Evidence of current impact of climate change on life: a walk from genes to the biosphere

We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade‐offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.     

Maternal source of variability in the embryo development of an annual killifish

Organisms inhabiting unpredictable environments often evolve diversified reproductive bet‐hedging strategies, expressed as production of multiple offspring phenotypes, thereby avoiding complete reproductive failure. To cope with unpredictable rainfall, African annual killifish from temporary savannah pools lay drought‐resistant eggs that vary widely in the duration of embryo development. We examined the sources of variability in the duration of individual embryo development, egg production and fertilization rate in Nothobranchius furzeri. Using a quantitative genetics approach (North Carolina type II design), we found support for maternal effects rather than polyandrous mating as the primary source of the variability in the duration of embryo development. The number of previously laid eggs appeared to serve as an internal physiological cue initiating a shift from rapid‐to‐slow embryo developmental mode. In annual killifish, extensive phenotypic variability in progeny traits is adaptive, as the conditions experienced by parents have limited relevance to the offspring generation. In contrast to genetic control, with high phenotypic expression and heritability, maternal control of traits under natural selection prevents standing genetic diversity from potentially detrimental effects of selection in fluctuating environments.     

植物的表型可塑性、异速生长及其入侵能力

表型可塑性是指同一个基因型对不同环境响应产生不同表型的特性,特定性状的可塑性本身可以遗传,也可以接受选择而发生进化。植物个体的异速生长是指生物体某一特征的相对生长速率不等于第二种特征的相对生长速率的特性,该特性是由物种的遗传性决定的一种固定特征,植物往往朝着最佳的异速生长曲线进化。植物特定基因型在不同环境下,诸如生物量分配和种群几何学上的一些表型差异,既可由异速生长造成,也可由表型可塑性造成。植物本身的异速生长是一种"外观可塑性",而异速生长曲线的改变才是真正的可塑性。植物的表型可塑性、异速生长对于入侵植物的适应具有重要意义。干扰等异质性生境下表型可塑性成为物种生存扩散的有利性状,表型可塑性强的物种更有可能成为广布种。植物本身的异速生长特性或其异速生长曲线的改变都能影响其入侵能力。     

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

Organisms often respond to environmental changes by producing alternative phenotypes. Epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression. Changes in DNA methylation, unlike DNA mutations, can be influenced by the environment; they are stable at the time scale of an individual and present different levels of heritability. These characteristics make DNA methylation a potentially important molecular process to respond to environmental change. The aim of this review is to present the implications of DNA methylation on phenotypic variations driven by environmental changes. More specifically, we explore epigenetic concepts concerning phenotypic change in response to the environment and heritability of DNA methylation, namely the Baldwin effect and genetic accommodation. Before addressing this point, we report major differences in DNA methylation across taxa and the role of this modification in producing and maintaining environmentally induced phenotypic variation. We also present the different methods allowing the detection of methylation polymorphism. We believe this review will be helpful to molecular ecologists, in that it highlights the importance of epigenetic processes in ecological and evolutionary studies.     

Comparing the consequences of natural selection,adaptive phenotypic plasticity,and matching habitat choice for phenotype–environment matching,population genetic structure,and reproductive isolation in meta‐populations

Organisms commonly experience significant spatiotemporal variation in their environments. In response to such heterogeneity, different mechanisms may act that enhance ecological performance locally. However, depending on the nature of the mechanism involved, the consequences for populations may differ greatly. Building on a previous model that investigated the conditions under which different adaptive mechanisms (co)evolve, this study compares the ecological and evolutionary population consequences of three very different responses to environmental heterogeneity: matching habitat choice (directed gene flow), adaptive plasticity (associated with random gene flow), and divergent natural selection. Using individual‐based simulations, we show that matching habitat choice can have a greater adaptive potential than plasticity or natural selection: it allows for local adaptation while protecting genetic polymorphism despite global mating or strong environmental changes. Our simulations further reveal that increasing environmental fluctuations and unpredictability generally favor the emergence of specialist genotypes but that matching habitat choice is better at preventing local maladaptation by individuals. This confirms that matching habitat choice can speed up the genetic divergence among populations, cause indirect assortative mating via spatial clustering, and hence even facilitate sympatric speciation. This study highlights the potential importance of directed dispersal in local adaptation and speciation, stresses the difficulty of deriving its operation from nonexperimental observational data alone, and helps define a set of ecological conditions which should favor its emergence and subsequent detection in nature.     

Natural selection, larval dispersal, and the geography of phenotype in the sea

Populations evolve generalist, specialist, and plastic strategies in response to environmental heterogeneity. Describing such within-species variation in phenotype and how it arises is central to understanding a variety of ecological and evolutionary topics. The literature on phenotypic differences among populations is highly biased; for every one article published on a marine species, at least 10 articles are published on a terrestrial species and eight focus on terrestrial plants. Here, I outline what we know from the marine literature about geographic variation in phenotype in the sea, with a principal focus on local adaptation. The theory of environmental "grain" predicts that the most likely evolutionary response (e.g., local adaptation, phenotypic plasticity, generalism, and balanced polymorphism) depends on the spatial scale of environmental variation relative to the distance that an organism disperses. Consistent with these predictions, phenotypic plasticity is stronger among invertebrates with geographically broad dispersal versus restricted dispersal (i.e., planktonic-dispersers versus direct-developers). However, contrary to predictions, the relative frequency, and spatial scale of local adaptation is not consistently greater among direct-developers relative to planktonic disperers. This indicates that the likelihood of local adaptation depends on other organismal or environmental traits. Two of the most vexing issues that remain include (1) predicting the extent to which barriers to dispersal are a cause versus consequence of phenotypic differentiation and (2) delineating the relative importance of evolutionary forces that favor or impede local adaptation. Understanding the mechanistic basis of the geography of phenotypic differences, or phenogeography, has gained recent momentum because of a need to predict impacts of global climatic change, anthropogenic disturbances, and dispersal of organisms to non-native habitats.     

The evolution of bet-hedging adaptations to rare scenarios

When faced with a variable environment, organisms may switch between different strategies according to some probabilistic rule. In an infinite population, evolution is expected to favor the rule that maximizes geometric mean fitness. If some environments are encountered only rarely, selection may not be strong enough for optimal switching probabilities to evolve. Here we calculate the evolution of switching probabilities in a finite population by analyzing fixation probabilities of alleles specifying switching rules. We calculate the conditions required for the evolution of phenotypic switching as a form of bet-hedging as a function of the population size N, the rate theta at which a rare environment is encountered, and the selective advantage s associated with switching in the rare environment. We consider a simplified model in which environmental switching and phenotypic switching are one-way processes, and mutation is symmetric and rare with respect to the timescale of fixation events. In this case, the approximate requirements for bet-hedging to be favored by a ratio of at least R are that sN>log(R) and thetaN>square root R .     

The Evolutionary Origin of Somatic Cells under the Dirty Work Hypothesis

Reproductive division of labor is a hallmark of multicellular organisms. However, the evolutionary pressures that give rise to delineated germ and somatic cells remain unclear. Here we propose a hypothesis that the mutagenic consequences associated with performing metabolic work favor such differentiation. We present evidence in support of this hypothesis gathered using a computational form of experimental evolution. Our digital organisms begin each experiment as undifferentiated multicellular individuals, and can evolve computational functions that improve their rate of reproduction. When such functions are associated with moderate mutagenic effects, we observe the evolution of reproductive division of labor within our multicellular organisms. Specifically, a fraction of the cells remove themselves from consideration as propagules for multicellular offspring, while simultaneously performing a disproportionately large amount of mutagenic work, and are thus classified as soma. As a consequence, other cells are able to take on the role of germ, remaining quiescent and thus protecting their genetic information. We analyze the lineages of multicellular organisms that successfully differentiate and discover that they display unforeseen evolutionary trajectories: cells first exhibit developmental patterns that concentrate metabolic work into a subset of germ cells (which we call “pseudo-somatic cells”) and later evolve to eliminate the reproductive potential of these cells and thus convert them to actual soma. We also demonstrate that the evolution of somatic cells enables phenotypic strategies that are otherwise not easily accessible to undifferentiated organisms, though expression of these new phenotypic traits typically includes negative side effects such as aging.     

Maternal effects on phenotypic plasticity in larvae of the salamander <Emphasis Type="Italic">Hynobius retardatus</Emphasis>

Maternal effects are widespread and influence a variety of traits, for example, life history strategies, mate choice, and capacity to avoid predation. Therefore, maternal effects may also influence phenotypic plasticity of offspring, but few studies have addressed the relationship between maternal effects and phenotypic plasticity of offspring. We examined the relationship between a maternally influenced trait (egg size) and the phenotypic plasticity of the induction rate of the broad-headed morph in the salamander Hynobius retardatus. The relationship between egg size and the induction of the broad-headed morph was tested across experimental crowding conditions (densities of low conspecifics, high conspecifics, and high heterospecific anuran), using eggs and larvae from eight natural populations with different larval densities of conspecifics and heterospecifics. The broad-headed morph has a large mouth that enables it to consume either conspecifics or heterospecifics, and this ability gives survival advantages over the normal morph. We have determined that there is phenotypic plasticity in development, as shown by an increase in the frequency of broad-headed morph in response to an increase in the density of conspecifics and heterospecifics. This reaction norm differed between populations. We also determined that the frequency of the broad-headed morph is affected by egg size in which larger egg size resulted in expression of the broad-headed morph. Furthermore, we determined that selection acting on the propensity to develop the broad-headed morph has produced a change in egg size. Lastly, we found that an increase in egg size alters the reaction norm to favor development of the broad-headed morph. For example, an equal change in experimental density produces a greater change in the frequency of the broad-headed morph in larvae developing from large eggs than it does in larvae developing from small eggs. Population differences in plasticity might be the results of differences in egg size between populations, which is caused by the adaptive integration of the plasticity and egg size. Phenotypic plasticity can not evolve independently of maternal effects.     

Selectionism and neutralism in molecular evolution

Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns|< or =1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.     

Biological responses to environmental heterogeneity under future ocean conditions

Organisms are projected to face unprecedented rates of change in future ocean conditions due to anthropogenic climate‐change. At present, marine life encounters a wide range of environmental heterogeneity from natural fluctuations to mean climate change. Manipulation studies suggest that biota from more variable marine environments have more phenotypic plasticity to tolerate environmental heterogeneity. Here, we consider current strategies employed by a range of representative organisms across various habitats – from short‐lived phytoplankton to long‐lived corals – in response to environmental heterogeneity. We then discuss how, if and when organismal responses (acclimate/migrate/adapt) may be altered by shifts in the magnitude of the mean climate‐change signal relative to that for natural fluctuations projected for coming decades. The findings from both novel climate‐change modelling simulations and prior biological manipulation studies, in which natural fluctuations are superimposed on those of mean change, provide valuable insights into organismal responses to environmental heterogeneity. Manipulations reveal that different experimental outcomes are evident between climate‐change treatments which include natural fluctuations vs. those which do not. Modelling simulations project that the magnitude of climate variability, along with mean climate change, will increase in coming decades, and hence environmental heterogeneity will increase, illustrating the need for more realistic biological manipulation experiments that include natural fluctuations. However, simulations also strongly suggest that the timescales over which the mean climate‐change signature will become dominant, relative to natural fluctuations, will vary for individual properties, being most rapid for CO₂ (~10 years from present day) to 4 decades for nutrients. We conclude that the strategies used by biota to respond to shifts in environmental heterogeneity may be complex, as they will have to physiologically straddle wide‐ranging timescales in the alteration of ocean conditions, including the need to adapt to rapidly rising CO₂ and also acclimate to environmental heterogeneity in more slowly changing properties such as warming.     

Local adaptation for enhanced salt tolerance reduces non‐adaptive plasticity caused by osmotic stress

Organisms often respond to environmental change via phenotypic plasticity, in which an individual modulates its phenotype according to the environment. Highly variable or changing environments can exceed physiological limits and generate maladapted plastic phenotypes, which is termed nonadaptive plasticity. In some cases, selection may reduce the negative or disruptive impacts of environmental stress and produce locally adapted populations. Salt is an increasingly prevalent contaminant of freshwater systems and can induce nonadaptive plastic phenotypes for freshwater organisms like amphibians. Hyla cinerea is a frog species with populations inhabiting brackish, coastal habitats, so we use this species to test whether coastal populations are locally adapted to tolerate saltwater by determining how salt exposure during the embryonic and larval stages alters mortality and plastic developmental and metamorphic phenotypes of coastal and inland populations. Coastal frogs have higher survival, faster growth rates, and metamorphose sooner than inland frogs across salinities. Coastal frogs also metamorphose smaller (likely a consequence of earlier metamorphosis) yet maintain constant size, while higher salinities reduce metamorphic size for inland frogs. Coastal frogs evolved to minimize nonadaptive and disruptive impacts of saltwater during larval development and accelerate the larval period to reduce time spent in a stressful environment.     

Parental investment in temporally varying environments

Summary Using a model that allows the mean and variance of investment by parents in offspring to evolve in response to change in degree of temporal environmental variation, this paper shows that both parental investment parameters should increase with increases in temporal variation. If offspring receiving greater parental investment are viable over a broader range of environmental conditions, then increased temporal environmental variation can select for increases in parental investment. The variance in parental investment also may increase with increases in temporal variation, but there is a threshold level of temporal variation that must be exceeded before variance in parental investment is adaptive. Thus phenotypic variance in parental investment is not adaptive in all temporally varying environments. Further, increased overlap among generations reduces the expected effects of temporal variation on the mean and variance in parental investment. Thus a negative correlation between length of reproductive life and both measures of investment is expected. There is support for the predictions of this model in some animal groups, but not among plants. Possible reasons for the lack of support among plants are discussed and directions for future research aimed at distinguishing adaptive and maladaptive phenotypic variance in parental investment are suggested.     

The Flask model: emergence of nutrient-recycling microbial ecosystems and their disruption by environment-altering 'rebel' organisms

Here we introduce a new model of life–environment interaction, which simulates an evolving microbial community in a 'Fask' of liquid with prescribed inputs of nutrients. The flask is seeded with a clonal population of 'microbes' that are subject to mutation on genetic loci that determine their nutrient uptake patterns, release patterns, and their effects on, and response to, other environmental variables. In contrast to existing models of life-environment interaction, notably Daisyworld, what benefits the individual organisms is decoupled from their 'global' (system-level) effects. A robust property of the model is the emergence of ecosystems that tend toward a state where nutrients are efficiently utilised and differentially recycled, with a correlated increase in total population. Organisms alter the environment as a free 'by-product' of their growth, and their growth is constrained by adverse environmental effects. This introduces environmental feedback, which can disrupt the model ecosystems, even though there are no constraints on the conditions to which the organisms can theoretically adapt. 'Rebel' organisms can appear that grow rapidly by exploiting an under-utilised resource, but in doing so shift the environment away from the state to which the majority of the community are adapted. The result can be a population crash with lossof recycling, followed by later recovery, or in extreme cases, a total extinction of the system. Numerous runs of these 'flask' ecosystems show that tighter environmental constraints on growth make the system more vulnerable to internally generated ecosystem extinction.     

Stressed mothers lay eggs with high corticosterone levels which produce low-quality offspring

Organisms frequently encounter stressful ecological conditions. In vertebrates, a major mechanism of physiological response to stress is mediated by the hypothalamic-pituitary-adrenal axis and results in increased secretion of glucocorticosteroids, which can have adverse consequences on diverse phenotypic traits affecting fitness. Maternal stress may thus have carry-over effects on progeny if it influences pre-natal offspring environment in terms of glucocorticosteroid concentration, although this hypothesis has never been tested in any species under field conditions. We manipulated stress experienced by female barn swallows Hirundo rustica, by exposing them to a predator during laying and measured egg corticosterone concentration. Stressed females laid eggs with greater corticosterone concentration than controls exposed to a herbivore. In another experiment, we injected physiological doses of corticosterone in the egg albumen and compared the phenotype of offspring originating from these eggs with their control siblings originating from either sham-inoculated or unmanipulated eggs and reared in the same nest. Eggs injected with corticosterone had lower hatchability and produced fledglings with smaller body size and slower plumage development than did control eggs. Nestling body size in our study population predicts long-term survival. Thus, maternal stress impaired offspring phenotype and viability by increasing transmission of glucocorticosteroids to the eggs. This study identifies a novel mechanism mediating early maternal effects whereby maternal stress affects offspring quality. These results are relevant to biological conservation because they disclose a mechanism that can link environmental conditions to population productivity and viability.     

Quantitative genetic and translocation experiments reveal genotype‐by‐environment effects on juvenile life‐history traits in two populations of Chinook salmon (Oncorhynchus tshawytscha)

Understanding the genetic architecture of phenotypic plasticity is required to assess how populations might respond to heterogeneous or changing environments. Although several studies have examined population‐level patterns in environmental heterogeneity and plasticity, few studies have examined individual‐level variation in plasticity. Here, we use the North Carolina II breeding design and translocation experiments between two populations of Chinook salmon to detail the genetic architecture and plasticity of offspring survival and growth. We followed the survival of 50 800 offspring through the larval stage and used parentage analysis to examine survival and growth through freshwater rearing. In one population, we found that additive genetic, nonadditive genetic and maternal effects explained 25%, 34% and 55% of the variance in larvae survival, respectively. In the second population, these effects explained 0%, 24% and 61% of the variance in larvae survival. In contrast, fry survival was regulated primarily by additive genetic effects, which indicates a shift from maternal to genetic effects as development proceeds. Fry growth also showed strong additive genetic effects. Translocations between populations revealed that offspring survival and growth varied between environments, the degree of which differed among families. These results indicate genetic differences among individuals in their degree of plasticity and consequently their ability to respond to environmental variation.     

Evolution of Adaptation and Mate Choice: Parental Relatedness Affects Expression of Phenotypic Variance in a Natural Population

Mating between relatives generally results in reduced offspring viability or quality, suggesting that selection should favor behaviors that minimize inbreeding. However, in natural populations where searching is costly or variation among potential mates is limited, inbreeding is often common and may have important consequences for both offspring fitness and phenotypic variation. In particular, offspring morphological variation often increases with greater parental relatedness, yet the source of this variation, and thus its evolutionary significance, are poorly understood. One proposed explanation is that inbreeding influences a developing organism’s sensitivity to its environment and therefore the increased phenotypic variation observed in inbred progeny is due to greater inputs from environmental and maternal sources. Alternatively, changes in phenotypic variation with inbreeding may be due to additive genetic effects alone when heterozygotes are phenotypically intermediate to homozygotes, or effects of inbreeding depression on condition, which can itself affect sensitivity to environmental variation. Here we examine the effect of parental relatedness (as inferred from neutral genetic markers) on heritable and nonheritable components of developmental variation in a wild bird population in which mate choice is often constrained, thereby leading to inbreeding. We found greater morphological variation and distinct contributions of variance components in offspring from highly related parents: inbred offspring tended to have greater environmental and lesser additive genetic variance compared to outbred progeny. The magnitude of this difference was greatest in late-maturing traits, implicating the accumulation of environmental variation as the underlying mechanism. Further, parental relatedness influenced the effect of an important maternal trait (egg size) on offspring development. These results support the hypothesis that inbreeding leads to greater sensitivity of development to environmental variation and maternal effects, suggesting that the evolutionary response to selection will depend strongly on mate choice patterns and population structure.     

Population size and identity influence the reaction norm of the rare,endemic plant Cochlearia bavarica across a gradient of environmental stress

Habitat degradation and loss can result in population decline and genetic erosion, limiting the ability of organisms to cope with environmental change, whether this is through evolutionary genetic response (requiring genetic variation) or through phenotypic plasticity (i.e., the ability of a given genotype to express a variable phenotype across environments). Here we address the question whether plants from small populations are less plastic or more susceptible to environmental stress than plants from large populations. We collected seed families from small (<100) versus large natural populations (>1,000 flowering plants) of the rare, endemic plant Cochlearia bavarica (Brassicaceae). We exposed the seedlings to a range of environments, created by manipulating water supply and light intensity in a 2 x 2 factorial design in the greenhouse. We monitored plant growth and survival for 300 days. Significant effects of offspring environment on offspring characters demonstrated that there is phenotypic plasticity in the responses to environmental stress in this species. Significant effects of population size group, but mainly of population identity within the population size groups, and of maternal plant identity within populations indicated variation due to genetic (plus potentially maternal) variation for offspring traits. The environment x maternal plant identity interaction was rarely significant, providing little evidence for genetically- (plus potentially maternally-) based variation in plasticity within populations. However, significant environment x population-size-group and environment x population-identity interactions suggested that populations differed in the amount of plasticity, the mean amount being smaller in small populations than in large populations. Whereas on day 210 the differences between small and large populations were largest in the environment in which plants grew biggest (i.e., under benign conditions), on day 270 the difference was largest in stressful environments. These results show that population size and population identity can affect growth and survival differently across environmental stress gradients. Moreover, these effects can themselves be modified by time-dependent variation in the interaction between plants and their environment.