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PubMed2026

Multilayered nucleotide organization reveals purifying selection and host-driven adaptation in CPV and FPV.

Since feline panleukopenia virus (FPV) is considered the most likely ancestor of canine parvovirus (CPV), comprehensive comparisons of nucleotide organization in corresponding viral genes between CPV and FPV may provide novel insights into the evolutionary dynamics underlying the divergence of these two viruses. Here, we characterize the evolutionary patterns of CPV and FPV genes across multiple levels of nucleotide organization. Both viruses exhibited highly conserved nucleotide usage at nonsynonymous sites, with Ka/Ks patterns consistent with strong purifying selection, whereas synonymous sites showed greater variability. CpG dinucleotides were markedly underrepresented across all four viral genes, suggesting host-associated selective pressure and/or intrinsic nucleotide compositional constraints. Extensive nonrandom biases in synonymous codon usage, codon neighboring nucleotide context, and codon pair usage further revealed fine-scale genomic optimization shaped by natural selection and nucleotide compositional constraints. Structural protein genes (VP1 and VP2) displayed stronger codon usage bias and higher tRNA adaptation than nonstructural genes. Moreover, CPV genes showed greater translational adaptation to feline hosts than to canine hosts. These findings highlight how closely related parvoviruses exploit flexible nucleotide organization to facilitate host adaptation while maintaining essential protein functions.

Animals↗
PubMed2003

Rapid evolution drives ecological dynamics in a predator-prey system.

Ecological and evolutionary dynamics can occur on similar timescales. However, theoretical predictions of how rapid evolution can affect ecological dynamics are inconclusive and often depend on untested model assumptions. Here we report that rapid prey evolution in response to oscillating predator density affects predator-prey (rotifer-algal) cycles in laboratory microcosms. Our experiments tested explicit predictions from a model for our system that allows prey evolution. We verified the predicted existence of an evolutionary tradeoff between algal competitive ability and defence against consumption, and examined its effects on cycle dynamics by manipulating the evolutionary potential of the prey population. Single-clone algal cultures (lacking genetic variability) produced short cycle periods and typical quarter-period phase lags between prey and predator densities, whereas multi-clonal (genetically variable) algal cultures produced long cycles with prey and predator densities nearly out of phase, exactly as predicted. These results confirm that prey evolution can substantially alter predator-prey dynamics, and therefore that attempts to understand population oscillations in nature cannot neglect potential effects from ongoing rapid evolution.

Animals↗
PubMed1999

Molecular evolution of Bov-B LINEs in vertebrates.

Since their discovery in family Bovidae (bovids), Bov-B LINEs, believed to be order-specific SINEs, have been found in all ruminants and recently also in Viperidae snakes. The distribution and the evolutionary relationships of Bov-B LINEs provide an indication of their origin and evolutionary dynamics in different species. The evolutionary origin of Bov-B LINE elements has been shown unequivocally to be in Squamata (squamates). The horizontal transfer of Bov-B LINE elements in vertebrates has been confirmed by their discontinuous phylogenetic distribution in Squamata (Serpentes and two lizard infra-orders) as well as in Ruminantia, by the high level of nucleotide identity, and by their phylogenetic relationships. The direction of horizontal transfer from Squamata to the ancestor of Ruminantia is evident from the genetic distances and discontinuous phylogenetic distribution of Bov-B LINE elements. The ancestor of Colubroidea snakes has been recognized as a possible donor of Bov-B LINE elements to Ruminantia. The timing of horizontal transfer has been estimated from the distribution of Bov-B LINE elements in Ruminantia and the fossil data of Ruminantia to be 40-50 My ago. The phylogenetic relationships of Bov-B LINE elements from the various Squamata species agrees with that of the species phylogeny, suggesting that Bov-B LINE elements have been stably maintained by vertical transmission since the origin of Squamata in the Mesozoic era.

Animals↗
PubMed1999

Horizontal transfer of non-LTR retrotransposons in vertebrates.

Since their discovery in family Bovidae (bovids), Bov-B LINEs, believed to be order-specific SINEs, have been found in all ruminants and recently also in Viperidae snakes. The distribution and the evolutionary relationships of Bov-B LINEs provide an indication of their origin and evolutionary dynamics in different species. The evolutionary origin of Bov-B LINE elements has been shown unequivocally to be in Squamata (squamates). The horizontal transfer of Bov-B LINE elements in vertebrates has been confirmed by their discontinuous phylogenetic distribution in Squamata (Serpentes and two lizard infra-orders) as well as in Ruminantia, by the high level of nucleotide identity, and by their phylogenetic relationships. The direction of horizontal transfer from Squamata to the ancestor of Ruminantia is evident from the genetic distances and discontinuous phylogenetic distribution of Bov-B LINE elements. The ancestral snake lineage (Boidae) has been recognized as a possible donor of Bov-B LINE elements to Ruminantia. The timing of horizontal transfer has been estimated from the distribution of Bov-B LINE elements in Ruminantia and the fossil data of Ruminantia to be 40-50 mya. The phylogenetic relationships of Bov-B LINE elements from the various Squamata species agrees with that of the species phylogeny, suggesting that Bov-B LINE elements have been stably maintained by vertical transmission since the origin of Squamata in the Mesozoic era.

Animals↗
PubMed2006

A symmetry of fixation times in evoultionary dynamics.

In this paper, we show that for evolutionary dynamics between two types that can be described by a Moran process, the conditional fixation time of either type is the same irrespective of the selective scenario. With frequency dependent selection between two strategies A and B of an evolutionary game, regardless of whether A dominates B, A and B are best replies to themselves, or A and B are best replies to each other, the conditional fixation times of a single A and a single B mutant are identical. This does not hold for Wright-Fisher models, nor when the mutants start from multiple copies.

Animals↗
PubMed1989

[Evolution of Alu repeats: dynamics of distribution in genome].

A mathematical model of evolutionary dynamics of Alu repeats' number in the human genome has been worked out. The model permitted us to observe the dynamics of propagation of Alu repeats within the genome and to evaluate such important parameters of the process mentioned as the rates of transposition (insertion of new copies into the genome) and excision of repeats. The peculiarities of the control of Alu repeats' number in the genome have been discussed, based on the data obtained.

Genome, Human↗
PubMed2005

Acquired immunity and stochasticity in epidemic intervals impede the evolution of host disease resistance.

Disease can generate intense selection pressure on host populations, but here we show that acquired immunity in a population subject to repeated disease outbreaks can impede the evolution of genetic disease resistance by maintaining susceptible genotypes in the population. Interference between the life-history schedule of a species and periodicity of the disease has unintuitive effects on selection intensity, and stochasticity in outbreak period further reduces the rate of spread of disease-resistance alleles. A general age-structured population genetic model was developed and parameterized using empirical data for phocine distemper virus (PDV) epizootics in harbor seals. Scenarios with acquired immunity had lower levels of epizootic mortality compared with scenarios without acquired immunity for the first PDV outbreaks, but this pattern was reversed after about five disease cycles. Without acquired immunity, evolution of disease resistance was more rapid, and long-term population size variation is efficiently dampened. Acquired immunity has the potential to significantly influence rapid evolutionary dynamics of a host population in response to age-structured disease selection and to alter predicted selection intensities compared with epidemiological models that do not consider such feedback. This may have important implications for evolutionary population dynamics in a range of human, agricultural, and wildlife disease settings.

Aging↗
PubMed2025

The ecology and evolution of microbial immune systems: a look on the wild vibrio side.

Natural populations of vibrio beyond the well-studied pandemic strains of Vibrio cholerae, provide a powerful model for investigating the eco-evolutionary dynamics of microbial immune systems. Their genetic diversity, ecological versatility, ease of culturability and the availability of time-series data enable detailed studies of phage-host interactions in natural contexts. This review synthesizes recent advances in vibriophage research, highlighting key findings and emerging tools. High-throughput assays and genomic tools have offered new perspectives on phage specificity, host range and the evolutionary pressures shaping these interactions. Theoretical frameworks, such as arms race and fluctuating selection dynamics, are informed by empirical data from vibrio-phage systems, with time-series sampling providing crucial insights into their temporal and spatial dynamics. A major finding is the role of mobile genetic elements (MGEs) in encoding bacterial defence systems, which shape phage-host coevolution. Discoveries like the phage satellite PICMI illustrate how MGEs facilitate the transfer of antiviral systems, influencing ecological and evolutionary dynamics. The paradox of generalist vibriophages, rare despite their broad host ranges, is also explored. By integrating experimental approaches with field observations, vibriophage research advances microbial ecology and informs sustainable applications in aquaculture and phage therapy, reinforcing vibrios as a versatile model system.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.

Bacteriophages↗
PubMed1993

Chaos and the evolution of cooperation.

The "iterated prisoner's dilemma" is the most widely used model for the evolution of cooperation in biological societies. Here we show that a heterogeneous population consisting of simple strategies, whose behavior is totally specified by the outcome of the previous round, can lead to persistent periodic or highly irregular (chaotic) oscillations in the frequencies of the strategies and the overall level of cooperation. The levels of cooperation jump up and down in an apparently unpredictable fashion. Small recurrent and simultaneous invasion attempts (caused by mutation) can change the evolutionary dynamics from converging to an evolutionarily stable strategy to periodic oscillations and chaos. Evolution can be twisted away from defection, toward cooperation. Adding "generous tit-for-tat" greatly increases the overall level of cooperation and can lead to long periods of steady cooperation. Since May's paper [May, R. M. (1976) Nature (London) 261, 459-467], "simple mathematical models with very complicated dynamics" have been found in many biological applications, but here we provide an example of a biologically relevant evolutionary game whose dynamics display deterministic chaos. The simulations bear some resemblance to the irregular cycles displayed by the frequencies of host genotypes and specialized parasites in evolutionary "arms races" [Hamilton, W. D., Axelrod, R. & Tanese, R. (1990) Proc. Natl. Acad. Sci. USA 87, 3566-3573; Seger, J. (1988) Philos. Trans. R. Soc. London B 319, 541-555].

Biological Evolution↗
PubMed2000

Adaptive dynamics in diploid, sexual populations and the evolution of reproductive isolation.

Evolutionary branching is the process whereby an initially monomorphic population evolves to a point where it undergoes disruptive selection and splits up into two phenotypically diverging lineages. We studied evolutionary branching in three models that are ecologically identical but that have different genetic systems. The first model is clonal, the second is sexual diploid with additive genetics on a single locus and the third is like the second but with an additional locus for mate choice. Evolutionary branching occurred under exactly the same ecological circumstances in all three models. After branching the evolutionary dynamics may be qualitatively different. In particular, in the diploid, sexual models there can be multiple evolutionary outcomes whereas in the corresponding clonal model there is only one. We showed that evolutionary branching favours the evolution of (partial) assortative mating and that this in turn effectively restores the results from the clonal model by rendering the alternative outcomes unreachable except for the one that also occurs in the clonal model. The evolution of assortative mating during evolutionary branching can be interpreted as the initial phase of sympatric speciation with phenotypic divergence and partial reproductive isolation.

Adaptation, Physiological↗
PubMed1999

Evolutionary consequences of niche construction and their implications for ecology.

Organisms regularly modify local resource distributions, influencing both their ecosystems and the evolution of traits whose fitness depends on such alterable sources of natural selection in environments. We call these processes niche construction. We explore the evolutionary consequences of niche construction using a two-locus population genetic model, which extends earlier analyses by allowing resource distributions to be influenced both by niche construction and by independent processes of renewal and depletion. The analysis confirms that niche construction can be a potent evolutionary agent by generating selection that leads to the fixation of otherwise deleterious alleles, supporting stable polymorphisms where none are expected, eliminating what would otherwise be stable polymorphisms, and generating unusual evolutionary dynamics. Even small amounts of niche construction, or niche construction that only weakly affects resource dynamics, can significantly alter both ecological and evolutionary patterns.

Alleles↗
PubMed2005

Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus.

Infectious disease emergence is under the simultaneous influence of both genetic and ecological factors. Yet, we lack a general framework for linking ecological dynamics of infectious disease with underlying molecular and evolutionary change. As a model, we illustrate the linkage between ecological and evolutionary dynamics in rabies virus during its epidemic expansion into eastern and southern Ontario. We characterized the phylogeographic relationships among 83 isolates of fox rabies virus variant using nucleotide sequences from the glycoprotein-encoding glycoprotein gene. The fox rabies virus variant descended as an irregular wave with two arms invading from northern Ontario into southern Ontario over the 1980s and 1990s. Correlations between genetic and geographic distance suggest an isolation by distance population structure for the virus. The divergence among viral lineages since the most recent common ancestor correlates with position along the advancing wave front with more divergent lineages near the origin of the epidemic. Based on divergence from the most recent common ancestor, the regional population can be partitioned into two subpopulations, each corresponding to an arm of the advancing wave. Subpopulation A (southern Ontario) showed reduced isolation by distance relative to subpopulation B (eastern Ontario). The temporal dynamics of subpopulation A suggests that the subregional viral population may have undergone several smaller waves that reduced isolation by distance. The use of integrated approaches, such as the geographical analysis of sequence variants, coupled with information on spatial dynamics will become indispensable aids in understanding patterns of disease emergence.

Animals↗
PubMedDate not supplied

Evolution: an axiomatic perspective.

In this paper we present an axiomatic theory of evolution which is inspired by the reading of a paper written by G.V. Schiaparelli in 1898. Schiaparelli was a famous astronomer, but he also studied the Darwinian ideas. We propose five axioms which can characterize the theory of evolution. We have also written these axioms using the language of the logic of predicates of first order with some constant monadic and dyadic predicates and appropriate functionals. But we can use other types of logic. So we can examine the concepts of species and of speciation. Then we introduce the interesting notion of generation distance. Moreover we give a theorem which establishes a geometrical model of our theory. If we analyze further the fourth axiom (which concerns the notion of generation distance) we can propose an elementary dynamical model by which we can represent possible evolutionary dynamics. These dynamics partially depend on random quantities.

Algorithms↗
PubMed2002

Evolution of cannibalistic traits: scenarios derived from adaptive dynamics.

The evolution of cannibalistic traits in consumer populations is studied in this paper with the approach of adaptive dynamics theory. The model is kept at its minimum complexity by eliminating some environmental characteristics, like heterogeneity and seasonalities, and by hiding the size-structure of the population. Evolutionary dynamics are identified through numerical bifurcation analysis, applied both to the ecological (resident-mutant) model and to the canonical equation of adaptive dynamics. The result is a rich catalog of evolutionary scenarios involving evolutionary stable strategies and branching points both in the monomorphic and dimorphic dynamics. The possibility of evolutionary extinction of highly cannibalistic populations is also ascertained. This allows one to explain why cannibalism can be a transient stage of evolution.

Adaptation, Physiological↗
PubMed2001

A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera:Papilionidae).

Although it is widely agreed that data from multiple sources are necessary to confidently resolve phylogenetic relationships, procedures for accommodating and incorporating heterogeneity in such data remain underdeveloped. We explored the use of partitioned, model-based analyses of heterogeneous molecular data in the context of a phylogenetic study of swallowtail butterflies (Lepidoptera: Papilionidae). Despite substantial basic and applied study, phylogenetic relationships among the major lineages of this prominent group remain contentious. We sequenced 3.3 kb of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidase I and II and 1.0 kb of elongation factor-1 alpha, respectively) from 22 swallowtails, including representatives of Baroniinae, Parnassiinae, and Papilioninae, and from several moth and butterfly outgroups. Using parsimony, we encountered considerable difficulty in resolving the deepest splits among these taxa. We therefore chose two outgroups with undisputed relationships to each other and to Papilionidae and undertook detailed likelihood analyses of alternative topologies. Following from previous studies that have demonstrated substantial heterogeneity in the evolutionary dynamics among process partitions of these genes, we estimated evolutionary parameters separately for gene-based and codon-based partitions. These values were then used as the basis for examining the likelihoods of possible resolutions and rootings under several partitioned and unpartitioned likelihood models. Partitioned models gave markedly better fits to the data than did unpartitioned models and supported different topologies. However, the most likely topology varied from model to model. The most likely ingroup topology under the best-fitting, six-partition GTR + gamma model favors a paraphyletic Parnassiinae. However, when examining the likelihoods of alternative rootings of this tree relative to rootings of the classical hypothesis, two rootings of the latter emerge as most likely. Of these two, the most likely rooting is within the Papilioninae, although a rooting between Baronia and the remaining Papilionidae is only nonsignificantly less likely.

Animals↗
PubMed2001

Lessons from the past: evolutionary impacts of mass extinctions.

Mass extinctions have played many evolutionary roles, involving differential survivorship or selectivity of taxa and traits, the disruption or preservation of evolutionary trends and ecosystem organization, and the promotion of taxonomic and morphological diversifications-often along unexpected trajectories-after the destruction or marginalization of once-dominant clades. The fossil record suggests that survivorship during mass extinctions is not strictly random, but it often fails to coincide with factors promoting survival during times of low extinction intensity. Although of very serious concern, present-day extinctions have not yet achieved the intensities seen in the Big Five mass extinctions of the geologic past, which each removed > or =50% of the subset of relatively abundant marine invertebrate genera. The best comparisons for predictive purposes therefore will involve factors such as differential extinction intensities among regions, clades, and functional groups, rules governing postextinction biotic interchanges and evolutionary dynamics, and analyses of the factors that cause taxa and evolutionary trends to continue unabated, to suffer setbacks but resume along the same trajectory, to survive only to fall into a marginal role or disappear ("dead clade walking"), or to undergo a burst of diversification. These issues need to be addressed in a spatially explicit framework, because the fossil record suggests regional differences in postextinction diversification dynamics and biotic interchanges. Postextinction diversifications lag far behind the initial taxonomic and morphological impoverishment and homogenization; they do not simply reoccupy vacated adaptive peaks, but explore opportunities as opened and constrained by intrinsic biotic factors and the ecological and evolutionary context of the radiation.

Animals↗
PubMed2006

Phanerozoic marine biodiversity dynamics in light of the incompleteness of the fossil record.

Long-term evolutionary dynamics have been approached through quantitative analysis of the fossil record, but without explicitly taking its incompleteness into account. Here we explore the temporal covariance structure of per-genus origination and extinction rates for global marine fossil genera throughout the Phanerozoic, both before and after corrections for the incompleteness of the fossil record. Using uncorrected data based on Sepkoski's compendium, we find significant autocovariance within origination and extinction rates, as well as covariance between extinction and origination, not one, but two, intervals later, corroborating evidence for the unexplained temporal gap found by past studies. However, these effects vanish when the data are corrected for the incompleteness of the fossil record. Instead, we observe significant covariance only between extinction and origination in the immediately following intervals. The gap in the response of the biosphere to extinction in the uncorrected fossil record thus appears to be an artifact of the incompleteness of the fossil record, specifically due to episodic variation in the probability that taxa will be preserved, on time scales comparable to the temporal resolution of Sepkoski's data. Our results also indicate that at that temporal resolution (the stage/substage of duration approximately = 5 million years), changes in origination and extinction do not persist for longer than one interval, except that elevated origination rates immediately after extinction may last for more than a single interval. Thus, although certain individual cases may deviate from the overall pattern, we find that in general the biosphere's response to perturbation is immediate geologically and usually short-lived.

Animals↗
PubMed2006

Stochastic dynamics of invasion and fixation.

We study evolutionary game dynamics in finite populations. We analyze an evolutionary process, which we call pairwise comparison, for which we adopt the ubiquitous Fermi distribution function from statistical mechanics. The inverse temperature in this process controls the intensity of selection, leading to a unified framework for evolutionary dynamics at all intensities of selection, from random drift to imitation dynamics. We derive a simple closed formula that determines the feasibility of cooperation in finite populations, whenever cooperation is modeled in terms of any symmetric two-person game. In contrast with previous results, the present formula is valid at all intensities of selection and for any initial condition. We investigate the evolutionary dynamics of cooperators in finite populations, and study the interplay between intensity of selection and the remnants of interior fixed points in infinite populations, as a function of a given initial number of cooperators, showing how this interplay strongly affects the approach to fixation of a given trait in finite populations, leading to counterintuitive results at different intensities of selection.

Animals↗