Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine

Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them to colonize harsh environments. In nature, microbes are regularly challenged by starvation, which is a particularly complex stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created by metabolic waste. Often overlooked are the additional complications introduced by eventual resource replenishment, as successful microbes must withstand rapid environmental shifts before swiftly capitalizing on replenished resources to avoid invasion by competing species. To understand how microbes navigate trade-offs between growth and survival, ultimately adapting to thrive in environments with extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days in repeated feast/famine conditions with cycles of 100-day starvation before resource replenishment. Using longitudinal population-genomic analysis, we found that evolution in response to extreme feast/famine is characterized by narrow adaptive trajectories with high mutational parallelism and notable mutational order. Genetic reconstructions reveal that early mutations result in trade-offs for biofilm and motility but trade-ups for growth and survival, as these mutations conferred positively correlated advantages during both short-term and long-term culture. Our results demonstrate how microbes can navigate the adaptive landscapes of regularly fluctuating conditions and ultimately follow mutational trajectories that confer benefits across diverse environments.

Effective fitness under fluctuating selection with genetic drift

The natural environment fluctuates for virtually every population of organisms. As a result, the fitness of a mutant may vary temporally. While commonly used for summarizing the effect of fluctuating selection on the mutant, geometric mean fitness can be misleading under some circumstances due to the influence of genetic drift. Here, we show by mathematical proof and computer simulation that, with genetic drift, the geometric mean fitness does not accurately reflect the overall effect of fluctuating selection. We propose an alternative measure based on the average expected allele frequency change caused by selection and demonstrate that this measure-effective fitness-better captures the overall effect of fluctuating selection in the presence of drift.

Pleiotropy drives evolutionary repair of the responsiveness of polarized cell growth to environmental cues

The ability of cells to translate different extracellular cues into different intracellular responses is vital for their survival in unpredictable environments. In Saccharomyces cerevisiae, cell polarity is modulated in response to environmental signals which allows cells to adopt varying morphologies in different external conditions. The responsiveness of cell polarity to extracellular cues depends on the integration of the molecular network that regulates polarity establishment with networks that signal environmental changes. The coupling of molecular networks often leads to pleiotropic interactions that can make it difficult to determine whether the ability to respond to external signals emerges as an evolutionary response to environmental challenges or as a result of pleiotropic interactions between traits. Here, we study how the propensity of the polarity network of S. cerevisiae to evolve toward a state that is responsive to extracellular cues depends on the complexity of the environment. We show that the deletion of two genes, BEM3 and NRP1, disrupts the ability of the polarity network to respond to cues that signal the onset of the diauxic shift. By combining experimental evolution with whole-genome sequencing, we find that the restoration of the responsiveness to these cues correlates with mutations in genes involved in the sphingolipid synthesis pathway and that these mutations frequently settle in evolving populations irrespective of the complexity of the selective environment. We conclude that pleiotropic interactions make a significant contribution to the evolution of networks that are responsive to extracellular cues.

Evolutionary rescue in a fluctuating environment: periodic versus quasi-periodic environmental changes

No environment is constant over time, and environmental fluctuations impact the outcome of evolutionary dynamics. Survival of a population not adapted to some environmental conditions is threatened unless, for example, a mutation rescues it, an eco-evolutionary process termed evolutionary rescue. We here investigate evolutionary rescue in an environment that fluctuates between a favourable state, in which the population grows, and a harsh state, in which the population declines. We develop a stochastic model that includes both population dynamics and genetics. We derive analytical predictions for the mean extinction time of a non-adapted population given that it is not rescued, the probability of rescue by a mutation, and the mean appearance time of a rescue mutant, which we validate using numerical simulations. We find that stochastic environmental fluctuations, resulting in quasi-periodic environmental changes, accelerate extinction and hinder evolutionary rescue compared with deterministic environmental fluctuations, resulting in periodic environmental changes. We demonstrate that high equilibrium population sizes and per capita growth rates maximize the chances of evolutionary rescue. We show that an imperfectly harsh environment, which does not fully prevent births but makes the death rate to birth rate ratio much greater than unity, has almost the same rescue probability as a perfectly harsh environment, which fully prevents births. Finally, we put our results in the context of antimicrobial resistance and conservation biology.

Internal cues for optimizing reproduction in a varying environment

In varying environments, it is beneficial for organisms to utilize available cues to infer the conditions they may encounter and express potentially favourable traits. However, external cues can be unreliable or too costly to use. We consider an alternative strategy where organisms exploit internal sources of information. Even without sensing environmental cues, their internal states may become correlated with the environment as a result of selection, which then form a memory that helps predict future conditions. To demonstrate the adaptive value of such internal cues in varying environments, we revisit the classic example of seed dormancy in annual plants. Previous studies have considered the germination fraction of seeds and its dependence on environmental cues. In contrast, we consider a model of germination fraction that depends on the seed age, which is an internal state that can serve as a memory. We show that, if the environmental variation has temporal structure, then age-dependent germination fractions will allow the population to have an increased long-term growth rate. The more the organisms can remember through their internal states, the higher the growth rate a population can potentially achieve. Our results suggest experimental ways to infer internal memory and its benefit for adaptation in varying environments.

Evolutionary coexistence in a fluctuating environment by specialization on resource level

Microbial communities in fluctuating environments, such as oceans or the human gut, contain a wealth of diversity. This diversity contributes to the stability of communities and the functions they have in their hosts and ecosystems. To improve stability and increase production of beneficial compounds, we need to understand the underlying mechanisms causing this diversity. When nutrient levels fluctuate over time, one possibly relevant mechanism is coexistence between specialists on low and specialists on high nutrient levels. The relevance of this process is supported by the observations of coexistence in the laboratory, and by simple models, which show that negative frequency dependence of two such specialists can stabilize coexistence. However, as microbial populations are often large and fast growing, they evolve rapidly. Our aim is to determine what happens when species can evolve; whether evolutionary branching can create diversity or whether evolution will destabilize coexistence. We derive an analytical expression of the invasion fitness in fluctuating environments and use adaptive dynamics techniques to find that evolutionarily stable coexistence requires a special type of trade-off between growth at low and high nutrients. We do not find support for the necessary evolutionary trade-off in data available for the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae on glucose. However, this type of data is scarce and might exist for other species or in different conditions. Moreover, we do find evidence for evolutionarily stable coexistence of the two species together. Since we find this coexistence in the scarce data that are available, we predict that specialization on resource level is a relevant mechanism for species diversity in microbial communities in fluctuating environments in natural settings.

Variation in shape and consistency of selection between populations of the threatened Hihi (Notiomystis cincta)

The shape and intensity of natural selection can vary between years, potentially resulting in a chronic reduction of fitness as individuals need to track a continually changing optimum of fitness (i.e., a "lag load"). In endangered species, often characterized by small population size, the lack of genetic diversity is expected to limit the response to this constant need to adjust to fluctuating selection, increasing the fitness burden and thus the risk of extinction. Here, we use long-term monitoring data to assess whether the type of selection for a key fitness trait (i.e., lay date) differs between two reintroduced populations of a threatened passerine bird, the hihi (Notiomystis cincta). We apply recent statistical developments to test for the presence or absence of fluctuation in selection in both the Tiritiri Mātangi Island and the Kārori sanctuary populations. Our results support the presence of stabilizing selection in Tiritiri Mātangi with a potential moving optimum for lay date. In Kārori our results favour a regime of directional selection. Although the shape of selection may differ, for both populations an earlier lay date generally increases fitness in both environments. Further, the moving optimum models of lay date on Tiritiri Mātangi, suggesting that selection varies between years, imply a substantial lag load in addition to the fitness burden caused by the population laying too late. Our results highlight the importance of characterizing the form and temporal variation of selection for each population to predict the effects of environmental change and to inform management.

Plasticity in social behaviour varies with reproductive status in an avian cooperative breeder

Cooperatively breeding vertebrates are common in unpredictable environments where the costs and benefits of providing offspring care fluctuate temporally. To balance these fitness outcomes, individuals of cooperatively breeding species often exhibit behavioural plasticity according to environmental conditions. Although individual variation in cooperative behaviours is well-studied, less is known about variation in plasticity of social behaviour. Here, we examine the fitness benefits, plasticity and repeatability of nest guarding behaviour in cooperatively breeding superb starlings (Lamprotornis superbus). After demonstrating that the cumulative nest guarding performed at a nest by all breeders and helpers combined is a significant predictor of reproductive success, we model breeder and helper behavioural reaction norms to test the hypothesis that individuals invest more in guarding in favourable seasons with high rainfall. Variation in nest guarding behaviour across seasons differed for individuals of different reproductive status: breeders showed plastic nest guarding behaviour in response to rainfall, whereas helpers did not. Similarly, we found that individual breeders show repeatability and consistency in their nest guarding behaviour while individual helpers did not. Thus, individuals with the potential to gain direct fitness benefits exhibit greater plasticity and individual-level repeatability in cooperative behaviour.

Antagonistic effects of long- and short-term environmental variation on species coexistence

Assessing the impact of environmental fluctuations on species coexistence is critical for understanding biodiversity loss and the ecological impacts of climate change. Yet determining how properties like the intensity, frequency or duration of environmental fluctuations influence species coexistence remains challenging, presumably because previous studies have focused on indefinite coexistence. Here, we model the impact of environmental fluctuations at different temporal scales on species coexistence over a finite time period by employing the concepts of time-windowed averaging and performance curves to incorporate temporal niche differences within a stochastic Lotka-Volterra model. We discover that short- and long-term environmental variability has contrasting effects on transient species coexistence, such that short-term variation favours species coexistence, whereas long-term variation promotes competitive exclusion. This dichotomy occurs because small samples (e.g. environmental changes over long time periods) are more likely to show large deviations from the expected mean and are more difficult to predict than large samples (e.g. environmental changes over short time periods), as described in the central limit theorem. Consequently, we show that the complex set of relationships among environmental fluctuations and species coexistence found in previous studies can all be synthesized within a general framework by explicitly considering both long- and short-term environmental variation.

A simple regulatory architecture allows learning the statistical structure of a changing environment

Bacteria live in environments that are continuously fluctuating and changing. Exploiting any predictability of such fluctuations can lead to an increased fitness. On longer timescales, bacteria can 'learn' the structure of these fluctuations through evolution. However, on shorter timescales, inferring the statistics of the environment and acting upon this information would need to be accomplished by physiological mechanisms. Here, we use a model of metabolism to show that a simple generalization of a common regulatory motif (end-product inhibition) is sufficient both for learning continuous-valued features of the statistical structure of the environment and for translating this information into predictive behavior; moreover, it accomplishes these tasks near-optimally. We discuss plausible genetic circuits that could instantiate the mechanism we describe, including one similar to the architecture of two-component signaling, and argue that the key ingredients required for such predictive behavior are readily accessible to bacteria.

High-throughput field phenotyping reveals genetic variation in photosynthetic traits in durum wheat under drought

Chlorophyll fluorescence (ChlF) is a powerful non-invasive technique for probing photosynthesis. Although proposed as a method for drought tolerance screening, ChlF has not yet been fully adopted in physiological breeding, mainly due to limitations in high-throughput field phenotyping capabilities. The light-induced fluorescence transient (LIFT) sensor has recently been shown to reliably provide active ChlF data for rapid and remote characterisation of plant photosynthetic performance. We used the LIFT sensor to quantify photosynthesis traits across time in a large panel of durum wheat genotypes subjected to a progressive drought in replicated field trials over two growing seasons. The photosynthetic performance was measured at the canopy level by means of the operating efficiency of Photosystem II ( Fq'/Fm' ) and the kinetics of electron transport measured by reoxidation rates ( Fr1' and Fr2' ). Short- and long-term changes in ChlF traits were found in response to soil water availability and due to interactions with weather fluctuations. In mild drought, Fq'/Fm' and Fr2' were little affected, while Fr1' was consistently accelerated in water-limited compared to well-watered plants, increasingly so with rising vapour pressure deficit. This high-throughput approach allowed assessment of the native genetic diversity in ChlF traits while considering the diurnal dynamics of photosynthesis.

Fitness cost from fluctuating ultraviolet radiation in Daphnia magna

Solar ultraviolet radiation (UVR) is an important environmental threat for organisms in aquatic systems, but its temporally variable nature makes the understanding of its effects ambiguous. The aim of our study was to assess potential fitness costs associated with fluctuating UVR in the aquatic zooplankter Daphnia magna. We investigated individual survival, reproduction and behaviour when exposed to different UVR treatments. Individuals exposed to fluctuating UVR, resembling natural variations in cloud cover, had the lowest fitness (measured as the number of offspring produced during their lifespan). By contrast, individuals exposed to the same, but constant UVR dose had similar fitness to control individuals (not exposed to UVR), but they showed a significant reduction in daily movement. The re-occurring threat response to the fluctuating UVR treatment thus had strong fitness costs for D. magna, and we found no evidence for plastic behavioural responses when continually being exposed to UVR, despite the regular, predictable exposure schedule. In a broader context, our results imply that depending on how variable a stressor is in nature, populations may respond with alternative strategies, a framework that could promote rapid population differentiation and local adaptation.

Can You Trust Who You See? The Evolution of Socially Cued Anticipatory Plasticity

AbstractThe social environment can affect development and fitness. However, we do not know how selection acts on individuals that cue developmental pathways using features of the social environment. Socially cued anticipatory plasticity (SCAP) is a hypothetical strategy whereby juveniles use social cues to alter development to match their adult phenotype to the social environment that they expect to encounter. While intuitively appealing, the evolution of such plasticity is a puzzle, because the cue changes when individuals use it. Can socially cued plasticity evolve when such a feedback occurs? We use individual-based simulations to model evolution of SCAP in an environment that fluctuates between favoring each of two discrete phenotypes. We found that socially cued plasticity evolved, but only when strong selection acted on survival rather than on fecundity differences between adult phenotypes. In this case, the social cue reliably predicted which phenotype would be favored on maturation. Surprisingly, costs to plasticity increased the range of conditions under which it was adaptive. In the absence of costs, evolution led to a state where SCAP individuals could not effectively respond to environmental changes. Costs to plasticity lowered the proportion of the population that used SCAP, which in turn increased the reliability of the social cue and allowed individuals that used socially cued plasticity to switch between the favored phenotypes more consistently. Our results suggest that the evolution of adaptive plasticity in response to social cues may represent a larger class of problems in which evolution is hard to predict because of feedbacks among critical processes.

Fluctuating optimum and temporally variable selection on breeding date in birds and mammals

Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.

Tolerance Patterns and Transcriptomic Response to Extreme and Fluctuating Salinities across Populations of the Intertidal Copepod Tigriopus californicus

AbstractPopulations that tolerate extreme environmental conditions with frequent fluctuations can give valuable insights into physiological limits and adaptation. In some estuarine and marine ecosystems, organisms must adapt to extreme and fluctuating salinities, but not much is known about how varying salinities impact local adaptation across a wide geographic range. We used eight geographically and genetically divergent populations of the intertidal copepod Tigriopus californicus to test whether northern populations have greater tolerance to low salinity stresses, as they experience greater precipitation and less evaporation. We used a common-garden experiment approach and exposed all populations to acute low (1 and 3 ppt) and high (110 and 130 ppt) salinities for 24 h and to a fluctuation between baseline salinity and moderate low (7 ppt) and high (80 ppt) salinities for over 49 h. We also performed RNA sequencing at several time points during the fluctuation between baseline and salinity of 7 ppt to understand the molecular basis of divergence between two populations with differing physiological responses. We present these novel findings: (1) acute low salinity conditions caused more deaths than high salinity; (2) molecular processes that elevate proline levels increased in salinity of 7 ppt, which contrasts with other physiological studies in T. californicus that mainly associated accumulation of proline with hyperosmotic stress; and (3) tolerance to a salinity fluctuation did not follow a latitudinal trend but was instead governed by a complex interplay of factors, including population and duration of salinity stress. This highlights the importance of including a wider variety of environmental conditions in empirical studies to understand local adaptation.

Reduced phenotypic plasticity evolves in less predictable environments

Phenotypic plasticity is a prominent mechanism for coping with variable environments, and a key determinant of extinction risk. Evolutionary theory predicts that phenotypic plasticity should evolve to lower levels in environments that fluctuate less predictably, because they induce mismatches between plastic responses and selective pressures. However, this prediction is difficult to test in nature, where environmental predictability is not controlled. Here, we exposed 32 lines of the halotolerant microalga Dunaliella salina to ecologically realistic, randomly fluctuating salinity, with varying levels of predictability, for 500 generations. We found that morphological plasticity evolved to lower degrees in lines that experienced less predictable environments. Evolution of plasticity mostly concerned phases with slow population growth, rather than the exponential phase where microbes are typically phenotyped. This study underlines that long‐term experiments with complex patterns of environmental change are needed to test theories about population responses to altered environmental predictability, as currently observed under climate change.

Microbial evolutionary strategies in a dynamic ocean

Marine microbes form the base of ocean food webs and drive ocean biogeochemical cycling. Yet little is known about the ability of microbial populations to adapt as they are advected through changing conditions. Here, we investigated the interplay between physical and biological timescales using a model of adaptation and an eddy-resolving ocean circulation climate model. Two criteria were identified that relate the timing and nature of adaptation to the ratio of physical to biological timescales. Genetic adaptation was impeded in highly variable regimes by nongenetic modifications but was promoted in more stable environments. An evolutionary trade-off emerged where greater short-term nongenetic transgenerational effects (low-γ strategy) enabled rapid responses to environmental fluctuations but delayed genetic adaptation, while fewer short-term transgenerational effects (high-γ strategy) allowed faster genetic adaptation but inhibited short-term responses. Our results demonstrate that the selective pressures for organisms within a single water mass vary based on differences in generation timescales resulting in different evolutionary strategies being favored. Organisms that experience more variable environments should favor a low-γ strategy. Furthermore, faster cell division rates should be a key factor in genetic adaptation in a changing ocean. Understanding and quantifying the relationship between evolutionary and physical timescales is critical for robust predictions of future microbial dynamics.

Temporally Autocorrelated Environmental Fluctuations Inhibit the Evolution of Stress Tolerance

As global environmental conditions continue to change at an unprecedented rate, many species will experience increases in natural and anthropogenic stress. Generally speaking, selection is expected to favor adaptations that reduce the negative impact of environmental stress (i.e., stress tolerance). However, natural environmental variables typically fluctuate, exhibiting various degrees of temporal autocorrelation, known as environmental colors, which may complicate evolutionary responses to stress. Here we combine experiments and theory to show that temporal environmental autocorrelation can determine long-term evolutionary responses to stress without affecting the total amount of stress experienced over time. Experimental evolution of RNA virus lineages in differing environmental autocorrelation treatments agreed closely with predictions from our theoretical models that stress tolerance is favored in less autocorrelated (whiter) environments but disfavored in more autocorrelated (redder) environments. This is explained by an interaction between environmental autocorrelation and a phenotypic trade-off between stress tolerance and reproductive ability. The degree to which environmental autocorrelation influences evolutionary trajectories depends on the shape of this trade-off as well as the relative level of tolerance exhibited by novel mutants. These results suggest that long-term evolutionary dynamics depend not only on the overall strength of selection but also on the way that selection is distributed over time.

Genomics of cellular proliferation in periodic environmental fluctuations

Living systems control cell growth dynamically by processing information from their environment. Although responses to a single environmental change have been intensively studied, little is known about how cells react to fluctuating conditions. Here, we address this question at the genomic scale by measuring the relative proliferation rate (fitness) of 3,568 yeast gene deletion mutants in out-of-equilibrium conditions: periodic oscillations between two environmental conditions. In periodic salt stress, fitness and its genetic variance largely depended on the oscillating period. Surprisingly, dozens of mutants displayed pronounced hyperproliferation under short stress periods, revealing unexpected controllers of growth under fast dynamics. We validated the implication of the high-affinity cAMP phosphodiesterase and of a regulator of protein translocation to mitochondria in this group. Periodic oscillations of extracellular methionine, a factor unrelated to salinity, also altered fitness but to a lesser extent and for different genes. The results illustrate how natural selection acts on mutations in a dynamic environment, highlighting unsuspected genetic vulnerabilities to periodic stress in molecular processes that are conserved across all eukaryotes.

What Kind of Maternal Effects Can Be Selected For in Fluctuating Environments?

Just as phenotypic plasticity can evolve when developing individuals get informational cues about their future adult environment, deterministic maternal effects, where offspring trait values depend on the maternal environment, can evolve when mothers gain reliable information about the environments their offspring will face. Randomizing maternal effects (a type of diversifying bet hedging), where offspring trait values are randomized, can evolve by natural selection even when information about future environments is unavailable. We investigate selection on both randomizing and deterministic maternal effects in environments that show correlated fluctuations between two environmental states. We compare the strength of selection for deterministic and randomizing maternal effects and explicitly consider maternal fitness costs of producing offspring with different phenotypes. Only a small set of environmental parameters allow randomizing maternal effects to outcompete deterministic maternal effects; not only must there be little or no information available about future environments, but the frequency of each environment must fall within a narrow range. By contrast, deterministic maternal effects can always invade an ancestral state lacking a maternal effect even if the amount of environmental information available is low. The long-term outcome may involve offspring trait value randomization but only if trait values first evolve to cause extreme differences in environment-specific fitness. Overall, deterministic maternal effects are more likely to evolve by natural selection than randomizing maternal effects.

Evolution in leaps: The punctuated accumulation and loss of cultural innovations

Archaeological accounts of cultural change reveal a fundamental conflict: Some suggest that change is gradual, accelerating over time, whereas others indicate that it is punctuated, with long periods of stasis interspersed by sudden gains or losses of multiple traits. Existing models of cultural evolution, inspired by models of genetic evolution, lend support to the former and do not generate trajectories that include large-scale punctuated change. We propose a simple model that can give rise to both exponential and punctuated patterns of gain and loss of cultural traits. In it, cultural innovation comprises several realistic interdependent processes that occur at different rates. The model also takes into account two properties intrinsic to cultural evolution: the differential distribution of traits among social groups and the impact of environmental change. In our model, a population may be subdivided into groups with different cultural repertoires leading to increased susceptibility to cultural loss, whereas environmental change may lead to rapid loss of traits that are not useful in a new environment. Taken together, our results suggest the usefulness of a concept of an effective cultural population size.

Barrancaceae: A new green algal lineage with structural and behavioral adaptations to a fluctuating environment

PREMISE OF THE STUDY

To enhance our knowledge of the diversity of microalgae, a phycological survey of the Canary Islands (Spain) was undertaken. Here we report the discovery of a (semi)terrestrial green filamentous alga isolated from a steep volcanic canyon on La Palma. This alga is continually exposed to changing weather conditions (floods vs. droughts) and thus provides a good opportunity to investigate possible adaptations to a semiterrestrial habitat with large fluctuations of environmental parameters.

METHODS

We used axenic cultures, simulated flood and drought stresses and studied their effect on the life history of the alga using light, confocal laser scanning and scanning electron microscopy including fluorescent staining. Furthermore, phylogenetic analyses using rDNA sequence comparisons were performed.

KEY RESULTS

Three specific life-history traits that likely represent adaptations to the fluctuating environment of the canyon were observed: (1) fragmentation through "filament splitting", a unique branching mechanism not reported before in algae and initiated by formation of oblique cross walls, (2) aplanospore formation, and (3) reproduction by multiflagellate zoospores with 4-24 flagella arranged in groups of four. Phylogenetic analyses identified the alga as Barranca multiflagellata gen. et sp. nov. (Barrancaceae fam. nov., Chaetophorales, Chlorophyceae). Moreover, the Chaetophoraceae Greville, 1824 was emended and a new family, Uronemataceae (fam. nov.) erected.

CONCLUSIONS

The discovery of Barrancaceae fam. nov. highlights the importance of investigating nonconventional habitats to explore microalgal diversity. The reproductive versatility demonstrated by Barranca suggests adaptation to a semiterrestrial habitat with large fluctuations in water availability.

Fate of a mutation in a fluctuating environment

Natural environments are never truly constant, but the evolutionary implications of temporally varying selection pressures remain poorly understood. Here we investigate how the fate of a new mutation in a fluctuating environment depends on the dynamics of environmental variation and on the selective pressures in each condition. We find that even when a mutation experiences many environmental epochs before fixing or going extinct, its fate is not necessarily determined by its time-averaged selective effect. Instead, environmental variability reduces the efficiency of selection across a broad parameter regime, rendering selection unable to distinguish between mutations that are substantially beneficial and substantially deleterious on average. Temporal fluctuations can also dramatically increase fixation probabilities, often making the details of these fluctuations more important than the average selection pressures acting on each new mutation. For example, mutations that result in a trade-off between conditions but are strongly deleterious on average can nevertheless be more likely to fix than mutations that are always neutral or beneficial. These effects can have important implications for patterns of molecular evolution in variable environments, and they suggest that it may often be difficult for populations to maintain specialist traits, even when their loss leads to a decline in time-averaged fitness.

Chemodetection in fluctuating environments: receptor coupling, buffering, and antagonism

Variability in the chemical composition of the extracellular environment can significantly degrade the ability of cells to detect rare cognate ligands. Using concepts from statistical detection theory, we formalize the generic problem of detection of small concentrations of ligands in a fluctuating background of biochemically similar ligands binding to the same receptors. We discover that in contrast with expectations arising from considerations of signal amplification, inhibitory interactions between receptors can improve detection performance in the presence of substantial environmental variability, providing an adaptive interpretation to the phenomenon of ligand antagonism. Our results suggest that the structure of signaling pathways responsible for chemodetection in fluctuating and heterogeneous environments might be optimized with respect to the statistics and dynamics of environmental composition. The developed formalism stresses the importance of characterizing nonspecific interactions to understand function in signaling pathways.

Evolution of phenotypic plasticity in colonizing species

I elaborate an hypothesis to explain inconsistent empirical findings comparing phenotypic plasticity in colonizing populations or species with plasticity from their native or ancestral range. Quantitative genetic theory on the evolution of plasticity reveals that colonization of a novel environment can cause a transient increase in plasticity: a rapid initial increase in plasticity accelerates evolution of a new optimal phenotype, followed by slow genetic assimilation of the new phenotype and reduction of plasticity. An association of colonization with increased plasticity depends on the difference in the optimal phenotype between ancestral and colonized environments, the difference in mean, variance and predictability of the environment, the cost of plasticity, and the time elapsed since colonization. The relative importance of these parameters depends on whether a phenotypic character develops by one-shot plasticity to a constant adult phenotype or by labile plasticity involving continuous and reversible development throughout adult life.

Rapid evolutionary adaptation to elevated salt concentrations in pathogenic freshwater bacteria Serratia marcescens

Rapid evolutionary adaptions to new and previously detrimental environmental conditions can increase the risk of invasion by novel pathogens. We tested this hypothesis with a 133-day-long evolutionary experiment studying the evolution of the pathogenic Serratia marcescens bacterium at salinity niche boundary and in fluctuating conditions. We found that S. marcescens evolved at harsh (80 g/L) and extreme (100 g/L) salt conditions had clearly improved salt tolerance than those evolved in the other three treatments (ancestral conditions, nonsaline conditions, and fluctuating salt conditions). Evolutionary theories suggest that fastest evolutionary changes could be observed in intermediate selection pressures. Therefore, we originally hypothesized that extreme conditions, such as our 100 g/L salinity treatment, could lead to slower adaptation due to low population sizes. However, no evolutionary differences were observed between populations evolved in harsh and extreme conditions. This suggests that in the study presented here, low population sizes did not prevent evolution in the long run. On the whole, the adaptive potential observed here could be important for the transition of pathogenic S. marcescens bacteria from human-impacted freshwater environments, such as wastewater treatment plants, to marine habitats, where they are known to infect and kill corals (e.g., through white pox disease).

Switching between apparently redundant iron-uptake mechanisms benefits bacteria in changeable environments

Bacteria often possess multiple siderophore-based iron uptake systems for scavenging this vital resource from their environment. However, some siderophores seem redundant, because they have limited iron-binding efficiency and are seldom expressed under iron limitation. Here, we investigate the conundrum of why selection does not eliminate this apparent redundancy. We focus on Pseudomonas aeruginosa, a bacterium that can produce two siderophores-the highly efficient but metabolically expensive pyoverdine, and the inefficient but metabolically cheap pyochelin. We found that the bacteria possess molecular mechanisms to phenotypically switch from mainly producing pyoverdine under severe iron limitation to mainly producing pyochelin when iron is only moderately limited. We further show that strains exclusively producing pyochelin grew significantly better than strains exclusively producing pyoverdine under moderate iron limitation, whereas the inverse was seen under severe iron limitation. This suggests that pyochelin is not redundant, but that switching between siderophore strategies might be beneficial to trade off efficiencies versus costs of siderophores. Indeed, simulations parameterized from our data confirmed that strains retaining the capacity to switch between siderophores significantly outcompeted strains defective for one or the other siderophore under fluctuating iron availabilities. Finally, we discuss how siderophore switching can be viewed as a form of collective decision-making, whereby a coordinated shift in behaviour at the group level emerges as a result of positive and negative feedback loops operating among individuals at the local scale.

Noncovalent Interaction Analysis in Fluctuating Environments

Noncovalent interactions play a central role in many chemical and biological systems. In a previous study, Johnson et al developed a NonCovalent Interaction (NCI) index to characterize and visualize different types of weak interactions. To apply the NCI analysis to fluctuating environments as in solution phase, we here develop a new Averaged NonCovalent Interaction (i.e., aNCI) index along with a fluctuation index to characterize magnitude of interactions and fluctuations. We applied aNCI for various systems including solute-solvent and ligand-protein noncovalent interactions. For water and benzene molecules in aqueous solution, solvation structures and the specific hydrogen bond patterns were visualized clearly. For the Cl^-+CH₃Cl S_N2 reaction in aqueous solution, charge reorganization influences over solvation structure along S_N2 reaction were revealed. For ligand-protein systems, aNCI can recover several key fluctuating hydrogen bond patterns that have potential applications for drug design. Therefore, aNCI, as a complementary approach to the original NCI method, can extract and visualize noncovalent interactions from thermal noise in fluctuating environments.

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 .

Herpes viruses hedge their bets

Static latency is the hallmark of all herpes viruses. The varicella zoster virus, for instance, causes varicella (chickenpox), and after a latent phase of between 5 and 40 years, it can give rise to herpes zoster (shingles). This latency and the subsequent reactivation has intrigued and puzzled virologists. Although several factors have been suggested, it is unknown what triggers reactivation. However, latency can be explained with a simple evolutionary model. Here, we demonstrate that a simple, yet efficient, bet-hedging strategy might have evolved in a number of viruses, especially those belonging to the herpes virus family and most importantly in varicella zoster virus. We show that the evolution of latency can be explained by the population dynamics of infectious diseases in fluctuating host populations.