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PubMed2006

Helminths as vectors of pathogens in vertebrate hosts: a theoretical approach.

Pathogens frequently use vectors to facilitate transmission between hosts and, for vertebrate hosts, the vectors are typically ectoparasitic arthropods. However, other parasites that are intimately associated with their hosts may also be ideal candidate vectors; namely the parasitic helminths. Here, we present empirical evidence that helminth vectoring of pathogens occurs in a range of vertebrate systems by a variety of helminth taxa. Using a novel theoretical framework we explore the dynamics of helminth vectoring and determine which host-helminth-pathogen characteristics may favour the evolution of helminth vectoring. We use two theoretical models: the first is a population dynamic model amalgamated from standard macro- and microparasite models, which serves as a framework for investigation of within-host interactions between co-infecting pathogens and helminths. The second is an evolutionary model, which we use to predict the ecological conditions under which we would expect helminth vectoring to evolve. We show that, like arthropod vectors, helminth vectors increase pathogen fitness. However, unlike arthropod vectors, helminth vectoring increases the pathogenic impact on the host and may allow the evolution of high pathogen virulence. We show that concomitant infection of a host with a helminth and pathogen are not necessarily independent of one another, due to helminth vectoring of microparasites, with profound consequences for pathogen persistence and the impact of disease on the host population.

Animals↗
PubMed1997

A thermodynamic approach to the compromise between power and efficiency in muscle contraction.

An analysis of muscle contraction based on irreversible thermodynamics is presented in this work. From reported experimental results, it is shown that a muscle, as an energy converter, does not obey linear phenomenological relations. Some more suitable nonlinear phenomenological relations are found and discussed from an evolutionary point of view. In those relations a parameter alpha appears which is related to the nonlinearity of the equations. It is suggested that this parameter determines the compromise between the power output and the efficiency reached by the muscle. By analysing the energetics of some suitable performance regimes, we suggest that the fact that alpha values greater than 0.4 are not found in muscles of higher species, can be interpreted as an evolutionary necessity.

Animals↗
PubMed2002

Evolutionary branching of dispersal strategies in structured metapopulations.

Dispersal polymorphism and evolutionary branching of dispersal strategies has been found in several metapopulation models. The mechanism behind those findings has been temporal variation caused by cyclic or chaotic local dynamics, or temporally and spatially varying carrying capacities. We present a new mechanism: spatial heterogeneity in the sense of different patch types with sufficient proportions, and temporal variation caused by catastrophes. The model where this occurs is a generalization of the model by Gyllenberg and Metz (2001). Their model is a size-structured metapopulation model with infinitely many identical patches. We present a generalized version of their metapopulation model allowing for different types of patches. In structured population models, defining and computing fitness in polymorphic situations is, in general, difficult. We present an efficient method, which can be applied also to other structured population or metapopulation models.

Biological Evolution↗
PubMed2004

The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.

All currently leading protein secondary structure prediction methods use a multiple protein sequence alignment to predict the secondary structure of the top sequence. In most of these methods, prior to prediction, alignment positions showing a gap in the top sequence are deleted, consequently leading to shrinking of the alignment and loss of position-specific information. In this paper we investigate the effect of this removal of information on secondary structure prediction accuracy. To this end, we have designed SymSSP, an algorithm that post-processes the predicted secondary structure of all sequences in a multiple sequence alignment by (i) making use of the alignment's evolutionary information and (ii) re-introducing most of the information that would otherwise be lost. The post-processed information is then given to a new dynamic programming routine that produces an optimally segmented consensus secondary structure for each of the multiple alignment sequences. We have tested our method on the state-of-the-art secondary structure prediction methods PHD, PROFsec, SSPro2 and JNET using the HOMSTRAD database of reference alignments. Our consensus-deriving dynamic programming strategy is consistently better at improving the segmentation quality of the predictions compared to the commonly used majority voting technique. In addition, we have applied several weighting schemes from the literature to our novel consensus-deriving dynamic programming routine. Finally, we have investigated the level of noise introduced by prediction errors into the consensus and show that predictions of edges of helices and strands are half the time wrong for all the four tested prediction methods.

Algorithms↗
PubMed2005

Coevolutionary arms races between bacteria and bacteriophage.

We propose a computational and theoretical framework for analyzing rapid coevolutionary dynamics of bacteriophage and bacteria in their ecological context. Bacteriophage enter host cells via membrane-bound surface receptors often responsible for nutrient uptake. As such, a selective pressure will exist for the bacteria to modify its receptor configuration and, in turn, for the phage to modify its tail fiber. A mathematical model of these trait adaptations is developed by using the framework of adaptive dynamics. Host strains differ in their efficiency of resource uptake and resistance to phage, whereas phage strains differ in their host preference for adsorption. We solve the evolutionary ecology model and find the conditions for coevolutionary branching and relevant dimensionless parameters leading to distinct quasispecies. We confirm these calculations using stochastic Monte Carlo simulations of populations evolving in a chemostat with fixed washout rate and inflow resource density. We find that multiple quasispecies of bacteria and phage can coexist in a homogeneous medium with a single resource. When diversification occurs, quasispecies of phage adsorb effectively to only a limited subset of the total number of quasispecies of bacteria, i.e., functional differences between quasispecies arise endogenously within the evolutionary ecology framework. Finally, we discuss means to relate predictions of this model to experimental studies in the chemostat, using the model organisms Escherichia coli and the virulent strain of lambda phage.

Adaptation, Biological↗
PubMed1999

Evolution and development of a central pattern generator for the swimming of a lamprey.

This article describes the design of neural control architectures for locomotion using an evolutionary approach. Inspired by the central pattern generators found in animals, we develop neural controllers that can produce the patterns of oscillations necessary for the swimming of a simulated lamprey. This work is inspired by Ekeberg's neuronal and mechanical model of a lamprey [11] and follows experiments in which swimming controllers were evolved using a simple encoding scheme [25, 26]. Here, controllers are developed using an evolutionary algorithm based on the SGOCE encoding [31, 32] in which a genetic programming approach is used to evolve developmental programs that encode the growing of a dynamical neural network. The developmental programs determine how neurons located on a two-dimensional substrate produce new cells through cellular division and how they form efferent or afferent interconnections. Swimming controllers are generated when the growing networks eventually create connections to the muscles located on both sides of the rectangular substrate. These muscles are part of a two-dimensional mechanical simulation of the body of the lamprey in interaction with water. The motivation of this article is to develop a method for the design of control mechanisms for animal-like locomotion. Such a locomotion is characterized by a large number of actuators, a rhythmic activity, and the fact that efficient motion is only obtained when the actuators are well coordinated. The task of the control mechanism is therefore to transform commands concerning the speed and direction of motion into the signals sent to the multiple actuators. We define a fitness function, based on several simulations of the controller with different commands settings, that rewards the capacity of modulating the speed and the direction of swimming in response to simple, varying input signals. Central pattern generators are thus evolved capable of producing the relatively complex patterns of oscillations necessary for swimming. The best solutions generate traveling waves of neural activity, and propagate, similarly to the swimming of a real lamprey, undulations of the body from head to tail propelling the lamprey forward through water. By simply varying the amplitude of two input signals, the speed and the direction of swimming can be modulated.

Algorithms↗
PubMed2000

Evolving together: the biology of symbiosis, part 1.

Symbioses, prolonged associations between organisms often widely separated phylogenetically, are more common in biology than we once thought and have been neglected as a phenomenon worthy of study on its own merits. Extending along a dynamic continuum from antagonistic to cooperative and often involving elements of both antagonism and mutualism, symbioses involve pathogens, commensals, and mutualists interacting in myriad ways over the evolutionary history of the involved "partners." In this first of 2 parts, some remarkable examples of symbiosis will be explored, from the coral-algal symbiosis and nitrogen fixation to the great diversity of dietary specializations enabled by the gastrointestinal microbiota of animals.

Journal Article↗
PubMed1999

Criticality and scaling in evolutionary ecology.

Fluctuations in ecological systems are known to involve a wide range of spatial and temporal scales, often displaying self-similar (fractal) properties. Recent theoretical approaches are trying to shed light on the nature of these complex dynamics. The results suggest that complexity in ecology and evolution comes from the network-like structure of multispecies communities that are close to instability. If true, these ideas might change our understanding of how complexity emerges in the biosphere and how macroevolutionary events could be decoupled from microevolutionary ones.

Journal Article↗
PubMed2004

Evolutionary trade-off between defence against grazing and competitive ability in a simple unicellular alga, Chlorella vulgaris.

Trade-offs between defence and other fitness components are expected in principle, and can have major qualitative impacts on ecological dynamics. Here we show that such a trade-off exists even in the simple unicellular alga Chlorella vulgaris. We grew algal populations for multiple generations in either the presence ('grazed algae') or absence ('non-grazed algae') of the grazing rotifer Brachionus calyciflorus, and then evaluated their defence and competitive abilities. Grazed algae were better defended, yielding rotifer growth rate 32% below that of animals fed non-grazed algae, but they also had diminished competitive ability, with a growth rate under nutrient-limiting conditions 28% below that of non-grazed algae. Grazed algae also had a smaller cell size and were more concentrated in carbon and nitrogen. Thus, C. vulgaris genotypes vary phenotypically in their position along a trade-off curve between defence against grazing and competitive ability. This genetic variation underlies rapid algal evolution that significantly alters the ecological predator-prey cycles between rotifers and algae.

Animals↗
PubMed2000

Permanence or change? The meaning of genetic variation.

Selected aspects of the evolutionary process and more specifically of the genetic variation are considered, with an emphasis in studies performed by my group. One key aspect of evolution seems to be the concomitant occurrence of dichotomic, contradictory (dialect) processes. Genetic variation is structured, and the dynamics of change at one level is not necessarily paralleled by that in another. The pathogenesis-related protein superfamily can be cited as an example in which permanence (the maintenance of certain key genetic features) coexists with change (modifications that led to different functions in different classes of organisms). Relationships between structure and function are exemplified by studies with hemoglobin Porto Alegre. The genetic structure of tribal populations may differ in important aspects from that of industrialized societies. Evolutionary histories also may differ when considered through the investigation of patrilineal or matrilineal lineages. Global evaluations taking into consideration all of these aspects are needed if we really want to understand the meaning of genetic variation.

Africa↗
PubMedDate not supplied

[Formation of evolutionary approach as an explanatory principle for ecology].

Although the connection of ecology with evolutionary idea and specifically with Darwinism was proclaimed for a long time it seems that Herbert Spencer's approach with its emphasize on natural equilibrium was much more often used as its real theoretical base. Elements of Darwinian approach appeared only in 1920-30s in works of those few researchers who studying the distribution and population dynamics of different species tried to understand general mechanisms providing their continuing existence. Later, in the middle of 1950s the first attempts were undertaken to consider the population life history (primarily the age specific schedule of death and reproduction) as a result of natural selection aimed to maintain the necessary level of fitness. A special attention in these studies that burgeoned in 1980-90s was paid to looking for various trade-offs between particular parameters of life history, e.g., between the survival of juveniles and fecundity of adults. The problem of life history optimization became central for the whole branch of science named "evolutionary ecology". Though traditionally this branch is connected with Darwinism, it is rooted rather in Spencer's ideas on moving equilibrium and deals more with static than dynamic. Disproportionately less attention was paid to the evolution of communities since these formations could be hardly interpreted as units of Darwinian selection. Moreover, the ecologists dealing with biosphere as a unified biogeochemical system began insist on "nondarwinian" nature of its evolution. The author considers this opinion as not sufficiently grounded. Darwin's ideas about unavoidable exponential growth, intrinsic for any population, consequent deficiency of resources, and differential survival and reproduction of individuals are still useful while studying the evolution of living organisms (phylogenetics) or the development of biosphere as a global ecosystem.

Animals↗
PubMed2004

Solution structure and backbone dynamics of the K18G/R82E Alicyclobacillus acidocaldarius thioredoxin mutant: a molecular analysis of its reduced thermal stability.

No general strategy for thermostability has been yet established, because the extra stability of thermophiles appears to be the sum of different cumulative stabilizing interactions. In addition, the increase of conformational rigidity observed in many thermophilic proteins, which in some cases disappears when mesophilic and thermophilic proteins are compared at their respective physiological temperatures, suggests that evolutionary adaptation tends to maintain corresponding states with respect to conformational flexibility. In this study, we accomplished a structural analysis of the K18G/R82E Alicyclobacillus acidocaldarius thioredoxin (BacTrx) mutant, which has reduced heat resistance with respect to the thermostable wild-type. Furthermore, we have also achieved a detailed study, carried out at 25, 45, and 65 degrees C, of the backbone dynamics of both the BacTrx and its K18G/R82E mutant. Our findings clearly indicate that the insertion of the two mutations causes a loss of energetically favorable long-range interactions and renders the secondary structure elements of the double mutants more similar to those of the mesophilic Escherichia coli thioredoxin. Moreover, protein dynamics analysis shows that at room temperature the BacTrx, as well as the double mutant, are globally as rigid as the mesophilic thioredoxins; differently, at 65 degrees C, which is in the optimal growth temperature range of A. acidocaldarius, the wild-type retains its rigidity while the double mutant is characterized by a large increase of the amplitude of the internal motions. Finally, our research interestingly shows that fast motions on the pico- to nanosecond time scale are not detrimental to protein stability and provide an entropic stabilization of the native state. This study further confirms that protein thermostability is reached through diverse stabilizing interactions, which have the key role to maintain the structural folding stable and functional at the working temperature.

Bacterial Proteins↗
PubMed1998

Coevolutionary chase in two-species systems with applications to mimicry.

We study a general dynamical model describing coevolution of two haploid populations with two alleles at a single locus under weak linear symmetric frequency-dependent selection. A novel and more realistic element of our modeling approach is that both species are allowed to evolve. We analyse conditions for "evolutionary chase" between two phenotypically similar species in which one species evolves to decrease its resemblance with the other species while this other species evolves to increase its resemblance with the first species. We apply our results to a series of simple population genetics models describing classical Müllerian and Batesian mimicries as well as intermediate cases. We show that one of the most important factors influencing the plausibility of non-equilibrium dynamics in systems of mimicry is the relationship between the strength of between-species and within-species interactions. This indicates that this relationship should be the focus of both experimental and theoretical work. Our results suggest that systematic studies of frequencies of different mimicry morphs through time may be very useful.

Animals↗
PubMed2005

Network thinking in ecology and evolution.

Although pairwise interactions have always had a key role in ecology and evolutionary biology, the recent increase in the amount and availability of biological data has placed a new focus on the complex networks embedded in biological systems. The increased availability of computational tools to store and retrieve biological data has facilitated wide access to these data, not just by biologists but also by specialists from the social sciences, computer science, physics and mathematics. This fusion of interests has led to a burst of research on the properties and consequences of network structure in biological systems. Although traditional measures of network structure and function have started us off on the right foot, an important next step is to create biologically realistic models of network formation, evolution, and function. Here, we review recent applications of network thinking to the evolution of networks at the gene and protein level and to the dynamics and stability of communities. These studies have provided new insights into the organization and function of biological systems by applying existing techniques of network analysis. The current challenge is to recognize the commonalities in evolutionary and ecological applications of network thinking to create a predictive science of biological networks.

Journal Article↗
PubMed2007

Cytochrome c(2) Exit Strategy: Dissociation Studies and Evolutionary Implications.

Small, water-soluble, type c cytochromes form a transient network connecting major bioenergetic membrane protein complexes in both photosynthesis and respiration. In the photosynthesis cycle of Rhodobacter sphaeroides, cytochrome c2 (cyt c2) docks to the reaction center (RC), undergoes electron transfer, and exits for the cytochrome bc1 complex. Translations of cyt c2 about the RC-cyt c2 docking interface and surrounding membrane reveal possible exit pathways. A pathway at a minimal elevation allowed by the architecture of the RC is analyzed using both an all-atom steered molecular dynamics simulation of the RC-cyt c2 complex and a bioinformatic analysis of the structures and sequences of cyt c. The structure-based phylogenetic analysis allows for the identification of structural elements that have evolved to satisfy the requirements of having multiple functional partners. The patterns of evolutionary variation obtained from the phylogenetic analysis of both docking partners of cyt c2 reveal conservation of key residues involved in the interaction interfaces that would be candidates for further experimental studies. Additionally, using the molecular mechanics Poisson-Boltzmann surface area method we calculate that the binding free energy of reduced cyt c2 to the RC is nearly 6 kcal/mol more favorable than with oxidized cyt c2. The redox-dependent variations lead to changes in structural flexibility, behavior of the interfacial water molecules, and eventually changes in the binding free energy of the complex.

Amino Acid Sequence↗
PubMed1999

What pair formation can do to the battle of the sexes: towards more realistic game dynamics.

In the various dynamic models of Dawkin's Battle of the Sexes, payoff matrices serve as the basic ingredients for the specification of a game-dynamic model. Here I model the sex war mechanistically, by expressing the costs of raising the offspring and performing a prolonged courtship via a time delay for the corresponding individuals, instead of via payoff matrices. During such a time delay an individual is not able to have new matings. Only after the delay has occurred, an individual (and its offspring) appears on the mating market again. From these assumptions I derive a pair-formation submodel, and a system of delay-differential equations describing the dynamics of the game. By a time-scale argument, I obtain an approximation of this system by means of a much simpler system of ordinary differential equations. Analysis of this simplified system shows that the model can give rise to two non-trivial asymptotically stable equilibrium points: an interior equilibrium where both female strategies and both male strategies are present, and a boundary equilibrium where only one of the female strategies and both male strategies are present. This behaviour is qualitatively different from that of models of the battle of the sexes formulated in the traditional framework of game-dynamic equations. In other words, the addition of a most elementary further assumption about individual life history fundamentally changes the model predictions. These results show that in analysing evolutionary games one should pay careful attention to the specific mechanisms involved in the conflict. In general, I advocate deriving simple models for evolutionary games, starting from more complex, mechanistic building blocks. The wide-spread method of modelling games at a high phenomenological level, through payoff matrices, can be misleading.

Animals↗
PubMed2004

The impact of nonlinear functional responses on the long-term evolution of food web structure.

We investigate the long-term web structure emerging in evolutionary food web models when different types of functional responses are used. We find that large and complex webs with several trophic layers arise only if the population dynamics is such that it allows predators to focus on their best prey species. This can be achieved using modified Lotka-Volterra or Holling/Beddington functional responses with effective couplings that depend on the predator's efficiency at exploiting the prey, or a ratio-dependent functional response with adaptive foraging. In contrast, if standard Lotka-Volterra or Holling/Beddington functional responses are used, long-term evolution generates webs with almost all species being basal, and with additionally many links between these species. Interestingly, in all cases studied, a large proportion of weak links result naturally from the evolution of the food webs.

Animals↗
PubMed2003

The evolutionary adaptation of HIV-1 to specific immunity.

Recent evidence of the evolutionary adaptation of HIV-1 to the specific immune system is reviewed. Longitudinal studies of patients show that a neutralizing antibody (NAb) response specific to autologous virus is detectable within 1-2 months of infection and that viral variants resistant to neutralization arise and spread in the viral population within the subsequent three months, and that this general pattern is repeated. There is strong evidence that amino acid replacements in gp120 glycan-binding motifs affect viral sensitivity to neutralization and are selected by NAbs. Longitudinal studies of humans have also provided good evidence of amino acid replacements in cytotoxic T lymphocyte (CTL) epitopes that allow the virus to escape detection by CTLs. But, the clearest evidence of adaptation to CTL surveillance at the molecular level comes from experiments with SIV-infected rhesus macaques. These show unequivocally that amino acid replacements in CTL epitopes are the result of positive selection and that these escape mutants have a lower class I major histocompatibility complex (MHC) binding affinity or are less likely to be recognized by CTLs than non-escape variants. To improve our ability to predict HIV's evolutionary responses to selection by the specific immune system it is suggested that future work focus on the details of the adaptive response to antibody surveillance, the temporal dynamics of specific immune responses, the relative importance of antibody and CTL selection, and the effects of superinfection, viral recombination, and viral protein functional constraints on immune escape.

Adaptation, Physiological↗