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Results for “Evolutionary trajectories”

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PubMed2005

Thermodynamic stability of ecosystems.

The stability of ecosystems during periods of stasis in their macro-evolutionary trajectory is studied from a non-equilibrium thermodynamic perspective. Individuals of the species are considered as units of entropy production and entropy exchange in an open thermodynamic system. Within the framework of the classical theory of irreversible thermodynamics, and under the condition of constant external constraints, such a system will naturally evolve toward a globally stable thermodynamic stationary state. It is thus suggested that the ecological steady state, or stasis, is a particular case of the thermodynamic stationary state, and that the evolution of community stability through natural selection is a manifestation of non-equilibrium thermodynamic directives. Furthermore, it is argued that punctuation of stasis leading to ecosystem succession, may be a manifestation of non-equilibrium "phase transitions" brought on by a change of external constraints through a thermodynamic critical point.

Animals↗
PubMed2005

Adaptive evolution by optimizing expression levels in different environments.

Organisms adapt to environmental changes through the fixation of mutations that enhance reproductive success. A recent study by Dekel and Alon demonstrated that Escherichia coli adapts to different growth conditions by fine-tuning protein levels, as predicted by a simple cost-benefit model. A study by Fong et al. showed that independent evolutionary trajectories lead to similar adaptive endpoints. Initial mutations on the path to adaptation altered the mRNA levels of numerous genes. Subsequent optimization through compensatory mutations restored the expression of most genes to baseline levels, except for a small set that retained differential levels of expression. These studies clarify how adaptation could occur by the alteration of gene expression.

Bacteria↗
PubMed2026

The genomic alchemist's arsenal: A comprehensive review of gene recruitment, regulatory rewiring, and the evolutionary arms race in snake envenomation.

Snake venom represents a striking example of evolutionary innovation, in which ancestral physiological gene networks have been co-opted into potent biochemical weapons. Advances in multi-omics, single-cell genomics, and structural bioinformatics have catalyzed a conceptual shift from descriptive toxin cataloging to a systems-level understanding of venom evolution, regulation, and function. This Review integrates genomic, cellular, and structural perspectives to delineate the molecular architecture underpinning venom diversification and target-site co-evolution. Emphasis is placed on regulatory mechanisms driving rapid expression plasticity, including super-enhancer activity, transposable element insertion, spatial heterogeneity within the venom gland, and non-coding RNA-mediated modulation. At the protein level, the review examines how hypervariable toxins engage in structural arms races with prey targets, and how multi-toxin complex formation, functional synergy, and molecular dynamics simulations inform models of lethality and resistance. A comparative framework is provided by contrasting high-potency predatory snake venoms with low-potency defensive venoms of hymenopterans such as bees and wasps, revealing how ecological selective pressures shape toxin potency, composition, and target specificity across taxa. Finally, current translational strategies are evaluated, with a focus on the relative merits of recombinant human monoclonal antibodies versus catalytic-site small-molecule inhibitors as deployable interventions for snakebite. By synthesizing evolutionary genomics, structural biology, comparative toxinology, and synthetic antivenomics, this Review outlines a predictive framework for anticipating venom evolutionary trajectories and for designing broad-spectrum, next-generation therapeutics.

Animals↗
PubMed2004

Quantitative genetic models of sexual selection.

Modeling of R.A. Fisher's ideas about the evolution of male ornamentation using quantitative genetics began in the 1980s. Following an initial period of enthusiasm, interest in these models began to wane when theoretical studies seemed to show that the rapid evolution of ornaments would not occur if there were costs associated with female mate choice. Recent theoretical work has shown, however, that runaway evolution and other kinds of extensive diversification of ornaments and preferences can occur, even when female choice is costly. These new models highlight crucial parameters that profoundly influence evolutionary trajectories, but these parameters have been neglected in empirical studies. Here, we review quantitative genetic models of sexual selection with the aim of fostering communication and synergism between theoretical and empirical enterprises. We also point out several areas in which additional empirical work could distinguish between alternative models of evolution.

Journal Article↗
PubMed2005

Tackling the population genetics of clonal and partially clonal organisms.

Many clonal organisms experience occasional events of sexual recombination, with profound consequences for their population dynamics and evolutionary trajectories. With the recent development of polymorphic genetic markers and new statistical methods, we now have an unprecedented ability to detect recombination in organisms that are thought to reproduce strictly, or essentially asexually. However, it is not always obvious which methodology to apply. Consequently, biologists might decide how to analyse their data without clear guidelines. Here, we discuss the available methods, focusing on those best suited when working with limited genetic information, such as a few genetic markers or DNA sequences. We conclude by commenting on the prospects offered by some recent conceptual advances and the access to high throughput technologies in an increasing number of model organisms.

Journal Article↗
PubMed1991

The evolution of viruses. Competition between horizontal and vertical transmission of mobile genes.

The transmission dynamics of viruses in a replicating cell population is investigated, assuming that viral mutants differ in their efficiencies of horizontal and vertical transmission. As a genetic result we find that competition between such different viral strategies need not select for increasing basic reproductive rates. We illustrate evolutionary trajectories that lead to increased viral latency even at the expense of lower basic reproductive rates and lower equilibrium abundance. In some cases oscillations in the prevalence of different mutants are obtained.

Biological Evolution↗
PubMed2001

Spatial distribution, cellular integration and stage development of Parkin protein in Xenopus brain.

Parkin is an ubiquitin-protein ligase molecule abundantly expressed in mammalian brains. Deletional mutations of Parkin protein produce a disease-related parkinsonian phenotype which is inherited with an autosomal recessive mode of transmission. To gain a greater insight into the evolutionary trajectory of the protein among vertebrate species, we describe here the (i) distribution pattern, (ii) sizing of specific fragments and (iii) embryonic development of Parkin in Xenopus laevis utilizing two antibodies to the N- and C-terminal sequence of the human Parkin protein. Parkin immunoreactivity was distributed in a heterogeneous fashion throughout the adult frog brain. The telencephalon, including the olfactory bulb, striatum and nucleus accumbens, harbored high numbers of Parkin-containing cells. High numbers of immunoreactive neurons were also present in discrete regions of the thalamus and hypothalamus. Relatively moderate expression of Parkin protein was noted in the nucleus anterodorsalis tegmenti, nucleus reticularis medius and torus semicircularis. The substantia nigra exhibited a distinctive heterogeneous pattern of Parkin-immunoreactivity, especially within presumptive dopamine neurons. The cerebellum also showed high expression of Parkin-positive material. Characterization of the subcellular distribution of the protein indicated both a cytoplasmic and nuclear integration of Parkin-immunoreactivity. This pattern of subcellular localization was similar to that observed in human brain material, perhaps reflecting distinct structural phosphorylation sites of the Parkin protein. Western blot analysis identified three specific bands with molecular weights varying from 50 to 65 kDa in adult Xenopus brain. However, studies on the temporal expression of Parkin during development showed a complete absence of cellular immunoreactivity which was especially conspicuous during late premetamorphic stages of frog development. These results suggest that the ubiquitination activity of Parkin is limited or non-existent during embryogenesis, but appears to assume a more functional role during adulthood as reflected by the high distribution pattern of the protein within major circuits of the amphibian brain.

Amino Acid Sequence↗
PubMed2002

OB-fold domains: a snapshot of the evolution of sequence, structure and function.

The OB-fold is found in all three kingdoms and is well represented in both sequence and structural databases. The OB-fold is a five-stranded closed beta barrel and the majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. Recently, a number of new structures with OB-folds have been reported that augment the variation seen for this set of proteins whilst conserving the characteristic fold and binding face. The conservation of fold and a functional binding face amongst many structures provides a model for investigating the evolutionary trajectory of sequence, structure and function.

Animals↗
PubMed2001

Evolution of functionality in lattice proteins.

We study the evolution of protein functionality using a two-dimensional lattice model. The characteristics particular to evolution, such as population dynamics and early evolutionary trajectories, have a large effect on the distribution of observed structures. Only subtle differences are observed between the distribution of structures evolved for function and those evolved for their ability to form compact structures.

Evolution, Molecular↗
PubMed2000

Evolution of placentation among squamate reptiles: recent research and future directions.

Squamate reptiles are uniquely suited to study of evolution of reproductive mode and pattern of embryonic nutrition. Viviparous species have evolved from oviparous ancestors on numerous occasions, patterns of nutritional provision to embryos range widely from lecithotrophy, at one end of a continuum, to placentotrophy at the other, and structure and function of the maternal-embryonic relationship is highly constrained resulting in parallel evolutionary trajectories among taxa. Embryos of oviparous species primarily receive nourishment from yolk, but also mobilize a significant quantity of calcium from the eggshell. Most viviparous species also are predominantly lecithotrophic, yet all viviparous species are placentotrophic to some degree. Similarities in embryonic development and nutritional pattern between oviparous species and most viviparous species suggest that the pattern of nutrition of oviparous squamates is an exaptation for the evolution of viviparity and that placentotrophy and viviparity evolve concomitantly. The few species of squamates that rely substantially on placentotrophy have structural modifications of the interface between the embryo and mother that are interpreted as adaptations to enhance nutritional exchange. Recent studies have extended understanding of the diversity of embryonic nutrition and placental structure and have resulted in hypotheses for transitions in the evolution of placentotrophy, yet data are available for few species. Indirect tests of these hypotheses, by comparison of structural-functional relationships among clades in which viviparity has evolved, awaits further study of the reproductive biology of squamates.

Animals↗
PubMed2002

Intracellular battlegrounds: conflict and cooperation between transposable elements.

Transposable elements (TEs) are genomic parasites that amplify their own representation on hosts' chromosomes by inserting into new positions. It is traditionally thought that their copy number is regulated by purifying selection that eliminates hosts with higher than average TE abundance. Here, we stress that selection due to beneficial or harmful interactions between TEs introduces a whole new dimension, with implications for TE evolutionary trajectories and TE loads on hosts. This framework poses new questions requiring conceptual and experimental advances. Considering primarily Drosophila data, we make a case for within host selection on TEs by thinking expansively about the lifecycle of several TE families.

Animals↗
PubMed2005

The coevolutionary dynamics of obligate ant social parasite systems--between prudence and antagonism.

In this synthesis we apply coevolutionary models to the interactions between socially parasitic ants and their hosts. Obligate social parasite systems are ideal models for coevolution, because the close phylogenetic relationship between these parasites and their hosts results in similar evolutionary potentials, thus making mutual adaptations in a stepwise fashion especially likely to occur. The evolutionary dynamics of host-parasite interactions are influenced by a number of parameters, for example the parasite's transmission mode and rate, the genetic structure of host and parasite populations, the antagonists' migration rates, and the degree of mutual specialisation. For the three types of obligate ant social parasites, queen-tolerant and queen-intolerant inquilines and slavemakers, several of these parameters, and thus the evolutionary trajectory, are likely to differ. Because of the fundamental differences in lifestyle between these social parasite systems, coevolution should further select for different traits in the parasites and their hosts. Queen-tolerant inquilines are true parasites that exert a low selection pressure on their host, because of their rarity and the fact that they do not conduct slave raids to replenish their labour force. Due to their high degree of specialisation and the potential for vertical transmission, coevolutionary theory would predict interactions between these workerless parasites and their hosts to become even more benign over time. Queen-intolerant inquilines that kill the host queen during colony take-over are best described as parasitoids, and their reproductive success is limited by the existing worker force of the invaded host nest. These parasites should therefore evolve strategies to best exploit this fixed resource. Slavemaking ants, by contrast, act as parasites only during colony foundation, while their frequent slave raids follow a predator prey dynamic. They often exploit a number of host species at a given site, and theory predicts that their associations are best described in terms of a highly antagonistic coevolutionary arms race.

Animals↗
PubMedDate not supplied

Generalized topological spaces in evolutionary theory and combinatorial chemistry.

The search spaces in combinatorial chemistry as well as the sequence spaces underlying (molecular) evolution are conventionally thought of as graphs. Recombination, however, implies a nongraphical structure of the combinatorial search spaces. These structures, and their implications for search process itself, are heretofore not well understood in general. In this contribution we review a very general formalism from point set topology and discuss its application to combinatorial search spaces, fitness landscapes, evolutionary trajectories, and artificial chemistries.

Base Sequence↗
PubMed2001

Quantitative genetics of signal evolution: a comparison of the pheromonal signal in two populations of the cabbage looper, Trichoplusia ni.

Pheromones are important in reproductive isolation among populations of moths, but the genetics associated with diversification of pheromonal signals is poorly understood. To gain insight into processes that may lead to diversification we examined the genetic architecture underlying the production of the sex pheromone of the cabbage looper moth, Trichoplusia ni. We compared genetic parameters of two populations; one with a wild-type pheromone phenotype (N) and one where a single-gene mutation affecting the pheromone blend produced by females had been established (M). Using a half-sib breeding design we estimated heritabilities, coefficients of additive genetic variation, and phenotypic, genetic, and environmental correlations of the pheromone components. In both populations, narrow sense heritabilities were generally moderate and genetic correlations were mostly positive. Comparisons between the two populations showed that, while the pattern of phenotypic correlations showed significant agreement between populations, the patterns of genetic (co)variation (i.e. the shapes of the within population matrix) were dissimilar between the two populations. The presence of additive genetic variation in both populations indicates that there is the potential for further evolution of individual pheromone components. However, because of the differences between the populations in the pattern of genetic variation and covariation, the populations will evolve along different evolutionary trajectories even under identical selection pressures. These results suggest that single gene mutations, once established, can be associated with further alterations in the genetic architecture and this has implications for the evolution of pheromone communication.

Animals↗
PubMed1996

Modelling phenotypic plasticity. II. Do genetic correlations matter?

Predictions of the evolutionary trajectory of reaction norms and interpretation of empirical results are usually based on two mathematically equivalent ways of partitioning phenotypic variance into its genetic, environmental, and interaction components: the genotype by environment interaction estimated by means of an analysis of variance, or the interenvironment genetic correlation (i.e. the genetic correlation between the expressions of the same trait in two environments). Both these quantities are supposed to indicate the amount of genetic variability for plasticity in natural population. I point out that not only are the qualitative predictions based on these statistical methods sometimes in conflict with each other, but that both may fail to predict rates of evolution and equilibria under some circumstances, because they ignore the details of the genetic machinery. It is shown that, ultimately, the only way to predict reliably the evolution of plasticity is actually to know its specific genetic basis and the genotypic constitution of the population, however inconvenient this may be from both theoretical and empirical standpoints. The discussion is framed in terms of a simple one-locus two-allele model that mimics the real case of the pennant/vestigial system describing plasticity of wing length to temperature in Drosophila melanogaster.

Alleles↗
PubMed2002

The role of parasites in sympatric and allopatric host diversification.

Exploiters (parasites and predators) are thought to play a significant role in diversification, and ultimately speciation, of their hosts or prey. Exploiters may drive sympatric (within-population) diversification if there are a variety of exploiter-resistance strategies or fitness costs associated with exploiter resistance. Exploiters may also drive allopatric (between-population) diversification by creating different selection pressures and increasing the rate of random divergence. We examined the effect of a virulent viral parasite (phage) on the diversification of the bacterium Pseudomonas fluorescens in spatially structured microcosms. Here we show that in the absence of phages, bacteria rapidly diversified into spatial niche specialists with similar patterns of diversity across replicate populations. In the presence of phages, sympatric diversity was greatly reduced, as a result of phage-imposed reductions in host density decreasing competition for resources. In contrast, allopatric diversity was greatly increased as a result of phage-imposed selection for resistance, which caused populations to follow divergent evolutionary trajectories. These results show that exploiters can drive diversification between populations, but may inhibit diversification within populations by opposing diversifying selection that arises from resource competition.

Animals↗
PubMed2001

Predicting the unpredictable: transmission of drug-resistant HIV.

We use a mathematical model to understand (from 1996 to 2001) and to predict (from 2001 to 2005) the evolution of the epidemic of drug-resistant HIV in San Francisco. We predict the evolutionary trajectories for 1,000 different drug-resistant strains with each strain having a different fitness relative to a drug-sensitive strain. We calculate that the current prevalence of resistance is high, and predict it will continue to rise. In contrast, we calculate that transmission of resistance is currently low, and predict it will remain low. We show that the epidemic of resistance is being generated mainly by the conversion of drug-sensitive cases to drug-resistant cases, and not by the transmission of resistant strains. We also show that transmission of resistant strains has not increased the overall number of new HIV infections. Our results indicate that transmission of resistant strains is, and will remain, a relatively minor public health problem.

Anti-HIV Agents↗
PubMed2004

Modeling the emergence of the 'hot zones': tuberculosis and the amplification dynamics of drug resistance.

'Hot zones' are areas that have >5% prevalence (or incidence) of multidrug-resistant tuberculosis (MDRTB). We present a new mathematical model (the amplifier model) that tracks the emergence and evolution of multiple (pre-MDR, MDR and post-MDR) strains of drug-resistant Mycobacterium tuberculosis. We reconstruct possible evolutionary trajectories that generated hot zones over the past three decades, and identify the key causal factors. Results are consistent with recently reported World Health Organization (WHO) data. Our analyses yield three important insights. First, paradoxically we found that areas with programs that successfully reduced wild-type pansensitive strains often evolved into hot zones. Second, some hot zones emerged even when MDR strains were substantially less fit (and thus less transmissible) than wild-type pansensitive strains. Third, levels of MDR are driven by case-finding rates, cure rates and amplification probabilities. To effectively control MDRTB in the hot zones, it is essential that the WHO specify a goal for minimizing the amplification probability.

Biological Evolution↗