Evolution in alternating environments with tunable interlandscape correlations

Natural populations are often exposed to temporally varying environments. Evolutionary dynamics in varying environments have been extensively studied, although understanding the effects of varying selection pressures remains challenging. Here, we investigate how cycling between a pair of statistically related fitness landscapes affects the evolved fitness of an asexually reproducing population. We construct pairs of fitness landscapes that share global fitness features but are correlated with one another in a tunable way, resulting in landscape pairs with specific correlations. We find that switching between these landscape pairs, depending on the ruggedness of the landscape and the interlandscape correlation, can either increase or decrease steady‐state fitness relative to evolution in single environments. In addition, we show that switching between rugged landscapes often selects for increased fitness in both landscapes, even in situations where the landscapes themselves are anticorrelated. We demonstrate that positively correlated landscapes often possess a shared maximum in both landscapes that allows the population to step through sub‐optimal local fitness maxima that often trap single landscape evolution trajectories. Finally, we demonstrate that switching between anticorrelated paired landscapes leads to ergodic‐like dynamics where each genotype is populated with nonzero probability, dramatically lowering the steady‐state fitness in comparison to single landscape evolution.     

Adaptation and habitat selection in the eco-evolutionary process

The struggle for existence occurs through the vital rates of population growth. This basic fact demonstrates the tight connection between ecology and evolution that defines the emerging field of eco-evolutionary dynamics. An effective synthesis of the interdependencies between ecology and evolution is grounded in six principles. The mechanics of evolution specifies the origin and rules governing traits and evolutionary strategies. Traits and evolutionary strategies achieve their selective value through their functional relationships with fitness. Function depends on the underlying structure of variation and the temporal, spatial and organizational scales of evolution. An understanding of how changes in traits and strategies occur requires conjoining ecological and evolutionary dynamics. Adaptation merges these five pillars to achieve a comprehensive understanding of ecological and evolutionary change. I demonstrate the value of this world-view with reference to the theory and practice of habitat selection. The theory allows us to assess evolutionarily stable strategies and states of habitat selection, and to draw the adaptive landscapes for habitat-selecting species. The landscapes can then be used to forecast future evolution under a variety of climate change and other scenarios.     

The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes

When facing the challenge of developing an individual that best fits its environment, nature demonstrates an interesting combination of two fundamentally different adaptive mechanisms: genetic evolution and phenotypic plasticity. Following numerous computational models, it has become the accepted wisdom that lifetime acclimation (e.g. via learning) smooths the fitness landscape and consequently accelerates evolution. However, analytical studies, focusing on the effect of phenotypic plasticity on evolution in simple unimodal landscapes, have often found that learning hinders the evolutionary process rather than accelerating it. Here, we provide a general framework for studying the effect of plasticity on evolution in multipeaked landscapes and introduce a rigorous mathematical analysis of these dynamics. We show that the convergence rate of the evolutionary process in a given arbitrary one-dimensional fitness landscape is dominated by the largest descent (drawdown) in the landscape and provide numerical evidence to support an analogous dominance also in multidimensional landscapes. We consider several schemes of phenotypic plasticity and examine their effect on the landscape drawdown, identifying the conditions under which phenotypic plasticity is advantageous. The lack of such a drawdown in unimodal landscapes vs. its dominance in multipeaked landscapes accounts for the seemingly contradictory findings of previous studies.     

The ascent of the abundant: how mutational networks constrain evolution

Evolution by natural selection is fundamentally shaped by the fitness landscapes in which it occurs. Yet fitness landscapes are vast and complex, and thus we know relatively little about the long-range constraints they impose on evolutionary dynamics. Here, we exhaustively survey the structural landscapes of RNA molecules of lengths 12 to 18 nucleotides, and develop a network model to describe the relationship between sequence and structure. We find that phenotype abundance—the number of genotypes producing a particular phenotype—varies in a predictable manner and critically influences evolutionary dynamics. A study of naturally occurring functional RNA molecules using a new structural statistic suggests that these molecules are biased toward abundant phenotypes. This supports an “ascent of the abundant” hypothesis, in which evolution yields abundant phenotypes even when they are not the most fit.     

Fitness landscapes emerging from pharmacodynamic functions in the evolution of multidrug resistance

Adaptive evolution often involves beneficial mutations at more than one locus. In this case, the trajectory and rate of adaptation is determined by the underlying fitness landscape, that is, the fitness values and mutational connectivity of all genotypes under consideration. Drug resistance, especially resistance to multiple drugs simultaneously, is also often conferred by mutations at several loci so that the concept of fitness landscapes becomes important. However, fitness landscapes underlying drug resistance are not static but dependent on drug concentrations, which means they are influenced by the pharmacodynamics of the drugs administered. Here, I present a mathematical framework for fitness landscapes of multidrug resistance based on Hill functions describing how drug concentrations affect fitness. I demonstrate that these ‘pharmacodynamic fitness landscapes’ are characterized by pervasive epistasis that arises through (i) fitness costs of resistance (even when these costs are additive), (ii) nonspecificity of resistance mutations to drugs, in particular cross‐resistance, and (iii) drug interactions (both synergistic and antagonistic). In the latter case, reciprocal drug suppression may even lead to reciprocal sign epistasis, so that the doubly resistant genotype occupies a local fitness peak that may be difficult to access by evolution. Simulations exploring the evolutionary dynamics on some pharmacodynamic fitness landscapes with both constant and changing drug concentrations confirm the crucial role of epistasis in determining the rate of multidrug resistance evolution.     

Adaptive Patch Searching Strategies in Fragmented Landscapes

The search strategies dispersers employ to search for new habitat patches affect individuals’ search success and subsequently landscape connectivity and metapopulation viability. Some evidence indicates that individuals within the same species may display a variety of behavioural patch searching strategies rather than one species-specific strategy. This may result from landscape heterogeneity. We modelled the evolution of individual patch searching strategies in different landscapes. Specifically, we analysed whether evolution can favour different, co-existing, behavioural search strategies within one population and to what extent this coexistence of multiple strategies was dependent on landscape configuration. Using an individual-based simulation model, we studied the evolution of patch searching strategies in three different landscape configurations: uniform, random and clumped. We found that landscape configuration strongly influenced the evolved search strategy. In uniform landscapes, one fixed search strategy evolved for the entire spatially structured population, while in random and clumped landscapes, a set of different search strategies emerged. The coexistence of several search strategies also strongly depended on the dispersal mortality. We show that our result can affect landscape connectivity and metapopulation dynamics. Co-ordinating editor: N. Yamamura     

The living state of matter.

Progress in biology has been extremely fast in the second half of the twentieth century in terms of numbers and quality of data. However less attention has been paid to the revision of existing theories on living beings structure and dynamics in development and evolution. Within this frame, the discussion on the very definition of life is lagging in the sometimes ideological debate between mechanistic and holistic views often without serious trials to integrate the overwhelming amount of new data into the different theoretical frameworks. The aim of this short review is to try to define a series of parameters specific of the living state of matter on the basis of existing evidence. The analysis starts from mathematical, physical and experimental studies on DNA constraints in nucleotide distributions and the interactions with proteins in some basic processes of life. The data discussed seem to show that short and long range correlations in DNA, particularly significant in non coding regions and increasing during evolution may have been fixed because of the need of structural landscapes complementarity for DNA-protein recognition and complex dynamics. The need for highly efficient and frequent recognition between the molecules has been extended to gene expression, protein-protein, protein-ligand complex formation and to signal transduction pointing out to the relevance of plasticity on one hand, complementarity on the other. Compartmentalisation and individuality are then taken as critical conditions favouring such processes in the hierarchical networks of all levels, from the cell to organisms, populations, ecosystems, the biosphere. Finally the specific meaning in life of useful (correlated) and disruptive noise is discussed along with the dynamics of evolutionary change in terms of homeorrhetic, plastic maintenance of flexible equilibria continuously challenged by internal and external signals.     

Predictability of evolutionary trajectories in fitness landscapes

Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness landscape. We report an exhaustive analysis of fitness landscapes constructed with an off-lattice model of protein folding where fitness is equated with robustness to misfolding. This model mimics the essential features of the interactions between amino acids, is consistent with the key paradigms of protein folding and reproduces the universal distribution of evolutionary rates among orthologous proteins. We introduce mean path divergence as a quantitative measure of the degree to which the starting and ending points determine the path of evolution in fitness landscapes. Global measures of landscape roughness are good predictors of path divergence in all studied landscapes: the mean path divergence is greater in smooth landscapes than in rough ones. The model-derived and experimental landscapes are significantly smoother than random landscapes and resemble additive landscapes perturbed with moderate amounts of noise; thus, these landscapes are substantially robust to mutation. The model landscapes show a deficit of suboptimal peaks even compared with noisy additive landscapes with similar overall roughness. We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding.     

A system for studying evolution of life-like virtual organisms

Background  

Fitness landscapes, the dependences of fitness on the genotype, are of critical importance for the evolution of living beings. Unfortunately, fitness landscapes that are relevant to the evolution of complex biological functions are very poorly known. As a result, the existing theory of evolution is mostly based on postulated fitness landscapes, which diminishes its usefulness. Attempts to deduce fitness landscapes from models of actual biological processes led, so far, to only limited success.     

Simulating protein evolution in sequence and structure space

Naturally occurring proteins comprise a special subset of all plausible sequences and structures selected through evolution. Simulating protein evolution with simplified and all-atom models has shed light on the evolutionary dynamics of protein populations, the nature of evolved sequences and structures, and the extent to which today's proteins are shaped by selection pressures on folding, structure and function. Extensive mapping of the native structure, stability and folding rate in sequence space using lattice proteins has revealed organizational principles of the sequence/structure map important for evolutionary dynamics. Evolutionary simulations with lattice proteins have highlighted the importance of fitness landscapes, evolutionary mechanisms, population dynamics and sequence space entropy in shaping the generic properties of proteins. Finally, evolutionary-like simulations with all-atom models, in particular computational protein design, have helped identify the dominant selection pressures on naturally occurring protein sequences and structures.     

On the evolution of dispersal via heterogeneity in spatial connectivity

Dispersal has long been recognized as a mechanism that shapes many observed ecological and evolutionary processes. Thus, understanding the factors that promote its evolution remains a major goal in evolutionary ecology. Landscape connectivity may mediate the trade-off between the forces in favour of dispersal propensity (e.g. kin-competition, local extinction probability) and those against it (e.g. energetic or survival costs of dispersal). It remains, however, an open question how differing degrees of landscape connectivity may select for different dispersal strategies. We implemented an individual-based model to study the evolution of dispersal on landscapes that differed in the variance of connectivity across patches ranging from networks with all patches equally connected to highly heterogeneous networks. The parthenogenetic individuals dispersed based on a flexible logistic function of local abundance. Our results suggest, all else being equal, that landscapes differing in their connectivity patterns will select for different dispersal strategies and that these strategies confer a long-term fitness advantage to individuals at the regional scale. The strength of the selection will, however, vary across network types, being stronger on heterogeneous landscapes compared with the ones where all patches have equal connectivity. Our findings highlight how landscape connectivity can determine the evolution of dispersal strategies, which in turn affects how we think about important ecological dynamics such as metapopulation persistence and range expansion.     

The frequency of fitness peak shifts is increased at expanding range margins due to mutation surfing

Dynamic species' ranges, those that are either invasive or shifting in response to environmental change, are the focus of much recent interest in ecology, evolution, and genetics. Understanding how range expansions can shape evolutionary trajectories requires the consideration of nonneutral variability and genetic architecture, yet the majority of empirical and theoretical work to date has explored patterns of neutral variability. Here we use forward computer simulations of population growth, dispersal, and mutation to explore how range-shifting dynamics can influence evolution on rugged fitness landscapes. We employ a two-locus model, incorporating sign epistasis, and find that there is an increased likelihood of fitness peak shifts during a period of range expansion. Maladapted valley genotypes can accumulate at an expanding range front through a phenomenon called mutation surfing, which increases the likelihood that a mutation leading to a higher peak will occur. Our results indicate that most peak shifts occur close to the expanding front. We also demonstrate that periods of range shifting are especially important for peak shifting in species with narrow geographic distributions. Our results imply that trajectories on rugged fitness landscapes can be modified substantially when ranges are dynamic.     

Urban landscapes can change virus gene flow and evolution in a fragmentation‐sensitive carnivore

Urban expansion has widespread impacts on wildlife species globally, including the transmission and emergence of infectious diseases. However, there is almost no information about how urban landscapes shape transmission dynamics in wildlife. Using an innovative phylodynamic approach combining host and pathogen molecular data with landscape characteristics and host traits, we untangle the complex factors that drive transmission networks of feline immunodeficiency virus (FIV) in bobcats (Lynx rufus). We found that the urban landscape played a significant role in shaping FIV transmission. Even though bobcats were often trapped within the urban matrix, FIV transmission events were more likely to occur in areas with more natural habitat elements. Urban fragmentation also resulted in lower rates of pathogen evolution, possibly owing to a narrower range of host genotypes in the fragmented area. Combined, our findings show that urban landscapes can have impacts on a pathogen and its evolution in a carnivore living in one of the most fragmented and urban systems in North America. The analytical approach used here can be broadly applied to other host–pathogen systems, including humans.     

Riverine landscape diversity

1. This review is presented as a broad synthesis of riverine landscape diversity, beginning with an account of the variety of landscape elements contained within river corridors. Landscape dynamics within river corridors are then examined in the context of landscape evolution, ecological succession and turnover rates of landscape elements. This is followed by an overview of the role of connectivity and ends with a riverine landscape perspective of biodiversity. 2. River corridors in the natural state are characterised by a diverse array of landscape elements, including surface waters (a gradient of lotic and lentic waterbodies), the fluvial stygoscape (alluvial aquifers), riparian systems (alluvial forests, marshes, meadows) and geomorphic features (bars and islands, ridges and swales, levees and terraces, fans and deltas, fringing floodplains, wood debris deposits and channel networks). 3. Fluvial action (erosion, transport, deposition) is the predominant agent of landscape evolution and also constitutes the natural disturbance regime primarily responsible for sustaining a high level of landscape diversity in river corridors. Although individual landscape features may exhibit high turnover, largely as a function of the interactions between fluvial dynamics and successional phenomena, their relative abundance in the river corridor tends to remain constant over ecological time. 4. Hydrological connectivity, the exchange of matter, energy and biota via the aqueous medium, plays a major though poorly understood role in sustaining riverine landscape diversity. Rigorous investigations of connectivity in diverse river systems should provide considerable insight into landscape‐level functional processes. 5. The species pool in riverine landscapes is derived from terrestrial and aquatic communities inhabiting diverse lotic, lentic, riparian and groundwater habitats arrayed across spatio‐temporal gradients. Natural disturbance regimes are responsible for both expanding the resource gradient in riverine landscapes as well as for constraining competitive exclusion. 6. Riverine landscapes provide an ideal setting for investigating how complex interactions between disturbance and productivity structure species diversity patterns.     

Predicting the Evolution of Sex on Complex Fitness Landscapes

Most population genetic theories on the evolution of sex or recombination are based on fairly restrictive assumptions about the nature of the underlying fitness landscapes. Here we use computer simulations to study the evolution of sex on fitness landscapes with different degrees of complexity and epistasis. We evaluate predictors of the evolution of sex, which are derived from the conditions established in the population genetic literature for the evolution of sex on simpler fitness landscapes. These predictors are based on quantities such as the variance of Hamming distance, mean fitness, additive genetic variance, and epistasis. We show that for complex fitness landscapes all the predictors generally perform poorly. Interestingly, while the simplest predictor, ΔVar_HD, also suffers from a lack of accuracy, it turns out to be the most robust across different types of fitness landscapes. ΔVar_HD is based on the change in Hamming distance variance induced by recombination and thus does not require individual fitness measurements. The presence of loci that are not under selection can, however, severely diminish predictor accuracy. Our study thus highlights the difficulty of establishing reliable criteria for the evolution of sex on complex fitness landscapes and illustrates the challenge for both theoretical and experimental research on the origin and maintenance of sexual reproduction.     

The influence of variation and of developmental constraints on the rate of multivariate phenotypic evolution

A model of multivariate phenotypic evolution is analysed under the assumption that all characters have the same variance or at least constant ratios of variance. The rate of evolution is examined as a function of the amount of phenotypic variance in a variety of adaptive landscapes (fitness functions). It is demonstrated that the effect of variation depends on the type of adaptive landscape. In “well behaved” adaptive landscapes the rate of evolution can theoretically increase without limits, depending on the amount of heritable phenotypic variation. However, in other adaptive landscapes there are upper limits to the rate of evolution which cannot be exceeded if phenotypic variation is developmentally unconstrained, i. e. if it is the same for all characters. Further it is shown that the maximal rate of evolution becomes small if the number of characters becomes large. Fitness functions of this type are called malignant. It is argued that malignant fitness functions are more adequate models for the evolution of typical organismic systems, because they are models of functionally interdependent characters. It is concluded that there are upper limits to the rate of phenotypic evolution if the variation of functionally interdependent characters is developmentally unconstrained. The possible role of developmental constraints in adaptive phenotypic evolution is discussed.     

Functional performance of turtle humerus shape across an ecological adaptive landscape

The concept of the adaptive landscape has been invaluable to evolutionary biologists for visualizing the dynamics of selection and adaptation, and is increasingly being used to study morpho‐functional data. Here, we construct adaptive landscapes to explore functional trade‐offs associated with variation in humerus morphology among turtles adapted to three different locomotor environments: marine, semiaquatic, and terrestrial. Humerus shape from 40 species of cryptodire turtles was quantified using a pseudolandmark approach. Hypothetical shapes were extracted in a grid across morphospace and four functional traits (strength, stride length, mechanical advantage, and hydrodynamics) measured on those shapes. Quantitative trait modeling was used to construct adaptive landscapes that optimize the functional traits for each of the three locomotor ecologies. Our data show that turtles living in different environments have statistically different humeral shapes. The optimum adaptive landscape for each ecology is defined by a different combination of performance trade‐offs, with turtle species clustering around their respective adaptive peak. Further, species adhere to pareto fronts between marine–semiaquatic and semiaquatic–terrestrial optima, but not between marine–terrestrial. Our study demonstrates the utility of adaptive landscapes in informing the link between form, function, and ecological adaptation, and establishes a framework for reconstructing turtle ecological evolution using isolated humeri from the fossil record.     

Antigen-antibody interactions and structural flexibility of a femtomolar-affinity antibody

The femtomolar-affinity mutant antibody (4M5.3) generated by directed evolution is interesting because of the potential of antibody engineering. In this study, the mutant and its wild type (4-4-20) were compared in terms of antigen-antibody interactions and structural flexibility to elucidate the effects of directed evolution. For this purpose, multiple steered molecular dynamics (SMD) simulations were performed. The pulling forces of SMD simulations elucidated the regions that form strong attractive interactions in the binding pocket. Structural analysis in these regions showed two important mutations for improving attractive interactions. First, mutation of Tyr102(H) to Ser (sequence numbering of Protein Data Bank entry 1FLR ) played a role in resolving the steric hindrance on the pathway of the antigen in the binding pocket. Second, mutation of Asp31(H) to His played a role in resolving electrostatic repulsion. Potentials of mean force (PMFs) of both the wild type and the mutant showed landscapes that do not include obvious intermediate states and go directly to the bound state. These landscapes were regarded as funnel-like binding free energy landscapes. Furthermore, the structural flexibility based on the fluctuations of the positions of atoms was analyzed. It was shown that the fluctuations in the positions of the antigen and residues in contact with antigen tend to be smaller in the mutant than in the wild type. This result suggested that structural flexibility decreases as affinity is improved by directed evolution. This suggestion is similar to the relationship between affinity and flexibility for in vivo affinity maturation, which was suggested by Romesberg and co-workers [Jimenez, R., et al. (2003) Proc. Natl. Acad. Sci. U.S.A.100, 92-97]. Consequently, the relationship was found to be applicable up to femotomolar affinity levels.     

Temporal variability of aphid biological control in contrasting landscape contexts

Landscape complexity may provide ecosystem services to agriculture through the provision of natural enemies of agricultural pests. Strong positive effect of adjacent semi-natural habitats on natural enemies in croplands has been evidenced, but the resulting impact on biological control remains unclear. Taking into account the temporal dynamics of pest and natural enemies in agricultural landscapes provides better resolution to the studies and better understanding of the biological control service.In this study, the population dynamics of aphids and two groups of predators (coccinellid and carabid beetles) were examined. Insects were sampled in 20 wheat fields, surrounded by structurally simple and complex landscapes in Chilean central valley. Considering the whole sampling period, the diversity of aphids and natural enemies were similar in wheat crops surrounded by both types of landscapes, and the abundance of ladybirds was higher in crops in the complex landscapes. The dynamics of predators was more advanced in complex landscapes than in the simple ones, whereas the dynamics of aphids were similar in both types of landscape. Negative correlation between abundance of predators and aphid population growth rate in both landscape contexts were observed suggesting a control of the pest population by the predators. Different temporal patterns were observed in these correlations in the two landscape contexts, which suggests differences in the biological control related to the landscape composition.The present study shows that colonization of crops by natural enemies occurs sooner in structurally complex landscapes and suggests that this early colonization may facilitate an early and efficient control of aphid populations, nevertheless the biological control efficiency seems to be higher in structurally simple landscapes later in the season.