Functional genomic analysis of corals from natural CO2‐seeps reveals core molecular responses involved in acclimatization to ocean acidification

Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here, we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long‐term acclimatization to natural variation in pCO₂. In the coral host, only 61 genes were differentially expressed in response to pCO₂ environment, but the pattern of change was highly consistent between replicate populations, likely reflecting the core expression homeostasis response to ocean acidification. Functional annotations highlight lipid metabolism and a change in the stress response capacity of corals as key parts of this process. Specifically, constitutive downregulation of molecular chaperones was observed, which may impact response to combined climate change‐related stressors. Elevated CO₂ has been hypothesized to benefit photosynthetic organisms but expression changes of in hospite Symbiodinium in response to acidification were greater and less consistent among reef populations. This population‐specific response suggests hosts may need to adapt not only to an acidified environment, but also to changes in their Symbiodinium populations that may not be consistent among environments, adding another challenging dimension to the physiological process of coping with climate change.     

Organism activity levels predict marine invertebrate survival during ancient global change extinctions

Multistressor global change, the combined influence of ocean warming, acidification, and deoxygenation, poses a serious threat to marine organisms. Experimental studies imply that organisms with higher levels of activity should be more resilient, but testing this prediction and understanding organism vulnerability at a global scale, over evolutionary timescales, and in natural ecosystems remain challenging. The fossil record, which contains multiple extinctions triggered by multistressor global change, is ideally suited for testing hypotheses at broad geographic, taxonomic, and temporal scales. Here, I assess the importance of activity level for survival of well‐skeletonized benthic marine invertebrates over a 100‐million‐year‐long interval (Permian to Jurassic periods) containing four global change extinctions, including the end‐Permian and end‐Triassic mass extinctions. More active organisms, based on a semiquantitative score incorporating feeding and motility, were significantly more likely to survive during three of the four extinction events (Guadalupian, end‐Permian, and end‐Triassic). In contrast, activity was not an important control on survival during nonextinction intervals. Both the end‐Permian and end‐Triassic mass extinctions also triggered abrupt shifts to increased dominance by more active organisms. Although mean activity gradually returned toward pre‐extinction values, the net result was a permanent ratcheting of ecosystem‐wide activity to higher levels. Selectivity patterns during ancient global change extinctions confirm the hypothesis that higher activity, a proxy for respiratory physiology, is a fundamental control on survival, although the roles of specific physiological traits (such as extracellular pCO₂ or aerobic scope) cannot be distinguished. Modern marine ecosystems are dominated by more active organisms, in part because of selectivity ratcheting during these ancient extinctions, so on average may be less vulnerable to global change stressors than ancient counterparts. However, ancient extinctions demonstrate that even active organisms can suffer major extinction when the intensity of environmental disruption is intense.     

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2‐acidified sea water

Ocean acidification is the increase in seawater pCO₂ due to the uptake of atmospheric anthropogenic CO₂, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO₂, and associated decrease in pH, represents a climate change‐related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal‐level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular‐level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild‐caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA‐seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms.     

Community‐level effects of rapid experimental warming and consumer loss outweigh effects of rapid ocean acidification

Climate change and consumer loss simultaneously affect marine ecosystems, but we have limited understanding of the relative importance of these factors and the interactions between them. Moreover, effects of environmental change are mediated by organism traits or life histories, which determine their sensitivity. Yet, trait‐based analyses have rarely been used to understand the effects of climate change, especially in the marine environment. Here we used a five‐week mesocosm experiment to assess the single and interactive effects of 1) rapid ocean warming, 2) rapid ocean acidification, and 3) simulated consumer loss, on the diversity and composition of macrofauna communities in eelgrass Zostera marina beds. Experimental warming (ambient versus + 3.2°C) and loss of a key consumer (the omnivorous crustacean, Gammarus locusta) both increased macrofauna richness and abundance, and altered overall species trait distributions and life history composition. Warming and consumer‐loss favored poorly defended epifaunal crustaceans (tube‐building amphipods), and species that brood their offspring. We suggest these organisms were favored because warming and consumer‐loss caused increased metabolism, food supply and, potentially, settling substrate, and lowered predation pressure from the omnivorous G. locusta. Importantly, we found no single, or interactive, effects of the rapid ocean acidification (ambient versus ?0.35 pH units). We suggest this result reflects natural variability in the native habitat and, potentially, the short duration of the experiment: organisms in these communities routinely experience rapid diurnal pH fluctuations that exceed the mean ocean acidification predicted for the coming century (and used in our experiments). In summary, our study indicates that macrofauna in shallow vegetated ecosystems will be significantly more affected by rapid warming and consumer diversity loss than by rapid ocean acidification.     

Plasticity and local adaptation explain lizard cold tolerance

How does climate variation limit the range of species and what does it take for species to colonize new regions? In this issue of Molecular Ecology, Campbell‐Staton et al. ( 2018 ) address these broad questions by investigating cold tolerance adaptation in the green anole lizard (Anolis carolinensis) across a latitudinal transect. By integrating physiological data, gene expression data and acclimation experiments, the authors disentangle the mechanisms underlying cold adaptation. They first establish that cold tolerance adaptation in Anolis lizards follows the predictions of the oxygen‐ and capacity‐limited thermal tolerance hypothesis, which states that organisms are limited by temperature thresholds at which oxygen supply cannot meet demand. They then explore the drivers of cold tolerance at a finer scale, finding evidence that northern populations are adapted to cooler thermal regimes and that both phenotypic plasticity and heritable genetic variation contribute to cold tolerance. The integration of physiological and gene expression data further highlights the varied mechanisms that drive cold tolerance adaptation in Anolis lizards, including both supply‐side and demand‐side adaptations that improve oxygen economy. Altogether, their work provides new insight into the physiological and genetic mechanisms underlying adaptation to new climatic niches and demonstrates that cold tolerance in northern lizard populations is achieved through the synergy of physiological plasticity and local genetic adaptation for thermal performance.     

Putting the genes into community genetics

As part of the long‐term fusion of evolutionary biology and ecology (Ford, 1964), the field of community genetics has made tremendous progress in describing the impacts of plant genetic variation on community and ecosystem processes. In the “genes‐to‐ecosystems” framework (Whitham et al., 2003), genetically based traits of plant species have ecological consequences, but previous studies have not identified specific plant genes responsible for community phenotypes. The study by Barker et al. (2019) in this issue of Molecular Ecology uses an impressive common garden experiment of trembling aspen (Figure 1) to test for the genetic basis of tree traits that shape the insect community composition. Using a Genome‐Wide Association Study (GWAS), they found that genomic regions associated with phytochemical traits best explain variation in herbivore community composition, and identified specific genes associated with different types of leaf‐modifying herbivores and ants. This is one of the first studies to identify candidate genes underlying the heritable plant traits that explain patterns of insect biodiversity.     

Generality in multispecies responses to ocean acidification revealed through multiple hypothesis testing

Decades of research have demonstrated that many calcifying species are negatively affected by ocean acidification, a major anthropogenic threat in marine ecosystems. However, even closely related species may exhibit different responses to ocean acidification and less is known about the drivers that shape such variation in different species. Here, we examine the drivers of physiological performance under ocean acidification in a group of five species of turf‐forming coralline algae. Specifically, quantitating the relative weight of evidence for each of ten hypotheses, we show that variation in coralline calcification and photosynthesis was best explained by allometric traits. Across ocean acidification conditions, larger individuals (measured as noncalcified mass) had higher net calcification and photosynthesis rates. Importantly, our approach was able to not only identify the aspect of size that drove the performance of coralline algae, but also determined that responses to ocean acidification were not dependent on species identity, evolutionary relatedness, habitat, shape, or structural composition. In fact, we found that failure to test multiple, alternative hypotheses would underestimate the generality of physiological performances, leading to the conclusion that each species had different baseline performance under ocean acidification. Testing among alternative hypotheses is an essential step toward determining the generalizability of experiments across taxa and identifying common drivers of species responses to global change.     

The physiology of rapid ecological specialization: A look at the Midas cichlids

Understanding the process of speciation is a primary goal of evolutionary biology, yet the question of whether speciation can reach completion in the presence of gene flow remains controversial. For more than 50 years, the cichlids of Africa, and more recently those in South and Central America, have served as model systems for the study of speciation in nature. Cichlids are distinguished by their enormous species richness, their diversity of behavioural and trophic adaptations, and their rapid rate of divergence. In both Africa and South and Central America, the repeated interaction of geology, new founder events and adaptive evolution has created a series of natural experiments with speciation occurring both within and between waterbodies of differing ages. In the “From the Cover” paper in this issue of the Journal of Molecular Ecology, Raffini, Schneider, Franchini, Kautt and Meyer move beyond the question of which mechanisms drive speciation, and instead show that divergent morphologies and physiologies translate into adaptive traits. They investigate differences in physiology and gene expression profiles in a benthic/limnetic species pair of Midas cichlidsin a 24,000‐year‐old Nicaraguan crater lake. While recently diverged, these two species demonstrate significant ecological, but limited genetic differentiation. The authors find that the distinct morphotypes translate into relevant differences in swimming performance and metabolic rates that correspond to differential gene expression profiles. Hence, the authors take an integrative approach examining the impacts of morphological differences on performance and niche partitioning: an approach that can advance our understanding of the drivers of morphological and physiological divergence during speciation.     

Making the most of population genomic data to understand the importance of chromosomal inversions for adaptation and speciation

Chromosomal inversions are increasingly found to differentiate locally adapted populations. This adaptive role is predictable because reduced recombination protects allelic combinations from gene flow. However, we are far from understanding how frequently inversions contribute to local adaptation and how widespread this phenomenon is across species. In a “From the Cover” article in this issue of Molecular Ecology, Huang, Andrew, Owens, Ostevik, and Rieseberg (2020) provide an important step towards this goal not only by finding adaptive inversions in a sunflower ecotype, but also by reversing the approach used to investigate the link between adaptation and inversions. Most studies compare two phenotypes and uncover divergence at a few regions, of which some can subsequently be identified as inversions. In contrast, Huang et al first catalogue putative inversions and then test genotype–environment associations, which allows them to ask systematically whether inversions may be adaptive and in which ecological contexts. They achieve that by revisiting a previous reduced‐representation sequencing (RAD‐sequencing) data set, demonstrating the suitability of this method to detect inversions in species with limited genomic resources. As such, Huang et al pave the way for a better understanding of the evolutionary role of structural genomic variation and highlight that accounting for inversions in population genomics is now possible, and much needed, in a wider range of organisms.     

Effects of multiple drivers of ocean global change on the physiology and functional gene expression of the coccolithophore Emiliania huxleyi

Ongoing ocean global change due to anthropogenic activities is causing multiple chemical and physical seawater properties to change simultaneously, which may affect the physiology of marine phytoplankton. The coccolithophore Emiliania huxleyi is a model species often employed in the study of the marine carbon cycle. The effect of ocean acidification (OA) on coccolithophore calcification has been extensively studied; however, physiological responses to multiple environmental drivers are still largely unknown. Here we examined two‐way and multiple driver effects of OA and other key environmental drivers—nitrate, phosphate, irradiance, and temperature—on the growth, photosynthetic, and calcification rates, and the elemental composition of E. huxleyi. In addition, changes in functional gene expression were examined to understand the molecular mechanisms underpinning the physiological responses. The single driver manipulation experiments suggest decreased nitrate supply being the most important driver regulating E. huxleyi physiology, by significantly reducing the growth, photosynthetic, and calcification rates. In addition, the interaction of OA and decreased nitrate supply (projected for year 2100) had more negative synergistic effects on E. huxleyi physiology than all other two‐way factorial manipulations, suggesting a linkage between the single dominant driver (nitrate) effects and interactive effects with other drivers. Simultaneous manipulation of all five environmental drivers to the conditions of the projected year 2100 had the largest negative effects on most of the physiological metrics. Furthermore, functional genes associated with inorganic carbon acquisition (RubisCO, AEL1, and δCA) and calcification (CAX3, AEL1, PATP, and NhaA2) were most downregulated by the multiple driver manipulation, revealing linkages between responses of functional gene expression and associated physiological metrics. These findings together indicate that for more holistic projections of coccolithophore responses to future ocean global change, it is necessary to understand the relative importance of environmental drivers both individually (i.e., mechanistic understanding) and interactively (i.e., cumulative effect) on coccolithophore physiology.     

FUNCTIONAL GENETIC DIVERGENCE IN HIGH CO2 ADAPTED EMILIANIA HUXLEYI POPULATIONS

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short‐term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well‐established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO₂. After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO₂‐adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment “high light” did not reveal such genetic divergence whereas growth in a low‐salinity environment revealed strong pleiotropic effects in high CO₂ adapted populations, indicating divergent genetic bases for adaptation to high CO₂. This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments.     

Formalizing the definition of meta‐analysis in Molecular Ecology

Meta‐analysis, the statistical synthesis of pertinent literature to develop evidence‐based conclusions, is relatively new to the field of molecular ecology, with the first meta‐analysis published in the journal Molecular Ecology in 2003 (Slate & Phua 2003). The goal of this article is to formalize the definition of meta‐analysis for the authors, editors, reviewers and readers of Molecular Ecology by completing a review of the meta‐analyses previously published in this journal. We also provide a brief overview of the many components required for meta‐analysis with a more specific discussion of the issues related to the field of molecular ecology, including the use and statistical considerations of Wright's F_ST and its related analogues as effect sizes in meta‐analysis. We performed a literature review to identify articles published as ‘meta‐analyses’ in Molecular Ecology, which were then evaluated by at least two reviewers. We specifically targeted Molecular Ecology publications because as a flagship journal in this field, meta‐analyses published in Molecular Ecology have the potential to set the standard for meta‐analyses in other journals. We found that while many of these reviewed articles were strong meta‐analyses, others failed to follow standard meta‐analytical techniques. One of these unsatisfactory meta‐analyses was in fact a secondary analysis. Other studies attempted meta‐analyses but lacked the fundamental statistics that are considered necessary for an effective and powerful meta‐analysis. By drawing attention to the inconsistency of studies labelled as meta‐analyses, we emphasize the importance of understanding the components of traditional meta‐analyses to fully embrace the strengths of quantitative data synthesis in the field of molecular ecology.     

Roe deer on ice: Selection despite limited effective population size through the Pleistocene

Roe deer (Capreolus spp.) are a little odd. They are one of only a few placental mammals—and the only genus among even‐toed ungulates—capable of putting embryonic development “on ice”, also known as embryonic diapause (Figure 1). It would seem such an unusual trait is probably the product of natural selection, but a big question is, how does selection for important traits, such as diapause, interact with the historical demography of a species? In a ‘From the Cover’ article in this issue of Molecular Ecology, de Jong et al. (2020) demonstrate that selection is acting on genes associated with reproductive biology in roe deer, despite heightened genetic drift due to reduced effective population size through the Pleistocene.     

Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland Honeyeater (Phylidonyris novaehollandiae)

Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex‐specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall‐related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits – shorter, deeper bills, longer tarsi, and longer wings – would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex‐biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill‐head length, deeper bills, and shorter tarsi. Bill depth in males in high‐rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill‐head length, bill‐nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale.