Habitats,stress, and evolutionary rates

Habitats of organisms are expressed as an interaction between stress intensity, magnitude of environmental fluctuations, and energy availability from resources. Under this model organisms should evolve broad biological properties defined by such physical characteristics. When energy is severely restricted under the continuing constant stress of adversity-selection, or in widely fluctuating and highly stressful environments, little evolutionary change is expected; relict species and ‘living fossils’ are the respective expectations. In rather stable abiotic environments where resources are limited habitat preferences may develop leading to specialization and ultimately adaptive radiations. On the other hand major new innovations are more likely in highly disturbed resource-rich habitats. Evidence from the living and fossil biota is presented which is consistent with these conclusions.     

Developmental variability and the limits of adaptation: Interactions with stress

1. Little evolutionary change may occur at species borders since the cost of accommodating environmental stresses is high. Extreme examples of such stasis include cave animals in stable stressed environments and ‘living fossils’ in widely fluctuating stressed environments. 2. Variability from the molecular to the organismic level tends to be high under extreme stress. At the developmental level, the fitness of such variants may be low. This means that much developmental variability in natural populations may have little evolutionary significance. 3. Rapid evolutionary change of morphological traits is most likely to be based upon genes acting late in a developmental pathway under conditions which are ecologically and energetically permissive. 4. Although some increases in resistance to temperature extremes have been recorded in laboratory selection experiments, major extensions of extremes in natural populations appear difficult to achieve. The energetic costs of surviving extremes at species borders implies that the evolution of major developmental and morphological shifts is more likely to be a feature of populations of more equable habitats.     

Environments and evolution: interactions between stress, resource inadequacy and energetic efficiency

Evolutionary change is interpreted in terms of the near-universal ecological scenario of stressful environments. Consequently, there is a premium on the energetically efficient exploitation of resources in a resource-inadequate world. Under this environmental model, fitness can be approximated to energetic efficiency especially towards the limits of survival. Furthermore, fitness at one stage of the life-cycle should correlate with fitness at other stages, especially for development time, survival and longevity; 'good genotypes' under stress should therefore be at a premium. Conservation in the wild depends primarily on adaptation to abiotically changing habitats since towards the limits of survival, genomic variation is rarely restrictive. The balance between energetic costs under variable environments and energy from resources provides a model for interpreting evolutionary stasis, punctuational and gradual change, and specialist diversification. Ultimately, a species should be in an equilibrium between the physiology of an organism and its adaptation to the environment. The primary key to understanding evolutionary change should therefore be ecological, highlighting energy availability in a stressed world; this approach is predictive for various patterns of evolutionary change in the living and fossil biota.     

Simulated shifts in trophic niche breadth modulate range loss of alpine butterflies under climate change

Species currently track suitable abiotic and biotic conditions under ongoing climate change. Adjustments of trophic interactions may provide a mechanism for population persistence, an option that is rarely included in model projections. Here, we model the future distribution, of butterflies in the western Alps of Switzerland under climate change, simulating potential diet expansion resulting from adaptive behavior or new host opportunities. We projected the distribution of 60 butterfly and 298 plant species with species distribution models (SDMs) under three climate change scenarios. From known host plants, we allowed a potential diet expansion based on phylogenetic constraints. We assessed whether diet expansion could reduce the rate of expected regional species extinction under climate change. We found that the risk of species extinctions decreased with a concave upward decreasing shape when expanding the host plant range. A diet expansion to even a few phylogenetically closely related host plants would significantly decrease extinction rates. Yet, even when considering expansion toward all plant species available in the study area, the overall regional extinction risk would remain high. Ecological or evolutionary shifts to new host plants may attenuate extinction risk, but the severe decline of suitable abiotic conditions is still expected to drive many species to local extinction.     

Conservation strategies: adaptation to stress and the preservation of genetic diversity

The level of genetic diversity in free-living populations is not normally restrictive for conservation, since it tends to be enhanced in stressed outlier populations. At the physiological level, this enhancement is supported by the favouring of heterozygotes, especially when energy demands needed to adapt to stress are high. Therefore ecophysiological considerations are important for conservation strategies, whereby survival depends upon the metabolic potential of organisms to counter the energy cost of stress in their environments. While abiotic stresses are primary, biotic stresses, in particular competition, can be consolidated into this model as second-order effects. Irrespective of levels of genetic diversity, any species can be incorporated into this approach to conservation. I therefore regard the monitoring of stress response traits to be primary to the preservation of genetic diversity in developing conservation strategies. In arriving at this conclusion, Fisher's 1930 discussions of the environment and consequences for adaptation, as presented in the Genetical Theory of Natural Selection, play an initiating role.     

Predicting loss of evolutionary history: Where are we?

The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.     

Chlorogenic Acid Metabolism: The Evolution and Roles in Plant Response to Abiotic Stress

During the evolution, plants acquired the ability to synthesize different phenylpropanoid compounds like chlorogenic acid (CGA), which plays vital roles in resistance mechanisms to abiotic stresses. These environmental factors, including heavy metal, cold, heat, ultraviolet (UV) light, drought, and salinity affect the plant physiological processes, resulting in massive losses of agriculture production. As plants evolve from green algae to bryophytes, ferns, gymnosperms and angiosperms, phenylpropanoids are produced and accumulated in different tissues, giving the plant the capacity to counteract the harmful effects of the adverse environments. Studies have been performed on the metabolic evolution of rosmarinic acid, flavonoids and lignin, showing that the biosynthesis of phenylpropanoids begins in green algae until the emersion of genes found in angiosperms; however, the evolution of the CGA pathway has not yet been reviewed. We hypothesize that CGA could also be synthesized from algae to angiosperms. In the present review, the evolutionary analysis of CGA pathway and the function of this compound in plant tolerance to abiotic stresses are summarized. Bioinformatics analyzes were carried out on CGA-related genes across 37 plant species and revealed that the metabolic pathway starts in algae and gradually increases until it becomes complete in angiosperms. The key genes exhibited different expression patterns in stress and plant tissues. Interestingly, some genes accumulated rapidly during evolution and were more sensitive to environmental stresses, while others appeared only later in angiosperms. Further studies are needed to better understand the evolution of the CGA metabolic pathway in plants under environmentally stressed conditions.     

Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants

DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.     

Combinatorial Interactions of Biotic and Abiotic Stresses in Plants and Their Molecular Mechanisms: Systems Biology Approach

Plants are continually facing biotic and abiotic stresses, and hence, they need to respond and adapt to survive. Plant response during multiple and combined biotic and abiotic stresses is highly complex and varied than the individual stress. These stresses resulted alteration of plant behavior through regulating the levels of microRNA, heat shock proteins, epigenetic variations. These variations can cause many adverse effects on the growth and development of the plant. Further, in natural conditions, several abiotic stresses causing factors make the plant more susceptible to pathogens infections and vice-versa. A very intricate and multifaceted interactions of various biomolecules are involved in metabolic pathways that can direct towards a cross-tolerance and improvement of plant’s defence system. Systems biology approach plays a significant role in the investigation of these molecular interactions. The valuable information obtained by systems biology will help to develop stress-resistant plant varieties against multiple stresses. Thus, this review aims to decipher various multilevel interactions at the molecular level under combinatorial biotic and abiotic stresses and the role of systems biology to understand these molecular interactions.     

The evolutionary significance of mass extinctions

Local extinctions of populations, species or groups of species in a particular area are commonly observed by biologists. There are also historical records of the total extinction of single species such as the Dodo, the Great Auk and the Tasmanian Wolf. Mass extinctions are on a much larger scale, and their study is based on the fossil record. The aims of this review are to explore the nature of mass extinctions and their evolutionary significance. The key questions are: what is mass extinction, what are the causes of mass extinctions, do mass extinctions follow a regular pattern, and how do mass extinctions affect our understanding of evolutionary processes?     

The future of evolutionary diversity in reef corals

One-third of the world''s reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in conjunction with geographical distributions of living reef coral species to model how extinctions are likely to affect evolutionary diversity across different ecoregions. Based on two measures—phylogenetic diversity and phylogenetic species variability—we highlight regions with the largest losses of evolutionary diversity and hence of potential conservation interest. Notably, the projected loss of evolutionary diversity is relatively low in the most species-rich areas such as the Coral Triangle, while many regions with fewer species stand to lose much larger shares of their diversity. We also suggest that for complex ecosystems like coral reefs it is important to consider changes in phylogenetic species variability; areas with disproportionate declines in this measure should be of concern even if phylogenetic diversity is not as impacted. These findings underscore the importance of integrating evolutionary history into conservation planning for safeguarding the future diversity of coral reefs.     

Escalation and extinction selectivity: morphology versus isotopic reconstruction of bivalve metabolism

Studies that have tested and failed to support the hypothesis that escalated species (e.g., those with predation-resistant adaptations) are more susceptible to elimination during mass extinctions have concentrated on the distribution and degree of morphological defenses in molluscan species. This morphological approach to determining level of escalation in bivalves may be oversimplified because it does not account for metabolic rate, which is an important measure of escalation that is less readily accessible for fossils. Shell growth rates in living bivalves are positively correlated with metabolic rate and thus are potential indicators of level of escalation. To evaluate this approach, we used oxygen isotopes to reconstruct shell growth rates for two bivalve species (Macrocallista marylandica and Glossus markoei) from Miocene-aged sediments of Maryland. Although both species are classified as non-escalated based on morphology, the isotopic data indicate that M. marylandica was a faster-growing species with a higher metabolic rate and G. markoei was a slower-growing species with a lower metabolic rate. Based on these results, we predict that some morphologically non-escalated species in previous tests of extinction selectivity should be reclassified as escalated because of their fast shell growth rates (i.e., high metabolic rates). Studies that evaluate the level of escalation of a fauna should take into account the energetic physiology of taxa to avoid misleading results.     

Evolutionary suicide

The great majority of species that lived on this earth have gone extinct. These extinctions are often explained by invoking changes in the environment, to which the species has been unable to adapt. Evolutionary suicide is an alternative explanation to such extinctions. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist. In this paper different models, where evolutionary suicide occurs are discussed, and the theory behind the phenomenon is reviewed.     

Analysis of adaptive ribosomal gene diversity in wild plant populations from contrasting climatic environments

Plant populations may contain variation that reflects adaptation to local environmental conditions. Clues to adaptive evolution of plants may be found in the genomes of species growing in diverse environments or across steep environmental gradients, and under stress. We have examined populations of wild relatives of barley and rice across diverse environmental gradients. Greater diversity, in a nuclear biotic stress defense gene and in chloroplast genes, was found in the more stressed, hotter and dryer environments. This may reflect the greater heterogeneity of these environments. Adaptation of plants to different abiotic stresses (temperatures and levels of water availability) may also require significant adaptation to the different biotic (pest and disease) pressures in these environments.¹   Plants growing across environmental gradients revealed greater diversity in a defense gene (Isa) in more stressed, hotter and dryer environments.² Chloroplast genome diversity also exhibited a similar variation with environment.³ We now report analysis of nuclear ribosomal genes from the same wild population. Two contrasting environments did not show significant differences in the level of diversity. However the pattern of SNP distribution within the rDNA did vary with greater SNP density in the RNA coding sequences compared with the internal transcribed spacers.     

Polyploidy: an evolutionary and ecological force in stressful times

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.     

CSR ecological strategies and plant mating systems: outcrossing increases with competitiveness but stress‐tolerance is related to mixed mating

A number of plant traits influence the success of fertilization and reproduction in plants. Collectively these traits represent ecological syndromes that are of evolutionary significance. However, while an association between mating system and colonizing ability has been proposed, the existence of a broader relationship between mating system and a species’ position in ecological succession has not been extensively investigated. Grime's CSR theory stresses that an ecological succession can involve changes from colonizing to either competitive or stress‐tolerant strategies. How distinct dimensions of competitiveness and stress tolerance covary with mating systems has still not been considered. We designed a comparative approach to evaluate the link between mating system, life form and CSR strategies for 1996 herbaceous and woody species. We found that CSR strategies are significantly related to mating systems. Ruderal species – colonizers in early succession – were mostly selfers while more competitive species were more often outcrossers. On the other hand, greater physiological stress tolerance was associated with mixed mating systems. Outcrossing is classically expected to be advantageous for most life history strategies other than colonizers, but we suggest that reproductive assurance can counterbalance this effect in stressful environments where populations are sparse and pollinators are rare. Therefore, our results emphasize that competition and abiotic stresses are not equivalent selective pressures on the evolution of mating systems. Finally, we found plant life span to convey additional information on mating system variation, supporting its role for mating system evolution. These findings encourage further investigation of the evolutionary role of ecological strategies as syndromes of traits and suggest that the emergence of large databases of plant traits will help address the major evolutionary hypotheses on such syndromes.     

Understanding extinction debts: spatio–temporal scales,mechanisms and a roadmap for future research

Extinction debt refers to delayed species extinctions expected as a consequence of ecosystem perturbation. Quantifying such extinctions and investigating long‐term consequences of perturbations has proven challenging, because perturbations are not isolated and occur across various spatial and temporal scales, from local habitat losses to global warming. Additionally, the relative importance of eco‐evolutionary processes varies across scales, because levels of ecological organization, i.e. individuals, (meta)populations and (meta)communities, respond hierarchically to perturbations. To summarize our current knowledge of the scales and mechanisms influencing extinction debts, we reviewed recent empirical, theoretical and methodological studies addressing either the spatio–temporal scales of extinction debts or the eco‐evolutionary mechanisms delaying extinctions. Extinction debts were detected across a range of ecosystems and taxonomic groups, with estimates ranging from 9 to 90% of current species richness. The duration over which debts have been sustained varies from 5 to 570 yr, and projections of the total period required to settle a debt can extend to 1000 yr. Reported causes of delayed extinctions are 1) life‐history traits that prolong individual survival, and 2) population and metapopulation dynamics that maintain populations under deteriorated conditions. Other potential factors that may extend survival time such as microevolutionary dynamics, or delayed extinctions of interaction partners, have rarely been analyzed. Therefore, we propose a roadmap for future research with three key avenues: 1) the microevolutionary dynamics of extinction processes, 2) the disjunctive loss of interacting species and 3) the impact of multiple regimes of perturbation on the payment of debts. For their ability to integrate processes occurring at different levels of ecological organization, we highlight mechanistic simulation models as tools to address these knowledge gaps and to deepen our understanding of extinction dynamics.     

Evolutionary innovations driving abiotic stress tolerance in C4 grasses and cereals

Grasslands dominate the terrestrial landscape, and grasses have evolved complex and elegant strategies to overcome abiotic stresses. The C₄ grasses are particularly stress tolerant and thrive in tropical and dry temperate ecosystems. Growing evidence suggests that the presence of C₄ photosynthesis alone is insufficient to account for drought resilience in grasses, pointing to other adaptations as contributing to tolerance traits. The majority of grasses from the Chloridoideae subfamily are tolerant to drought, salt, and desiccation, making this subfamily a hub of resilience. Here, we discuss the evolutionary innovations that make C₄ grasses so resilient, with a particular emphasis on grasses from the Chloridoideae (chloridoid) and Panicoideae (panicoid) subfamilies. We propose that a baseline level of resilience in chloridoid ancestors allowed them to colonize harsh habitats, and these environments drove selective pressure that enabled the repeated evolution of abiotic stress tolerance traits. Furthermore, we suggest that a lack of evolutionary access to stressful environments is partially responsible for the relatively poor stress resilience of major C₄ crops compared to their wild relatives. We propose that chloridoid crops and the subfamily more broadly represent an untapped reservoir for improving resilience to drought and other abiotic stresses in cereals.

Chloridoid grasses have evolved unique adaptations to adverse environments and represent an untapped reservoir for improving resilience to drought and other abiotic stresses in cereals.     

Introduction pathway and climate trump ecology and life history as predictors of establishment success in alien frogs and toads

A major goal for ecology and evolution is to understand how abiotic and biotic factors shape patterns of biological diversity. Here, we show that variation in establishment success of nonnative frogs and toads is primarily explained by variation in introduction pathways and climatic similarity between the native range and introduction locality, with minor contributions from phylogeny, species ecology, and life history. This finding contrasts with recent evidence that particular species characteristics promote evolutionary range expansion and reduce the probability of extinction in native populations of amphibians, emphasizing how different mechanisms may shape species distributions on different temporal and spatial scales. We suggest that contemporary changes in the distribution of amphibians will be primarily determined by human-mediated extinctions and movement of species within climatic envelopes, and less by species-typical traits.