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PubMed1995

Evolutionary dynamics of the FMR1 locus.

Rare haplotypes for close flanking markers are associated with increased allele size and frequency of the fragile X mutation. Exceptional founder haplotypes can be identified, but many haplotypes with rare alleles contribute to full mutations. A transition matrix constructed from the data predicts that a population with reduced variability will manifest a slowly increasing frequency of premutations and full mutations, reach a distribution close to the observed one after a few hundred generations, and then slowly be depleted of these alleles. This prediction is opposite to less well supported inference of increasing frequency of progressive amplification, but the data are inadequate to reach any firm conclusions. Factors that may determine the evolution of these systems, but cannot now be evaluated, are discussed.

Biological Evolution↗
PubMed1999

Evolutionary dynamics of HIV-induced subversion of the immune response.

Human immunodeficiency virus (HIV) disease progression is characterized by a slow but steady decline in the number of CD4+ T cells. It results in the development of AIDS when the immune response collapses and the virus grows uncontrolled. Pathogenicity of HIV may be due to viral escape from cellular immune responses as well as virus-induced immune impairment. Here we discuss how the dynamic interactions between the virus population and the immune response may lead to the development of AIDS. In particular we argue that in vivo evolution of HIV may be the driving force successively weakening the immune system. This may lead to increased levels of viraemia as well as to the evolution of more virulent phenotypes which indicate progression to AIDS. These insights are important for understanding the disease process itself and for designing effective treatment regimes.

HIV Infections↗
PubMed2002

Evolutionary dynamics of viral attenuation.

The genetic trajectory leading to viral attenuation was studied in a canine parvovirus (CPV) strain grown on dog kidney cells for 115 transfers. Consensus sequences of viral populations at passages 0, 3, 30, 50, 80, and 115 were obtained from PCR products covering 86% of the genome; clones from each of the 80th and 115th passages were also sequenced, covering 69% of the genome. Sixteen changes were fixed in the 115th-passage virus sample. Levels of polymorphism were strikingly different over time, in part because of a plaque-cloning step at passage 112 that reduced variation: passage 80 had 19 variants common among the clones, but passage 115 had only a single common variant. Several mutations increased in the culture at the same time, with most reaching fixation only after the 80th passage. The pattern of evolution was consistent with recombination and not with separate selective sweeps of individual mutations. Thirteen of the changes observed were identical to or at the same positions as changes observed in other isolates of CPV or feline panleukopenia virus.

Adaptation, Physiological↗
PubMed2026

Evolutionary dynamics of HIV-1 recombinants: analysis of contemporary and historical viral populations in East Africa.

BACKGROUND: Understanding the genetic evolution of HIV-1 Transmitted/Founder (T/F) virus is crucial for developing effective treatment and prevention strategies due to its rapid mutation and recombination rates. METHODS: This study compared the genetic diversity of 24 contemporary T/F viruses collected between 2016 and 2021 in Uganda and Kenya with 29 historical T/F sequences sampled between 2006 and 2011. RESULTS: Subtype analysis based on near-full-length (NFL) HIV-1 T/F genomes revealed that 57.1% (12/21) of contemporary viruses were recombinants, predominantly involving Subtype A1, D, and increasing Subtype C, with 33.3% (7/21) being A1D recombinants (A1 > D) and 19% (4/21) classified as complex recombinants involving three or more subtypes. Historical viruses showed a similar overall proportion (69%) but were mainly A1D mosaics (D > A1) with recombination confined primarily to the envelope region. In contrast, contemporary viruses shifted towards more complex recombinant patterns affecting additional genomic regions, including pol and accessory genes. Phylogenetic analysis demonstrated that contemporary viruses clustered into distinct, well-supported (98% bootstrap) sub-branches, suggesting divergency attributed to an imbalance in their proportions of subtype A1 and D sequences as well as a different content of A1 and D segments in the A1/D mosaic recombinants. CONCLUSIONS: These findings underscore the dynamic and shifting nature of HIV-1 genetic diversity in East Africa, highlighting the need for continuous molecular surveillance and region-specific treatment guidelines.

HIV-1↗
PubMed2001

Evolutionary dynamics of host-plant specialization: a case study of the tribe Nymphalini.

Two general patterns that have emerged from the intense studies on insect-host plant associations are a predominance of specialists over generalists and a taxonomic conservatism in host-plant use. In most insect-host plant systems, explanations for these patterns must be based on biases in the processes of host colonizations, host shifts, and specialization, rather than cospeciation. In the present paper, we investigate changes in host range in the nymphalid butterfly tribe Nymphalini, using parsimony optimizations of host-plant data on the butterfly phylogeny. In addition, we performed larval establishment tests to search for larval capacity to feed and survive on plants that have been lost from the female egg-laying repertoire. Optimizations suggested an ancestral association with Urticaceae, and most of the tested species showed a capacity to feed on Urtica dioica regardless of actual host-plant use. In addition, there was a bias among the successful establishments on nonhosts toward plants that are used as hosts by other species in the Nymphalini. An increased likelihood of colonizing ancestral or related plants could also provide an alternative explanation for the observed pattern that some plant families appear to have been colonized independently several times in the tribe. We also show that there is no directionality in host range evolution toward increased specialization, that is, specialization is not a dead end. Instead, changes in host range show a very dynamic pattern.

Animals↗
PubMed2001

Evolutionary dynamics of the human immunoglobulin kappa locus and the germline repertoire of the Vkappa genes.

We have determined the entire nucleotide sequence of the human immunoglobulin kappa locus, comprising a total of 1,010,706 nucleotides. The 76 Vkappa genes found by a hybridization-based approach and their classification in 7 families were confirmed. A Vkappa orphon located near the locus was also sequenced. In addition, we identified 55 novel Vkappa relics and truncated pseudogenes, which establish 5 new families. Among these 132 Vkappa genes, 46 have open reading frames. According to the databases and the literature, 32 unique Vkappa genes and 5 identical gene pairs form VJ-joints, 27 unique genes and 4 gene pairs are transcribed, and 25 unique genes and 4 gene pairs produce functional proteins. The Vkappa gene locus contains a 360-kb inverted duplication, which harbors 118 Vkappa genes. A comparison of the duplicated Vkappa genes suggests positive selection on the complementarity-determining regions of the duplicated genes by point mutations. The entire duplication unit was divided into 13 blocks, each of which has its distinct nucleotide sequence identity to its duplication counterpart (98.1 - 99.9 %). An inversion-mediated mechanism is suggested to generate the high-homology blocks. Based on the homology blocks and the mutation rates, the inverted duplication is assumed to have taken place approximately 5 million years ago. An orphon Vkappa gene near the kappa locus and a cluster of five Vkappa orphons on chromosome 22 have no counterparts within the kappa locus. This suggests possible mechanisms of the transposition of orphon Vkappa genes.

Base Composition↗
PubMed1981

[V. M. Shimkevich's principle of methorisis and its relation to the evolutionary dynamics of the esophageal epithelium of fish].

In 31 species of Teleostei and Chondrostei a possibility to apply the principle of methorisis (displacement of borders between embryonic germs and, respectively, between their tissue derivatives) to the epithelial layer of the esophagus in these vertebrates has been considered. Appearance of the esophageal capillary networks is connected with the phenomenon of displacement. It is noted that food does not evidently affect directly the esophageal epithelium. Simultaneously, peculiarities in the structure of the esophageal epithelium of some Teleostei and Chondrostei are observed.

Animals↗
PubMed1997

Interplay of causation between suppliers and consumers in evolutionary trophic dynamics.

Natural selection, conceived as the process of small causes making small effects on the level of molecular evolutionary dynamics of a population, can yield global effects on the level of evolutionary trophic dynamics of populations, including those of mass extinctions. Occurrence of mass extinctions is due to the interplay of causation between suppliers and consumers in trophic dynamics. If the case of supplier causation is available such that resource exploitation by consumers on the upper trophic level follows in time resource presentation by suppliers on the lower, instead of resource exploitation followed by resource presentation, mass extinctions could be a norm of the evolutionary trophic dynamics.

Biological Evolution↗
PubMed2002

The adaptiveness of defence strategies against cuckoo parasitism.

Host bird species of the Eurasian Cuckoo, Cuculus canorus, often display egg-discrimination behaviour but chick-rejection behaviour has never been reported. In this paper, we analyse a host-cuckoo association in which both population dynamics and evolutionary dynamics are explored in a discrete-time model. We introduce four host types, each with their own defence behaviour, displaying either egg or chick rejection, neither or both, We also introduce fitness functions for each of these host types. Although we can characterize the long term behaviour in many cases by a simple heuristic argument which is in accordance with common views in ecology, there are a number of other phenomena that are not explained within this framework: we describe stable oscillatory behaviour and coexistence of two defensive host types. We analyse the scenarios in which chick rejection may establish itself and give a first explanation as to why this defence trait has never been recorded in nature. We find that chick rejectors generally are at an intrinsic disadvantage with respect to a host type that rejects eggs. Hosts benefit more from rejecting cuckoo eggs than cuckoo chicks, and our model suggests that this is chiefly responsible for the absence of chick rejection. Moreover, even though it seems that chick rejection must be useful as an extra defence, it is shown that hosts with both defence strategies are less likely to establish themselves in competition with egg-rejectors than hosts which reject chicks only. These results provide insight in the extent to which adaptations may be perfected by natural selection.

Adaptation, Biological↗
PubMed2002

Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis).

Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evolutionary dynamics of the duplicated defense genes hm1 and hm2 in maize and its wild ancestor Zea mays ssp. parviglumis. Both genes have been shown to confer resistance to the fungal pathogen Cochliobolus carbonum race 1, but the effectiveness of resistance differs between loci. The genes also display different population histories. The hm1 locus has the highest nucleotide diversity of any gene yet sampled in the wild ancestor of maize, and it contains a large number of indel polymorphisms. There is no evidence, however, that high diversity in hm1 is a product of nonneutral evolution. In contrast, hm2 has very low nucleotide diversity in the wild ancestor of maize. The distribution of hm2 polymorphic sites is consistent with nonneutral evolution, as indicated by Tajima's D and other neutrality tests. In addition, one hm2 haplotype is more frequent than expected under the equilibrium neutral model, suggesting hitchhiking selection. Both defense genes retain >80% of the level of genetic variation in maize relative to the wild ancestor, and this level is similar to other maize genes that were not subject to artificial selection during domestication.

Ascomycota↗
PubMed2001

Effects of population size and metapopulation dynamics on a mating-system polymorphism.

The evolutionary dynamics of neutral alleles under the Wright-Fisher model are well understood. Similarly, the effect of population turnover on neutral genetic diversity in a metapopulation has attracted recent attention in theoretical studies. Here we present the results of computer simulations of a simple model that considers the effects of finite population size and metapopulation dynamics on a mating-system polymorphism involving selfing and outcrossing morphs. The details of the model are based on empirical data from dimorphic populations of the annual plant Eichhornia paniculata, but the results are also of relevance to species with density-dependent selfing rates in general. In our model, the prior selfing rate is determined by two alleles segregating at a single diploid locus. After prior selfing occurs, some remaining ovules are selfed through competing self-fertilisation in finite populations as a result of random mating among gametes. Fitness differences between the mating-system morphs were determined by inbreeding depression and pollen discounting in a context-dependent manner. Simulation results showed evidence of frequency dependence in the action of pollen discounting and inbreeding depression in finite populations. In particular, as a result of selfing in outcrossers through random mating among gametes, selfers experienced a "fixation bias" through drift, even when the mating-system locus was selectively neutral. In a metapopulation, high colony turnover generally favoured the fixation of the outcrossing morph, because inbreeding depression reduced opportunities for colony establishment by selfers through seed dispersal. Our results thus demonstrate that population size and metapopulation processes can lead to evolutionary dynamics involving pollen and seed dispersal that are not predicted for large populations with stable demography.

Alleles↗
PubMed1995

Body surface adaptations to boundary-layer dynamics.

Evolutionary processes have adapted nektonic animals to interact efficiently with the water that surrounds them. Not all these adaptations serve the same purpose. This paper concentrates on reduction of drag due to friction in the boundary layer close to the body surface. Mucus, compliant skins, scales, riblets and roughness may influence the flow velocity gradient, the type of flow and the thickness of the boundary layer around animals, and may seriously affect their drag in a positive or negative way. The long-chain polymers found in mucus decrease the pressure gradient and considerably reduced drag due to friction. The effect is probably due to channelling of the flow particles in the direction of the main flow, resulting in a reduction of turbulence. Compliant surfaces could probably reduce drag by equalising and distributing pressure pulses. However, the existing evidence that drag reduction actually occurs is not convincing. There is no indication that instantaneous heating, reducing the viscosity in the boundary layer, is used by animals as a drag-reducing technique. Small longitudinal ridges on rows of scales on fish can reduce shear stress in the boundary by a maximum of 10% compared with the shear stress of a smooth surface. The mechanism is based on the impedance of cross flow under well-defined conditions. The effect has been visualized with the use of particle image velocimetry techniques. The function of the swords and spears of several fast, pelagic, predatory fish species is still enigmatic. The surface structure of the sword of a swordfish is shown to be both rough and porous. The height of the roughness elements on the tip of the sword is close to the critical value for the induction of a laminar-to-turbulent flow transition at moderate cruising speeds. A flow tank is described that is designed to visualize the effects of surface imperfections on flow in the boundary layer in direct comparison with a smooth flat wall. The flow in a 1 m long, 10 cm high and 1 cm wide channel is visualized by illuminating the particles in a thin laser light sheet. The first results show that a rough surface increases the shear stress in the boundary layer and makes it thinner. The function of the roughness on the sword of a swordfish is probably to reduce the total drag by generating premature turbulence and by boundary layer thinning, despite an increased friction over the surface of the sword. The function of the porous surface structures on the sword, and of the porous skins of sharks and of the castor oil fish, will probably be discovered soon using new particle image velocimetry techniques applied under strong magnification to visualize the local behaviour of the flow.

Adaptation, Physiological↗
PubMed2025

Fluctuating DNA methylation tracks cancer evolution at clinical scale.

Cancer development and response to treatment are evolutionary processes1,2, but characterizing evolutionary dynamics at a clinically meaningful scale has remained challenging3. Here we develop a new methodology called EVOFLUx, based on natural DNA methylation barcodes fluctuating over time4, that quantitatively infers evolutionary dynamics using only a bulk tumour methylation profile as input. We apply EVOFLUx to 1,976 well-characterized lymphoid cancer samples spanning a broad spectrum of diseases and show that initial tumour growth rate, malignancy age and epimutation rates vary by orders of magnitude across disease types. We measure that subclonal selection occurs only infrequently within bulk samples and detect occasional examples of multiple independent primary tumours. Clinically, we observe faster initial tumour growth in more aggressive disease subtypes, and that evolutionary histories are strong independent prognostic factors in two series of chronic lymphocytic leukaemia. Using EVOFLUx for phylogenetic analyses of aggressive Richter-transformed chronic lymphocytic leukaemia samples detected that the seed of the transformed clone existed decades before presentation. Orthogonal verification of EVOFLUx inferences is provided using additional genetic data, including long-read nanopore sequencing, and clinical variables. Collectively, we show how widely available, low-cost bulk DNA methylation data precisely measure cancer evolutionary dynamics, and provides new insights into cancer biology and clinical behaviour.

Humans↗
PubMed2026

Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.

UNLABELLED: Predator-mediated selection is an important ecological force shaping bacterial evolution, but its effects on genomic adaptation and virulence in opportunistic pathogens are not fully understood. Here, we used experimental evolution to study how exposure to the ciliate predator Tetrahymena thermophila affects Pseudomonas aeruginosa. Replicate populations were evolved for 60 days with or without the predator, followed by whole-genome shotgun metagenomic sequencing and phenotypic analyses. Both treatments showed strong selection and evidence of parallel evolution at gene and nucleotide levels, indicating constrained adaptation. However, predator exposure altered evolutionary dynamics. Predator-evolved populations showed a wider distribution of mutation frequencies, with many mutations persisting at intermediate frequencies, consistent with increased clonal interference and ongoing competition among lineages. In contrast, populations evolved without predators showed more high-frequency mutations, consistent with selective sweeps, although some low-frequency variants remained. Despite substantial genomic change, phenotypic outcomes were variable. Virulence in an invertebrate host model did not consistently increase. Instead, evolved isolates showed context-dependent changes, including modest decreases or occasional increases. Competition assays also showed no consistent fitness advantage for predator-evolved isolates, suggesting trade-offs between predator resistance and growth in other environments. Overall, predator-mediated selection reshaped evolutionary dynamics by maintaining diversity and altering the balance of lineages rather than producing uniform increases in virulence. These results highlight how ecological complexity influences adaptive evolution and the context-dependent nature of pathogen traits. IMPORTANCE: Opportunistic pathogens such as Pseudomonas aeruginosa often evolve in environmental settings before infecting hosts, raising questions about how ecological interactions influence virulence. Predator-mediated selection has been suggested to increase virulence via coincidental evolution, but evidence is inconsistent. Here, we show that exposure to a eukaryotic predator does not consistently elevate virulence but does reshape evolutionary dynamics by altering how mutations spread in populations. Predator-exposed populations retained more intermediate-frequency mutations, consistent with increased clonal interference and ongoing competition among lineages, whereas non-predator populations were dominated by selective sweeps. These differences were also reflected in functional targets of adaptation, with predator exposure favoring mutations in genes involved in environmental sensing and interaction. Together, these findings suggest that ecological complexity shapes the dynamics of adaptation rather than driving a single evolutionary outcome, highlighting that virulence is an emergent property influenced by underlying evolutionary processes.

Pseudomonas aeruginosa↗
PubMed2002

Consequences of plant-herbivore coevolution on the dynamics and functioning of ecosystems.

The potential consequences of plant-herbivore coevolution for ecosystem functioning are investigated using a simple nutrient-limited ecosystem model in which plant and herbivore traits are subject to adaptive dynamics. Although the ecological model is very simple and always reaches a stable equilibrium in the absence of evolution, coevolution can generate a great diversity of dynamical behaviors. The evolutionary dynamics can lead to a stable equilibrium. If the evolution of plants is fast enough, certain values of the trade-off parameters lead to complex evolutionary cycles bounded by physiological constraints. The dynamical behavior of the model is very different when the dynamics of inorganic nutrient is ignored and plant competition is modeled by a logistic growth function. This emphasizes the importance of including explicit nutrient dynamics in studies of plant-herbivore coevolution.

Adaptation, Biological↗