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Climate, energy and diversity.

In recent years, a number of species-energy hypotheses have been developed to explain global patterns in plant and animal diversity. These hypotheses frequently fail to distinguish between fundamentally different forms of energy which influence diversity in dissimilar ways. Photosynthetically active radiation (PAR) can be utilized only by plants, though their abundance and growth rate is also greatly influenced by water. The Gibbs free energy (chemical energy) retained in the reduced organic compounds of tissue can be utilized by all heterotrophic organisms. Neither PAR nor chemical energy influences diversity directly. Both, however, influence biomass and/or abundance; diversity may then increase as a result of secondary population dynamic or evolutionary processes. Temperature is not a form of energy, though it is often used loosely by ecologists as a proxy for energy; it does, however, influence the rate of utilization of chemical energy by organisms. It may also influence diversity by allowing a greater range of energetic lifestyles at warmer temperatures (the metabolic niche hypothesis). We conclude that there is no single species/energy mechanism; fundamentally different processes link energy to abundance in plants and animals, and diversity is affected secondarily. If we are to make progress in elucidating these mechanisms, it is important to distinguish climatic effects on species' distribution and abundance from processes linking energy supply to plant and animal diversity.

Animals↗

Macroevolutionary trends in the Dinosauria: Cope's rule.

Cope's rule is the tendency for body size to increase over time along a lineage. A set of 65 phylogenetically independent comparisons, between earlier and later genera, show that Cope's rule applied in dinosaurs: later genera were on average about 25% longer than the related earlier genera to which they were compared. The tendency for size to increase was not restricted to a particular clade within the group, nor to a particular time within its history. Small lineages were more likely to increase in size, and large lineages more likely to decrease: this pattern may indicate an intermediate optimum body size, but can also be explained as an artefact of data error. The rate of size increase estimated from the phylogenetic comparisons is significantly higher than the rate seen across the fauna as a whole. This difference could indicate that within-lineage selection for larger size was opposed by clade selection favouring smaller size, but data limitations mean that alternative explanations (which we discuss) cannot be excluded. We discuss ways of unlocking the full potential usefulness of phylogenies for studying the dynamics of evolutionary trends.

Animals↗

Local adaptation and population structure at a micro-geographical scale of a fungal parasite on its host plant.

Local adaptation, which has been detected for several wild pathosystems is influenced by gene flow and recombination. In this study, we investigate local adaptation and population structure at a fine scale in wild populations of a plant-pathogen fungus. We sampled hierarchically strains of Colletotrichum lindemuthianum in a wild population of its host. The analysis of AFLP patterns obtained for 86 strains indicated that: (i) many different haplotypes can be discriminated, although occurrence of recombination could not be shown; (ii) migration between adjacent plants seemed rare during the season; and (iii) neutral diversity is structured according to groups of plants and individual host plants. Furthermore, we tested for the occurrence of local adaptation using a cross-inoculation experiment. Our results showed local adaptation at the scale of the individual host plant. These results indicate that fine-scale dynamics has evolutionary consequences in this pathosystem.

Adaptation, Biological↗

Group performance and decision making.

Theory and research on small group performance and decision making is reviewed. Recent trends in group performance research have found that process gains as well as losses are possible, and both are frequently explained by situational and procedural contexts that differentially affect motivation and resource coordination. Research has continued on classic topics (e.g., brainstorming, group goal setting, stress, and group performance) and relatively new areas (e.g., collective induction). Group decision making research has focused on preference combination for continuous response distributions and group information processing. New approaches (e.g., group-level signal detection) and traditional topics (e.g., groupthink) are discussed. New directions, such as nonlinear dynamic systems, evolutionary adaptation, and technological advances, should keep small group research vigorous well into the future.

Cognition↗

Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environment.

BACKGROUND: In order to study the dynamics of evolutionary change, 12 populations of E. coli B were serially propagated for 20,000 generations in minimal glucose medium at constant 37 degrees C. Correlated changes in various other traits have been previously associated with the improvement in competitive fitness in the selective environment. This study examines whether these evolved lines changed in their ability to tolerate the stresses of prolonged freezing and repeated freeze-thaw cycles during adaptation to a benign environment. RESULTS: All 12 lines that evolved in the benign environment for 20,000 generations are more sensitive to freeze-thaw cycles than their ancestor. The evolved lines have an average mortality rate of 54% per daily cycle, compared to the ancestral rate of 34%. By contrast, there was no significant difference between the evolved lines and their ancestor in mortality during prolonged freezing. There was also some variability among the evolved lines in susceptibility to repeated freeze-thaw cycles. Those lines that had evolved higher competitive fitness in the minimal glucose medium at 37 degrees C also had higher mortality during freeze-thaw cycles. This variability was not associated, however, with differences among lines in DNA repair functionality and mutability. CONCLUSION: The consistency of the evolutionary declines in freeze-thaw tolerance, the correlation between fitness in glucose medium at 37 degrees C and mortality during freeze-thaw cycles, and the absence of greater declines in freeze-thaw survival among the hypermutable lines all indicate a trade-off between performance in minimal glucose medium at 37 degrees C and the capacity to tolerate this stress. Analyses of the mutations that enhance fitness at 37 degrees C may shed light on the physiological basis of this trade-off.

Adaptation, Physiological↗

Ancient host-pathogen associations maintained by specificity of chemotaxis and antibiosis.

Switching by parasites to novel hosts has profound effects on ecological and evolutionary disease dynamics. Switching requires that parasites are able to establish contact with novel hosts and to overcome host defenses. For most host-parasite associations, it is unclear as to what specific mechanisms prevent infection of novel hosts. Here, we show that parasitic fungal species in the genus Escovopsis, which attack and consume the fungi cultivated by fungus-growing ants, are attracted to their hosts via chemotaxis. This response is host-specific: Escovopsis spp. grow towards their natural host cultivars more rapidly than towards other closely related fungi. Moreover, the cultivated fungi secrete compounds that can suppress Escovopsis growth. These antibiotic defenses are likewise specific: in most interactions, cultivars can inhibit growth of Escovopsis spp. not known to infect them in nature but cannot inhibit isolates of their naturally infecting pathogens. Cases in which cultivars are susceptible to novel Escovopsis are limited to a narrow set of host-parasite strain combinations. Targeted chemotactic and antibiotic responses therefore explain why Escovopsis pathogens do not readily switch to novel hosts, consequently constraining long-term dynamics of host-parasite coevolution within this ancient association.

Animals↗

Molecular mechanisms underlying drug resistance in protozoan parasites: emerging mechanisms and therapeutic perspectives.

Protozoan parasitic infections, including malaria, leishmaniasis, and human African trypanosomiasis, remain major global public health challenges. In the absence of highly effective vaccines, disease control relies primarily on chemotherapy; however, the emergence and spread of drug-resistant parasite populations increasingly threaten treatment efficacy. This review synthesizes current evidence on the molecular mechanisms underlying drug resistance in Plasmodium, Leishmania, and Trypanosoma species through a systematic analysis of literature. The review identifies four interconnected mechanisms that drive the evolution of drug resistance. First, altered drug transport enables parasites to regulate intracellular drug concentrations through mutations, loss, or amplification of membrane transporters, including PfCRT in Plasmodium and AQP2 in Trypanosoma brucei. Second, target modification and genomic plasticity promote resistance through point mutations in drug targets, such as dhfr and dhps in Plasmodium, while kinetoplastids, particularly Leishmania, exploit extensive genomic plasticity, including aneuploidy, gene amplification, and translational reprogramming, to facilitate rapid adaptation under drug pressure. Third, metabolic reprogramming enhances parasite survival by increasing intracellular thiol production, strengthening antioxidant defense systems, and reshaping central carbon and lipid metabolism to mitigate drug-induced stress. Finally, stress response and persistence mechanisms enable subpopulations of parasites to enter dormant, persister-like states characterized by reduced metabolic activity and slowed proliferation, thereby evading both host immune responses and chemotherapeutic agents. Collectively, these findings demonstrate that drug resistance is a dynamic, multifactorial evolutionary process rather than a single molecular event. Addressing this growing challenge requires integrating genomic surveillance, molecular diagnostics, mathematical modeling of resistance transmission, and mechanistic insights into parasite persistence into future drug discovery and disease control strategies. Such an integrated approach is essential for improving the durability of antiprotozoal therapies and advancing global efforts to control neglected protozoan diseases.

antiprotozoal therapy↗

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.

Biological Evolution↗

Speciation in multidimensional evolutionary space.

Adaptive dynamics in two-dimensional phenotype space is investigated by computer simulation. The model assumes Lotka-Voltera-type competition and a stochastic mutation process. The carrying capacity has a single maximum in the origin of the strategy space and the competition coefficient decreases with strategy difference. Evolutionary branching, an asexual analog of adaptive speciation, is observed with suitable parameters. The branching at the singular point, which is a fixed point of the directional evolution, may occur into two or three, but not more, directions. Further branchings may occur after the initial separation. The probability of three-branching is studied as a function of several parameters. We conclude that the two-way branching is the predominant mode of adaptive speciation.

Adaptation, Physiological↗

The evolutionary ecology of dominance-recessivity.

An "adaptive dynamics" modelling approach to the evolution of dominance-recessivity is presented. In this approach, fitness derives from an explicit ecological scenario, and both evolutionary attractivity and invasibility of resident populations are examined. The ecology consists of a within-individual part representing a locus with regulated activity and a between-individual part that is a two-patch soft selection model. Evolutionary freedom is allowed at a single locus. The evolutionary analysis considers directed random walks on trait space, generated by repeated invasions of mutants. The phenotype of an individual is determined by allelic parameters. Mutations can have two effects: they either affect the affinity of the promoter sequence for transcription factors, or they affect the gene product. The dominance interaction between alleles derives from their promoter affinities. Additive genetics is evolutionarily unstable when selection and evolution maintain two alleles in the population. In such a situation, dominance interactions can become stationary and close to additive genetics or they continue to evolve at a very slow pace towards dominance-recessivity. The probability that a specific dominance interaction will evolve depends on the relative mutation rate of promoter compared to gene product and the distribution of mutational effect sizes. Either allele in the dimorphism can become dominant, and dominance-recessivity is always most likely to evolve. Evolution then approaches a population state where every phenotype has maximum viability in one of the two patches. When the within-individual part is replaced by a housekeeping locus that codes for a metabolic enzyme, evolution favours a population of two alleles under the same conditions as for a regulated locus. In the case of a housekeeping gene, however, the evolutionary dynamical system approaches a population state where the heterozygote and only one homozygote phenotype are equivalent to the optimum phenotypes in the two patches.

Alleles↗

Hierarchical classification with a competitive evolutionary neural tree.

A new, dynamic, tree structured network, the Competitive Evolutionary Neural Tree (CENT) is introduced. The network is able to provide a hierarchical classification of unlabelled data sets. The main advantage that the CENT offers over other hierarchical competitive networks is its ability to self determine the number, and structure, of the competitive nodes in the network, without the need for externally set parameters. The network produces stable classificatory structures by halting its growth using locally calculated heuristics. The results of network simulations are presented over a range of data sets, including Anderson's IRIS data set. The CENT network demonstrates its ability to produce a representative hierarchical structure to classify a broad range of data sets.

Journal Article↗

Evolutionary games and two species population dynamics.

Competition between species has long been modeled by population dynamics based on total numbers of each species. Recently, the evolution of strategy frequencies has been used successfully for competition models between individuals. In this paper, we illustrate that these two views of competition are compatible. It is shown that the rate of intra and interspecific competitions between individuals largely determines the population dynamics. Competition models over a single common resource and predator-prey models are developed from this individual competition approach. In particular, the equilibrium strategies in a co-evolving predator-prey system are shown to be more stable than the predicted strategy cycling of standard evolutionary game theory.

Animals↗

The mating system and gene dynamics of plateau pikas.

Evolutionary theory suggests that mating systems should have substantial effects on gene dynamics of local populations. In polygynous species, local 'breeding groups' may produce significant genetic structure, due to genetic differences among groups, and rate of loss of genetic variation from such populations may be considerably slowed. We examined possible influences of the variable mating system and family group structure on genetic properties of a population of plateau pikas (Ochotona curzoniae). Pika gene dynamics were examined via F-statistics and effective population sizes (N(e)), calculated from genetic correlations within and among individuals and families. Genetic correlations were estimated from mating patterns, population demography, and dispersal patterns. Substantial genetic structure within the population was indicated by a strongly positive F(LS). Genetic influence of natal dispersal out of pika families was indicated by a strongly negative inbreeding statistic (F(IL)=-0.34). Effective size of the population was not greatly different from the census population, whereas a traditional estimate of effective size of the population was much lower, indicating that the family structure of the pikas results in a slowed loss of genetic variation over time. Thus, even though mating patterns of plateau pikas were variable, family structure had a strong influence on pika gene dynamics.

Journal Article↗

Evolutionary conservation of protein backbone flexibility.

Internal protein dynamics is essential for biological function. During evolution, protein divergence is functionally constrained: properties more relevant for function vary more slowly than less important properties. Thus, if protein dynamics is relevant for function, it should be evolutionary conserved. In contrast with the well-studied evolution of protein structure, the evolutionary divergence of protein dynamics has not been addressed systematically before, apart from a few case studies. X-Ray diffraction analysis gives information not only on protein structure but also on B-factors, which characterize the flexibility that results from protein dynamics. Here we study the evolutionary divergence of protein backbone dynamics by comparing the C(alpha) flexibility (B-factor) profiles for a large dataset of homologous proteins classified into families and superfamilies. We show that C(alpha) flexibility profiles diverge slowly, so that they are conserved at family and superfamily levels, even for pairs of proteins with nonsignificant sequence similarity. We also analyze and discuss the correlations among the divergences of flexibility, sequence, and structure.

Amino Acid Sequence↗

Energetics and evolution: an emerging research domain.

The study of energetics is important to human biology because the availability and utilization of food energy influence health, survival, and reproduction. Over the last decade, human biologists, biological anthropologists, and other evolutionary scientists have increasingly come to recognize the importance of energy dynamics in shaping evolutionary processes. Thus far, different lines of energetics research have been conducted largely in isolation from one another. This thematic collection examines topics of evolutionary energetics from several different perspectives, drawing together research from human paleontology, comparative primate and mammalian biology, human population biology, and mathematical modeling. It represents a starting point for further integrative research on human evolutionary energetics.

Animals↗

Recently Evolved, Stage-Specific Genes Are Enriched at Life-Stage Transitions in Flies.

Understanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal, and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster (D. melanogaster) has been extensively studied, less is known about the evolutionary dynamics that could govern stage-specific gene expression. To address this question, we compared the distribution of stage-specific genes, that is, genes expressed in temporally restricted developmental stages, across the development of D. melanogaster and Aedes aegypti (A. aegypti). Using tau-scoring, a computational method to determine gene expression specificity, we found that, on average, a large proportion of genes (20%-30% of all protein-coding genes) in both species exhibit restricted expression to specific developmental stages. Phylostratigraphy analysis, a method to date the age of genes, further revealed that stage-specific genes fall into two major categories: highly conserved and recently evolved. Notably, many of the recently evolved and stage-specific genes identified in A. aegypti and D. melanogaster are restricted to Diptera order (20%-35% of all stage-specific genes), highlighting ongoing evolutionary processes that continue to shape life-stage transitions. Overall, our findings underscore the complex interplay between gene evolutionary age, expression specificity, and morphological transformations in development. These results suggest that the attraction of genes to critical life-stage transitions is an ongoing process that may not be constant across evolutionary time or uniform between different lineages, offering new insights into the adaptability and diversification of dipteran genomes.

Animals↗

[A mathematical model for the dynamics of primitive biological macromolecules and its evolutionary implications].

A mathematical model, adopted from the logistic equations for population growth and interspecific competition in ecology, was proposed for the dynamics of primitive biological macromolecules: [formula: see text] where Nm is the copy number of a kind of biological macromolecule in primitive environment at time t. rm is the intrinsic replicating capacity (rate) of the macromolecule. Km is the carrying capacity (resource limit) of the primitive environment. dNm/dt is the instantaneous rate of increase of copy number of the primitive biological macromolecule beta 12 and beta 21 are competition coefficients concerning the inhibition of macromolecule 2 on macromolecule 1 (beta 12), and macromolecule 1 on macromolecule 2 (beta 21) other lower indexes in the equations refer to macromolecule 1 or 2. By analysing the possible competition outcomes deduced from the model, a conclusion with evolutionary implications could be drawn that the biological diversity would be very low shortly after the origin of life in the primitive biosphere. In other words, the abundant biological macromolecules capable of replicating in the primitive biosphere would be quite unique in kinds, and this uniqueness would therefore be the initial basis of biological evolution which would then go from low biological diversity to high biological diversity. The model is also helpful for the understanding of the origin of repeated sequences which are widely present in the genomes of modern organisms.

Animals↗

The adaptive dynamics of function-valued traits.

This study extends the framework of adaptive dynamics to function-valued traits. Such adaptive traits naturally arise in a great variety of settings: variable or heterogeneous environments, age-structured populations, phenotypic plasticity, patterns of growth and form, resource gradients, and in many other areas of evolutionary ecology. Adaptive dynamics theory allows analysing the long-term evolution of such traits under the density-dependent and frequency-dependent selection pressures resulting from feedback between evolving populations and their ecological environment. Starting from individual-based considerations, we derive equations describing the expected dynamics of a function-valued trait in asexually reproducing populations under mutation-limited evolution, thus generalizing the canonical equation of adaptive dynamics to function-valued traits. We explain in detail how to account for various kinds of evolutionary constraints on the adaptive dynamics of function-valued traits. To illustrate the utility of our approach, we present applications to two specific examples that address, respectively, the evolution of metabolic investment strategies along resource gradients, and the evolution of seasonal flowering schedules in temporally varying environments.

Adaptation, Biological↗