from three native fish species (Lepomis gibbosus, Percina caprodes, and Perca flavescens) collected at multiple sites across a dissolved calcium gradient in the Upper St. Lawrence River. Contradicting the "passive response" scenario, we did not detect strong or consistent relationships between scalar calcium and water calcium. Instead, for a given proportional increase in water calcium across the wide environmental gradient, the corresponding proportional change in scalar calcium was much smaller. We thus favor the alternative "active homeostasis" scenario, wherein fish from calcium-poor water are better able to uptake, mobilize, and deposit calcium than are fish from calcium-rich water. We further highlight the importance of studying functional traits, such as scales, in their natural setting as opposed to only laboratory studies.

Phenotypic plasticity is not a cline: Thermal physiology of an intertidal barnacle over 20° of latitude

Our understanding of the plastic and evolutionary potential of ectothermic organisms and their populational impacts in the face of rapid global change remains limited. Studies attempting on the relationship between the magnitude of thermal variability across latitude and the degree of phenotypic plasticity exhibited by marine ectotherms are inconclusive. We state that the latter arises from the narrow range of thermal variability captured by the limited span of the latitudinal gradients studied to date. Using a mechanistic ecophysiological approach and a satellite-based assessment of the relevant environmental variables (i.e. temperature and food availability), we studied individuals of the intertidal barnacle Jehlius cirratus from seven local populations widely spread along the Humboldt current system that spanning two biogeographic regions. At the same time, we synthesized published information on the local abundance of our study species across a total of 76 sites representing 20° of latitude, and spanning from 18 to 42°S. We examined the effects of latitude and environmental variability on metabolic rate plasticity, thermal tolerance (thermal breadth and thermal safety margins) and their impacts on the abundance of this widespread marine invertebrate. We demonstrate that the phenotypic plasticity of metabolic rate in J. cirratus populations is not related to latitude. In turn, thermal breadth is explained by the temperature variability each population experiences. Furthermore, we found clinal variation with a poleward decrease of the critical thermal minimum, suggesting that episodic extreme low temperatures represent a ubiquitous selective force on the lower thermal limit for ectotherms. Across our study gradient, plasticity patterns indicate that populations at the equatorial extreme are more vulnerable to a warming climate, while populations located in the biogeographic transitional zone (i.e. high environmental heterogeneity), on the centre of the gradient, display higher levels of phenotypic plasticity and may represent a genetic buffer for the effects of ocean warming. Together, our results suggest the existence of a fitness trade-off involving the metabolic cost of plasticity and population density that is evident only across the vast latitudinal gradient examined.

Phenotypic plasticity under rapid global changes: The intrinsic force for future seagrasses survival

Coastal oceans are particularly affected by rapid and extreme environmental changes with dramatic consequences for the entire ecosystem. Seagrasses are key ecosystem engineering or foundation species supporting diverse and productive ecosystems along the coastline that are particularly susceptible to fast environmental changes. In this context, the analysis of phenotypic plasticity could reveal important insights into seagrasses persistence, as it represents an individual property that allows species' phenotypes to accommodate and react to fast environmental changes and stress. Many studies have provided different definitions of plasticity and related processes (acclimation and adaptation) resulting in a variety of associated terminology. Here, we review different ways to define phenotypic plasticity with particular reference to seagrass responses to single and multiple stressors. We relate plasticity to the shape of reaction norms, resulting from genotype by environment interactions, and examine its role in the presence of environmental shifts. The potential role of genetic and epigenetic changes in underlying seagrasses plasticity in face of environmental changes is also discussed. Different approaches aimed to assess local acclimation and adaptation in seagrasses are explored, explaining strengths and weaknesses based on the main results obtained from the most recent literature. We conclude that the implemented experimental approaches, whether performed with controlled or field experiments, provide new insights to explore the basis of plasticity in seagrasses. However, an improvement of molecular analysis and the application of multi-factorial experiments are required to better explore genetic and epigenetic adjustments to rapid environmental shifts. These considerations revealed the potential for selecting the best phenotypes to promote assisted evolution with fundamental implications on restoration and preservation efforts.

Acquiring an evolutionary perspective in marine ecotoxicology to tackle emerging concerns in a rapidly changing ocean

Tens of thousands of anthropogenic chemicals and wastes enter the marine environment each year as a consequence of the ever-increasing anthropogenic activities and demographic growth of the human population, which is majorly concentrated along coastal areas. Marine ecotoxicology has had a crucial role in helping shed light on the fate of chemicals in the environment, and improving our understanding of how they can affect natural ecosystems. However, chemical contamination is not occurring in isolation, but rather against a rapidly changing environmental horizon. Most environmental studies have been focusing on short-term within-generation responses of single life stages of single species to single stressors. As a consequence, one-dimensional ecotoxicology cannot enable us to appreciate the degree and magnitude of future impacts of chemicals on marine ecosystems. Current approaches that lack an evolutionary perspective within the context of ongoing and future local and global stressors will likely lead us to under or over estimations of the impacts that chemicals will exert on marine organisms. It is therefore urgent to define whether marine organisms can acclimate, i.e. adjust their phenotypes through transgenerational plasticity, or rapidly adapt, i.e. realign the population phenotypic performances to maximize fitness, to the new chemical environment within a selective horizon defined by global changes. To foster a significant advancement in this research area, we review briefly the history of ecotoxicology, synthesis our current understanding of the fate and impact of contaminants under global changes, and critically discuss the benefits and challenges of integrative approaches toward developing an evolutionary perspective in marine ecotoxicology: particularly through a multigenerational approach. The inclusion of multigenerational studies in Ecological Risk Assessment framework (ERA) would provide significant and more accurately information to help predict the risks of pollution in a rapidly changing ocean.

Plasticity in parental effects confers rapid larval thermal tolerance in the estuarine anemone Nematostella vectensis

Parental effects can prepare offspring for different environments and facilitate survival across generations. We exposed parental populations of the estuarine anemone, Nematostella vectensis, from Massachusetts to elevated temperatures and quantified larval mortality across a temperature gradient. We found that parental exposure to elevated temperatures resulted in a consistent increase in larval thermal tolerance, as measured by the temperature at which 50% of larvae die (LT50), with a mean increase in LT50 of 0.3°C. Larvae from subsequent spawns returned to baseline thermal thresholds when parents were returned to normal temperatures, indicating plasticity in these parental effects. Histological analyses of gametogenesis in females suggested that these dynamic shifts in larval thermal tolerance may be facilitated by maternal effects in non-overlapping gametic cohorts. We also compared larvae from North Carolina (a genetically distinct population with higher baseline thermal tolerance) and Massachusetts parents, and observed that larvae from heat-exposed Massachusetts parents had thermal thresholds comparable to those of larvae from unexposed North Carolina parents. North Carolina parents also increased larval thermal tolerance under the same high-temperature regime, suggesting that plasticity in parental effects is an inherent trait for N. vectensis Overall, we find that larval thermal tolerance in N. vectensis shows a strong genetic basis and can be modulated by parental effects. Further understanding of the mechanisms behind these shifts can elucidate the fate of thermally sensitive ectotherms in a rapidly changing thermal environment.

The Neurobiology of Ocean Change - insights from decapod crustaceans

The unprecedented rate of carbon dioxide accumulation in the atmosphere has led to increased warming, acidification and oxygen depletion in the world's oceans, with projected impacts also on ocean salinity. In this perspective article, we highlight potential impacts of these factors on neuronal responses in decapod crustaceans. Decapod crustaceans comprise more than 8,800 marine species which have colonized a wide range of habitats that are particularly affected by global ocean change, including estuarine, intertidal, and coastal areas. Many decapod species have large economic value and high ecological importance because of their global invasive potential and impact on local ecosystems. Global warming has already led to considerable changes in decapod species' behavior and habitat range. Relatively little is known about how the decapod nervous system, which is the ultimate driver of all behaviors, copes with environmental stressors. We use select examples to summarize current findings and evaluate the impact of current and expected environmental changes. While data indicate a surprising robustness against stressors like temperature and pH, we find that only a handful of species have been studied and long-term effects on neuronal activity remain mostly unknown. A further conclusion is that the combined effects of multiple stressors are understudied. We call for greater research efforts towards long-term effects on neuronal physiology and expansion of cross-species comparisons to address these issues.

Effects of temperature on physiological performance and behavioral thermoregulation in an invasive fish, the round goby

Invasive species exert negative impacts on biodiversity and ecosystems on a global scale, which may be enhanced in the future by climate change. Knowledge of how invasive species respond physiologically and behaviorally to novel and changing environments can improve our understanding of which traits enable the ecological success of these species, and potentially facilitate mitigation efforts. We examined the effects of acclimation to temperatures ranging from 5 to 28°C on aerobic metabolic rates, upper temperature tolerance (critical thermal maximum, CTmax), as well as temperature preference (Tpref) and avoidance (Tavoid) of the round goby (Neogobius melanostomus), one of the most impactful invasive species in the world. We show that round goby maintained a high aerobic scope from 15 to 28°C; that is, the capacity to increase its aerobic metabolic rate above that of its maintenance metabolism remained high across a broad thermal range. Although CTmax increased relatively little with acclimation temperature compared with other species, Tpref and Tavoid were not affected by acclimation temperature at all, meaning that round goby maintained a large thermal safety margin (CTmax-Tavoid) across acclimation temperatures, indicating a high level of thermal resilience in this species. The unperturbed physiological performance and high thermal resilience were probably facilitated by high levels of phenotypic buffering, which can make species readily adaptable and ecologically competitive in novel and changing environments. We suggest that these physiological and behavioral traits could be common for invasive species, which would only increase their success under continued climate change.

Effects of temperature on physiological performance and behavioral thermoregulation in an invasive fish, the round goby

Invasive species exert negative impacts on biodiversity and ecosystems on a global scale, which may be enhanced in the future by climate change. Knowledge of how invasive species respond physiologically and behaviorally to novel and changing environments can improve our understanding of which traits enable the ecological success of these species, and potentially facilitate mitigation efforts. We examined the effects of acclimation to temperatures ranging from 5 to 28°C on aerobic metabolic rates, upper temperature tolerance (critical thermal maximum, CT_max), as well as temperature preference (T _pref) and avoidance (T _avoid) of the round goby (Neogobius melanostomus), one of the most impactful invasive species in the world. We show that round goby maintained a high aerobic scope from 15 to 28°C; that is, the capacity to increase its aerobic metabolic rate above that of its maintenance metabolism remained high across a broad thermal range. Although CT_max increased relatively little with acclimation temperature compared with other species, T _pref and T _avoid were not affected by acclimation temperature at all, meaning that round goby maintained a large thermal safety margin (CT_max-T _avoid) across acclimation temperatures, indicating a high level of thermal resilience in this species. The unperturbed physiological performance and high thermal resilience were probably facilitated by high levels of phenotypic buffering, which can make species readily adaptable and ecologically competitive in novel and changing environments. We suggest that these physiological and behavioral traits could be common for invasive species, which would only increase their success under continued climate change.

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

BACKGROUND

Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and families within the phylum Annelida are still represented by a single specimen of a single species. The genus of interstitial annelids Ophryotrocha (Dorvilleidae, Errantia, Annelida) is among these neglected groups, despite its extensive use as model organism in numerous studies on the evolution of life history, physiological and ecological traits. To compensate for the paucity of genomic information in this genus, we here obtained novel complete mitochondrial genomes of six Ophryotrocha species using next generation sequencing. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3).

RESULTS

Surprisingly, gene order was not conserved among the six Ophryotrocha species investigated, and varied greatly as compared to those found in other annelid species within the class Errantia. The mitogenome phylogeny for the six Ophryotrocha species displayed a separation of gonochoric and hermaphroditic species. However, this separation was not observed in the phylogeny based on the COX1, 16S rDNA, and H3 genes. Parsimony and Bayesian ancestral trait reconstruction indicated that gonochorism was the most parsimonious ancestral reproductive mode in Ophryotrocha spp.

CONCLUSIONS

Our results highlight the remarkably high level of gene order variation among congeneric species, even in annelids. This encourages the need for additional mitogenome sequencing of annelid taxa in order to properly understand its mtDNA evolution, high biodiversity and phylogenetic relationships.

Benchmarking DNA methylation assays in a reef-building coral

Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is currently too costly to apply at the scales required for ecological research. Here, we evaluate different methods for measuring DNA methylation for ecological epigenetics. We compare whole genome bisulphite sequencing (WGBS) with methylated CpG binding domain sequencing (MBD-seq), and a modified version of MethylRAD we term methylation-dependent restriction site-associated DNA sequencing (mdRAD). We evaluate these three assays in measuring variation in methylation across the genome, between genotypes, and between polyp types in the reef-building coral Acropora millepora. We find that all three assays measure absolute methylation levels similarly for gene bodies (gbM), as well as exons and 1 Kb windows with a minimum Pearson correlation 0.66. Differential gbM estimates were less correlated, but still concurrent across assays. We conclude that MBD-seq and mdRAD are reliable and cost-effective alternatives to WGBS. The considerably lower sequencing effort required for mdRAD to produce comparable methylation estimates makes it particularly useful for ecological epigenetics.

Unfamiliar partnerships limit cnidarian holobiont acclimation to warming

Enhancing the resilience of corals to rising temperatures is now a matter of urgency, leading to growing efforts to explore the use of heat tolerant symbiont species to improve their thermal resilience. The notion that adaptive traits can be retained by transferring the symbionts alone, however, challenges the holobiont concept, a fundamental paradigm in coral research. Holobiont traits are products of a specific community (holobiont) and all its co-evolutionary and local adaptations, which might limit the retention or transference of holobiont traits by exchanging only one partner. Here we evaluate how interchanging partners affect the short- and long-term performance of holobionts under heat stress using clonal lineages of the cnidarian model system Aiptasia (host and Symbiodiniaceae strains) originating from distinct thermal environments. Our results show that holobionts from more thermally variable environments have higher plasticity to heat stress, but this resilience could not be transferred to other host genotypes through the exchange of symbionts. Importantly, our findings highlight the role of the host in determining holobiont productivity in response to thermal stress and indicate that local adaptations of holobionts will likely limit the efficacy of interchanging unfamiliar compartments to enhance thermal tolerance.

Inorganic carbon uptake strategies in coralline algae: Plasticity across evolutionary lineages under ocean acidification and warming

Dissolved inorganic carbon (DIC) assimilation is essential to the reef-building capacity of crustose coralline algae (CCA). Little is known, however, about the DIC uptake strategies and their potential plasticity under ongoing ocean acidification (OA) and warming. The persistence of CCA lineages throughout historical oscillations of pCO₂ and temperature suggests that evolutionary history may play a role in selecting for adaptive traits. We evaluated the effects of pCO₂ and temperature on the plasticity of DIC uptake strategies and associated energetic consequences in reef-building CCA from different evolutionary lineages. We simulated past, present, moderate (IPCC RCP 6.0) and high pCO₂ (RCP 8.5) and present and high (RCP 8.5) temperature conditions and quantified stable carbon isotope fractionation (¹³ε), organic carbon content, growth and photochemical efficiency. All investigated CCA species possess CO₂-concentrating mechanisms (CCMs) and assimilate CO₂ via diffusion to varying degrees. Under OA and warming, CCA either increased or maintained CCM capacity, which was associated with overall neutral effects on metabolic performance. More basal taxa, Sporolithales and Hapalidiales, had greater capacity for diffusive CO₂ use than Corallinales. We suggest that CCMs are an adaptation that supports a robust carbon physiology and are likely responsible for the endurance of CCA in historically changing oceans.

Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.)

BACKGROUND

Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment association tests were used to attempt to identify loci under selection in relation to local temperature data.

RESULTS

We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (FST = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as a distinct population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal.

CONCLUSIONS

As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.

Limited Genetic Connectivity Among Sargassum horneri (Phaeophyceae) Populations in the Chinese Marginal Seas Despite Their high Dispersal Capacity

Sargassum horneri is a habitat-forming species in the Northwest Pacific and an important contributor to seaweed rafts. In this study, 131 benthic samples and 156 floating samples were collected in the Yellow Sea and East China Sea (ECS) to test the effects of seaweed rafts on population structure and connectivity. Our results revealed high levels of genetic diversity in both benthic and floating samples based on concatenated mitochondrial markers (rpl5-rps3, rnl-atp9, and cob-cox2). Phylogenetic analyses consistently supported the existence of two lineages (lineages I and II), with divergence dating to c. 0.692 Mya (95% HPD: 0.255-1.841 Mya), indicating that long-term isolation may have occurred during the mid-Pleistocene (0.126-0.781 Mya). Extended Bayesian skyline plots demonstrated a constant population size over time in lineage I and slight demographic expansion in lineage II. Both lineages were found in each marginal sea (including both benthic and floating samples), but PCoA, FST , and AMOVA analyses consistently revealed deep genetic variation between regions. Highly structured phylogeographic pattern supports limited genetic connectivity between regions. IMA analyses demonstrated that asymmetric gene flow between benthic populations in the North Yellow Sea (NYS) and ECS was extremely low (ECS→NYS, 2Nm = 0.6), implying that high dispersal capacity cannot be assumed to lead to widespread population connectivity, even without dispersal barriers. In addition, there were only a few shared haplotypes between benthic and floating samples, suggesting the existence of hidden donors for the floating masses in the Chinese marginal seas.

Local thermal adaptation and limited gene flow constrain future climate responses of a marine ecosystem engineer

Rising ocean temperatures and extreme temperature events have precipitated declines and local extinctions in many marine species globally, but patterns of loss are often uneven across species ranges for reasons that are poorly understood. Knowledge of the extent of local adaptation and gene flow may explain such patterns and help predict future trajectories under scenarios of climate change. We test the extent to which local differentiation in thermal tolerance is influenced by gene flow and local adaptation using a widely distributed intertidal seaweed (Hormosira banksii) from temperate Australia. Population surveys across ~2,000 km of the species range revealed strong genetic structuring at regional and local scales (global F ST = 0.243) reflecting extremely limited gene flow, while common garden experiments (14-day exposures to 15, 18, 21°C) revealed strong site differences in early development and mortality in response to elevated temperature. Embryos from many sites spanning a longitudinal thermal gradient showed suppressed development and increased mortality to elevated water temperatures, but populations originating from warmer and more variable thermal environments tended to be less susceptible to warming. Notably, there was significant local-scale variation in the thermal responses of embryos within regions which was corroborated by the finding of small-scale genetic differences. We expect the observed genetic and phenotypic differentiation to lead to uneven responses to warming sea surface temperatures in this important marine foundation species. The study highlights the challenges of predicting species responses to thermal stress and the importance of management strategies that incorporate evolutionary potential for "climate-proofing" marine ecosystems.

Combined stress of ocean acidification and warming influence survival and drives differential gene expression patterns in the Antarctic pteropod, Limacina helicina antarctica

The ecologically important thecosome pteropods in the Limacina spp. complex have recently been the focus of studies examining the impacts global change factors - e.g., ocean acidification (OA) and ocean warming (OW) - on their performance and physiology. This focus is driven by conservation concerns where the health of pteropod populations is threatened by the high susceptibility of their shells to dissolution in low aragonite saturation states associated with OA and how coupling of these stressors may push pteropods past the limits of physiological plasticity. In this manipulation experiment, we describe changes in the transcriptome of the Antarctic pteropod, Limacina helicina antarctica, to these combined stressors. The conditions used in the laboratory treatments met or exceeded those projected for the Southern Ocean by the year 2100. We made two general observations regarding the outcome of the data: (1) Temperature was more influential than pH in terms of changing patterns of gene expression, and (2) these Antarctic pteropods appeared to have a significant degree of transcriptomic plasticity to respond to acute abiotic stress in the laboratory. In general, differential gene expression was observed amongst the treatments; here, for example, transcripts associated with maintaining protein structure and cell proliferation were up-regulated. To disentangle the effects of OA and OW, we used a weighted gene co-expression network analysis to explore patterns of change in the transcriptome. This approach identified gene networks associated with OW that were enriched for transcripts proposed to be involved in increasing membrane fluidity at warmer temperatures. Together these data provide evidence that L.h.antarctica has a limited capacity to acclimate to the combined conditions of OA and OW used in this study. This reduced scope of acclimation argues for continued study of how adaptation to polar aquatic environments may limit the plasticity of present-day populations in responding to future environmental change.

Transgenerational biochemical effects of seawater acidification on the Manila clam (Ruditapes philippinarum)

Ocean acidification can negatively impact marine bivalves. Pivotal to projecting their fate is the ability to acclimate and adapt to shifts in seawater chemistry. Transgenerational plasticity enables marine bivalves to acclimate, yet the underlying mechanisms at different levels of biological organization remain poorly understood. Here, we performed a transgenerational experiment to understand biochemical responses of the Manila clam, Ruditapes philippinarum, following exposure to moderately reduced seawater pH (from 8.1 to 7.7). Activities of tissue calcification-relevant enzymes, such as carbonic anhydrase (CA), acid phosphatase (ACP) and alkaline phosphatase (ALP), energy-metabolizing enzymes, such as Na⁺/K⁺-ATPase (NKA) and Ca²⁺/Mg²⁺-ATPase (CMA), as well as tissue energy reserves (glycogen, lipid and protein) were assayed. With decreasing seawater pH, adult R. philippinarum exhibited significantly increased CA activity, and especially the clams with a history of transgenerational exposure displaying significantly higher CA activity than those spawned from parents exposed to ambient seawater pH. Yet, ACP and ALP activities remained unaffected. Transgenerational exposure to reduced seawater pH led to significant increases of NKA activity, while no transgenerational response of CMA activity was observed. Tissue glycogen and lipid contents were significantly depleted under acidified conditions regardless of transgenerational exposure. Yet, transgenerational alleviation in the net protein degradation was found. These findings suggest that our current understanding of transgenerational responses is still limited by the achievable time-window possible in the laboratory. While the energetic budget is lower under acidified conditions, there is no evidence of transgenerational recovery in term of energetic budget. Therefore, this work demonstrates that the critical basis of ocean acidification resilience can most likely be explained in energetic terms.