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Results for “Evolutionary dynamics”

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PubMed2025

Five-Year (2017-2022) Evolutionary Dynamics of Human Coronavirus HKU1 in Southern France With Emergence of Viruses Harboring Spike H512R Substitution.

HCoV-HKU1 diversity and evolution were scarcely studied. We performed next-generation sequencing (NGS) and analysis of HCoV-HKU1 genomes over 5 years. NGS used Illumina technology on NovaSeq 6000 following whole genome PCR amplification by an in-house set of primers designed using Gemi and PrimalScheme. Genome assembly and analyses used CLC Genomics, Mafft, BioEdit, Nextstrain, Nextclade, MEGA, and iTol bioinformatic tools. Spike molecular modeling and dynamics simulations used Molegro Molecular Viewer and Hyperchem programs. Twenty-eight PCR systems allowed obtaining 158 HCoV-HKU1 genomes including 69 and 89 of genotypes A and B, respectively. Both genotypes co-circulated during the study period but one predominated each year. A total of 1683 amino acid substitutions including 80 in ≥ 10 genomes were detected in genotype A relatively to a 2004 reference. H512R in spike, first detected in 2009 and reported as involved in antibody neutralization, was found in all genotype A, almost always with V387I and K478N, and was predicted here to significantly improve cellular TMPRSS2 protein binding. Also, 1802 amino acid substitutions including 64 in ≥ 10 genomes were detected in genotype B relatively to a 2005 reference. This study substantially expands the global set of HCoV-HKU1 genomes. Genomics with protein structural analyses contributed to our understanding of HCoV-HKU1 evolution.

Humans↗
PubMed2001

The evolutionary dynamics of the lexical matrix.

The lexical matrix is an integral part of the human language system. It provides the link between word form and word meaning. A simple lexical matrix is also at the center of any animal communication system, where it defines the associations between form and meaning of animal signals. We study the evolution and population dynamics of the lexical matrix. We assume that children learn the lexical matrix of their parents. This learning process is subject to mistakes: (i) children may not acquire all lexical items of their parents (incomplete learning); and (ii) children might acquire associations between word forms and word meanings that differ from their parents' lexical items (incorrect learning). We derive an analytic framework that deals with incomplete learning. We calculate the maximum error rate that is compatible with a population maintaining a coherent lexical matrix of a given size. We calculate the equilibrium distribution of the number of lexical items known to individuals. Our analytic investigations are supplemented by numerical simulations that describe both incomplete and incorrect learning, and other extensions.

Adult↗
PubMed1999

Arms Races, Conflict Costs and Evolutionary Dynamics.

In conflicts and fights, the winner is often determined by the difference in resource-holding potential, e.g. size, weaponry, strength (RHP). I model the evolution of RHP in a symmetric game with continuous strategies. I show that there is a convergence stable ESS level of RHP if the cost of the trait increases faster than linearly, and that this is the only solution if the cost increases fast enough with RHP. Otherwise with slowly increasing cost, the solution is a cyclically fluctuating level of RHP. It is also shown that if the cost increases linearly with RHP, the only solution to the game is neutrally stable cycles, the amplitude determined by the initial conditions. The cycles come about because in a population drawn into an arms race of RHP, individuals after a while suffer costs so high that mutants with the lowest possible armament level may invade. Copyright 1999 Academic Press.

Journal Article↗
PubMed1999

Three mechanisms of host resistance to microparasites-avoidance, recovery and tolerance-show different evolutionary dynamics.

Parasite resistant hosts may avoid becoming infected, recover more quickly after infection or survive longer once infected. A model is constructed to examine the evolution of costly host resistance to directly transmitted microparasites and these three distinct mechanisms of avoidance, recovery and tolerance are compared. In each case polymorphism is more likely between very dissimilar strains and resistance (by which we mean the resistant strain alone) is always more likely to occur in hosts with high intrinsic productivity. However, the region where polymorphism occurs is relatively much smaller when resistance is through reduced pathogenicity. In particular, polymorphism with highly resistant strains requires correspondingly high costs. This is in contrast to avoidance or recovery resistance, where polymorphism can also occur when high resistance is associated with small costs due to the inability of highly resistant strains with low susceptibility or high recovery to support the parasite alone and hence resist invasion by the susceptible strain. Relatedly, resistance through avoidance and recovery is favoured in response to less pathogenic parasites.

Animals↗
PubMed2001

Genetic algorithm-based model of evolutionary dynamics of class II transposable elements.

We propose a new conceptual framework to study the dynamics of transposable elements. Based on a genetic algorithm, our model is designed as a self-organizing system. Our results show that transposable elements could emerge from a single endonuclease gene. The DNA repair mechanisms appear to condition the emergence success of class II TEs. Antagonist selective forces acting on transposable elements and their hosts induce by their opposition differences in the sequence evolution of the functional domains and of the copies.

Algorithms↗
PubMed1992

On the potential of simple repetitive DNA for fingerprinting in clinical, forensic, and evolutionary dynamic studies.

The purpose of this review is to discuss critically the practical meaning of a specific genome component, simple repetitive desoxyribonucleic acid (DNA) sequences as clinical and forensic and diagnostic and research tools. Previously, multilocus DNA fingerprinting was the major technology employed to visualize such simple repeat sequences. This technique enables many polymorphic loci to be simultaneously detected thus yielding vast amounts of information. With the advent of enzymatic DNA amplification via the polymerase chain reaction (PCR), individual simple repeat loci can be demonstrated, theoretically even from single DNA molecules and so a wealth of additional approaches have also become feasible. In general investigating, small, known, single copy parts of genomes have not posed truly insurmountable problems if enough material was available. There have even been a few (anecdotal) reports on the amplification of simple repeats from ancient DNA (see, e.g. [30]. Here we would like to after a solid basis for an earnest discussion of the applications of these simple repetitive sequences using various methodological approaches relevant for clinical diagnosis, setting aside the obvious unsolved mysteries of their biology.

Animals↗
PubMed1991

Simulation of local evolutionary dynamics of small populations.

A simple stochastic model assuming continuous traits, normally distributed modifications, selection for fertility and multiplicative fitness was used to simulate phenotypic evolution by "reproducing individuals" in a given fitness landscape. Of particular interest was how small populations cross saddles separating distinct adaptive peaks. The simulated evolution exhibits a strong dualism: at the same level of reproductive errors, sexual reproduction provides significantly better local adaptation and asexual reproduction provides significantly better adaptive dynamics.

Animals↗
PubMed1984

Evolutionary dynamics of zero-sum games.

Aim model in terms of differential equations is used to explain mammalian ovulation control, in particular regulation for a prescribed number of mature eggs.

Female↗
PubMed1988

Evolutionary dynamics of tryptophan tRNAs in Mycoplasma capricolum.

Mycoplasma capricolum uses two tryptophan codons, the "universal" nonsense codon UGA and the universal codon UGG. The bacterium contains two tryptophan tRNAs, one with anticodon UCA, (U: 2'-O-methyl U derivative), and the other with CCA (5'-C: partially 2'-O-methylated). tRNAUCA would translate codons UGA and probably UGG by wobbling. tRNACCA is much less charged by tryptophan in the cells than tRNAUCA, and the intracellular amount of tRNACCA is 5-10 times lower than that of tRNAUCA. The genes for these two tRNAs are separated by a terminator-like structure in a single operon. In vitro transcription experiments suggest that the predominance of tRNAUCA over tRNACCA results from the attenuation of transcription by this terminator-like structure.

Base Sequence↗
PubMed2003

Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications.

We determined the phylogenetic positions of 82 large nuclear pseudogenes of mitochondrial origin (numts) within the human genome. For each numt, two possibilities pertaining to its origin were considered: (1) independent insertion from the mitochondria into the nucleus, or (2) genomic duplication subsequent to the insertion. A significant increase in the rate of numt accumulation is seen after the divergence of Platyrrhini (New World monkeys) from the Catarrhini (Old World monkeys, apes and humans). By using pairwise phylogenetic analyses, we were able to demonstrate that this peak in numt accumulation is mostly the result of duplication of preexisting nuclear numts rather than the result of an increase in mitochondrial-sequence insertion. In fact, only about a third of all the numt repertoire in the human nuclear genome is due to insertions of mitochondrial sequences, the rest originated as duplications of preexisting numts. Hence, we conclude that numt insertion occurs at a much lower rate than previously reported. As expected under the assumption that genomic duplications occur at rates that are uninfluenced by content, older numts were found to be duplicated more times than recently inserted ones.

DNA Transposable Elements↗
PubMed2000

Evolutionary dynamics of HTLV-I.

Using mathematical models to describe the in vivo dynamics of HTLV-I infection, an explanation is offered for the slow rate of evolution of HTLV-I relative to HIV-1. In agreement with experimental findings, it is assumed that cell activation is required for successful replication in T helper cells and that HTLV-I induces a significant degree of bystander activation. It is found that the rate of evolution of HTLV-I is limited by the restricted availability of activated uninfected T cells, both at high and low proviral loads. This limits the within-host sequence diversity of HTLV-I and may therefore account for the slow rate of evolution of the virus in the population. Specific differences in the in vivo dynamics of HTLV-I and HIV-1 are identified which may account for the discrepancy in the rate of evolution of these two retroviruses.

Evolution, Molecular↗
PubMed2005

Characterisation of Fmrp in zebrafish: evolutionary dynamics of the fmr1 gene.

Fragile X syndrome is the most common inherited form of mental retardation. It is caused by the lack of the Fragile X Mental Retardation Protein (FMRP), which is encoded by the FMR1 gene. Although Fmr1 knockout mice display some characteristics also found in fragile X patients, it is a complex animal model to study brain abnormalities, especially during early embryonic development. Interestingly, the ortholog of the FMR1 gene has been identified not only in mouse, but also in zebrafish (Danio rerio). In this study, an amino acid sequence comparison of FMRP orthologs was performed to determine the similar regions of FMRP between several species, including human, mouse, frog, fruitfly and zebrafish. Further characterisation of Fmrp has been performed in both adults and embryos of zebrafish using immunohistochemistry and western blotting with specific antibodies raised against zebrafish Fmrp. We have demonstrated a strong Fmrp expression in neurons of the brain and only a very weak expression in the testis. In brain tissue, a different distribution of the isoforms of Fmrp, compared to human and mouse brain tissue, was shown using western blot analysis. Due to the high similarity between zebrafish Fmrp and human FMRP and their similar expression pattern, the zebrafish has great potential as a complementary animal model to study the pathogenesis of the fragile X syndrome, especially during embryonic development.

Amino Acid Sequence↗
PubMed1984

Evolutionary dynamics in frequency-dependent two-phenotype models.

General frequency-dependent selection models based on two phenotypic classes are analyzed with underlying one-locus multiallele phenotypic determination systems in diploid populations. It is proved that the mean phenotypic fitnesses tend to equality over discrete generations and genetic mutations if a phenotypic polymorphism is to be maintained. The exact conditions are examined. The present results are valid for a wide class of models whenever random groupings or assortative patterns based on phenotype and affecting fitness, linearly or not, are independent of sex, mating preferences, or kinship. They can also be applied to two-sex haploid models.

Diploidy↗
PubMed2004

Evolutionary dynamics of satellite DNA in species of the Genus Formica (Hymenoptera, Formicidae).

The satellite DNA has been characterized in eight species of the Formica genus. This satellite DNA is organized as tandemly repeated 129-bp monomers in all species and it presents internal inverted repeats. The results of all the analyses performed in the sequences sampled from Formica cunicularia, F. fusca, F. gerardi, F. rufibarbis, F. selysi, F. frontalis, and F. sanguinea suggest interspecific conservation of satellite DNA. Nevertheless, the results from the comparative analysis of the sequences sampled from F. subrufa and the remaining species studied suggest that the mechanisms producing concerted evolution have been efficient in these taxa. A CENP-B-like motif has been found in the satellite DNA from the species analysed, including F. subrufa. This satellite DNA is located in the pericentromeric regions of all chromosomes. We suggest that, although the evolution of the DNA satellite in ants could be similar to that in other organisms, there may be some particularities as a result of a haplodiploid system.

Animals↗
PubMed2006

On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins.

Protein sequences frequently contain regions composed of a reduced number of amino acids. Despite their presence in about half of all proteins and their unusual prevalence in the malaria parasite Plasmodium falciparum, the function and evolution of such low-complexity regions (LCRs) remain unclear. Here we show that LCR abundance and amino acid composition depend largely, but not exclusively, on genomic A+T content and obey power-law growth dynamics. Further, our results indicate that LCRs are analogous to microsatellites in that DNA replication slippage and unequal crossover recombination are important molecular mechanisms for LCR expansion. We support this hypothesis by demonstrating that the size of LCR insertions/deletions among orthologous genes depends upon length. Moreover, we show that LCRs enable intra-exonic recombination in a key family of cell-surface antigens in P. falciparum and thus likely facilitate the generation of antigenic diversity. We conclude with a mechanistic model for LCR evolution that links the pattern of LCRs within P. falciparum to its high genomic A+T content and recombination rate.

Amino Acids↗
PubMed2005

Evolutionary dynamics and highly optimized tolerance.

We develop a numerical model of a lattice community based on Highly Optimized Tolerance (HOT), which relates the evolution of complexity to robustness tradeoffs in an uncertain environment. With the model, we explore scenarios for evolution and extinction which are abstractions of processes which are commonly discussed in biological and ecological case studies. These include the effects of different habitats on the phenotypic traits of the organisms, the effects of different mutation rates on adaptation, fitness, and diversity, and competition between generalists and specialists. The model exhibits a wide variety of microevolutionary and macroevolutionary phenomena which can arise in organisms which are subject to random mutation, and selection based on fitness evaluated in a specific environment. Generalists arise in uniform habitats, where different disturbances occur with equal frequency, while specialists arise when the relative frequency of different disturbances is skewed. Fast mutators are seen to play a primary role in adaptation, while slow mutators preserve well-adapted configurations. When uniform and skewed habitats are coupled through migration of the organisms, we observe a primitive form of punctuated equilibrium. Rare events in the skewed habitat lead to extinction of the specialists, whereupon generalists invade from the uniform habitat, adapt to their new surroundings, ultimately leading their progeny to become vulnerable to extinction in a subsequent rare disturbance.

Adaptation, Physiological↗
PubMed2006

Evolutionary dynamics of the continuous iterated prisoner's dilemma.

The iterated prisoner's dilemma (IPD) has been widely used in the biological and social sciences to model dyadic cooperation. While most of this work has focused on the discrete prisoner's dilemma, in which actors choose between cooperation and defection, there has been some analysis of the continuous IPD, in which actors can choose any level of cooperation from zero to one. Here, we analyse a model of the continuous IPD with a limited strategy set, and show that a generous strategy achieves the maximum possible payoff against its own type. While this strategy is stable in a neighborhood of the equilibrium point, the equilibrium point itself is always vulnerable to invasion by uncooperative strategies, and hence subject to eventual destabilization. The presence of noise or errors has no effect on this result. Instead, generosity is favored because of its role in increasing contributions to the most efficient level, rather than in counteracting the corrosiveness of noise. Computer simulation using a single-locus infinite alleles Gaussian mutation model suggest that outcomes ranging from a stable cooperative polymorphism to complete collapse of cooperation are possible depending on the magnitude of the mutational variance. Also, making the cost of helping a convex function of the amount of help provided makes it more difficult for cooperative strategies to invade a non-cooperative equilibrium, and for the cooperative equilibrium to resist destabilization by non-cooperative strategies. Finally, we demonstrate that a much greater degree of assortment is required to destabilize a non-cooperative equilibrium in the continuous IPD than in the discrete IPD. The continuous model outlined here suggests that incremental amounts of cooperation lead to rapid decay of cooperation and thus even a large degree of assortment will not be sufficient to allow cooperation to increase when cooperators are rare. The extreme degree of assortment required to destabilize the non-cooperative equilibrium, as well as the instability of the cooperative equilibrium, may help explain why cooperation in Prisoner's Dilemmas is so rare in nature.

Altruism↗