Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria.

Selection of mutator alleles, increasing the mutation rate up to 10, 000-fold, has been observed during in vitro experimental evolution. This spread is ascribed to the hitchhiking of mutator alleles with favorable mutations, as demonstrated by a theoretical model using selective parameters corresponding to such experiments. Observations of unexpectedly high frequencies of mutators in natural isolates suggest that the same phenomenon could occur in the wild. But it remains questionable whether realistic in natura parameter values could also result in selection of mutators. In particular, the main parameters of adaptation, the size of the adapting population and the height and steepness of the adaptive peak characterizing adaptation, are very variable in nature. By simulation approach, we studied the effect of these parameters on the selection of mutators in asexual populations, assuming additive fitness. We show that the larger the population size, the more likely the fixation of mutator alleles. At a large population size, at least four adaptive mutations are needed for mutator fixation; moreover, under stronger selection stronger mutators are selected. We propose a model based on multiple mutations to illustrate how second-order selection can optimize population fitness when few favorable mutations are required for adaptation.

Effects of colonization processes on genetic diversity: differences between annual plants and tree species.

Tree species are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than trees. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for trees. This explanation is problematic because it relies on equilibrium hypotheses. Because trees have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest trees, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of trees are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in trees and annual species by much less diversity and much more differentiation than nuclear genes.

Organization and expression of the mitochondrial genome in the Nicotiana sylvestris CMSII mutant.

Previous analyses suggested that the Nicotiana sylvestris CMSII mutant carried a large deletion in its mitochondrial genome. Here, we show by cosmid mapping that the deletion is 60 kb in length and contains several mitochondrial genes or ORFs, including the complex I nad7 gene. However, due to the presence of large duplications in the progenitor mitochondrial genome, the only unique gene that appears to be deleted is nad7. RNA gel blot data confirm the absence of nad7 expression, strongly suggesting that the molecular basis for the CMSII abnormal phenotype, poor growth and male sterility, is the altered complex I structure. The CMSII mitochondrial genome appears to consist essentially of one of two subgenomes resulting from recombination between direct short repeats. In the progenitor mitochondrial genome both recombination products are detected by PCR and, reciprocally, the parental fragments are detected at the substoichiometric level in the mutant. The CMSII mtDNA organization has been maintained through six sexual generations.

Dynamics of plant mitochondrial genome: model of a three-level selection process.

The plant mitochondrial genome is composed of a set of molecules of various sizes that generate each other through recombination between repeated sequences. Molecular observations indicate that these different molecules are present in an equilibrium state. Different compositions of molecules have been observed within species. Recombination could produce deleted molecules with a high replication rate but bearing little useful information for the cell (such as "petite" mutants in yeast). In this paper we use a multilevel model to examine selection among rapidly replicating incomplete molecules and relatively slowly replicating complete molecules. Our model simulates the evolution of mitochondrial information through a three-level selection process including intermolecular, intermitochondrial, and intercellular selection. The model demonstrates that maintenance of the mitochondrial genome can result from multilevel selection, but maintenance is difficult to explain without the existence of selection at the intermitochondrial level. This study shows that compartmentation into mitochondria is useful for maintenance of the mitochondrial information. Our examination of evolutionary equilibria shows that different equilibria (with different combinations of molecules) can be obtained when recombination rates are lower than a threshold value. This may be interpreted as a drift-mutation balance.

From metabolism to polymorphism in bacterial populations: a theoretical study.

Stable polymorphisms are commonly observed in experimental bacterial populations grown in homogeneous media. Evidence is accumulating that metabolic interactions might be the main mechanism underlying the emergence and maintenance of such polymorphisms. To date, however, attempts to model the evolution of bacterial polymorphism have not considered metabolism as a possible component of polymorphism maintenance. Here, we propose a simulation approach to model the evolution of selected polymorphisms in a bacterial population. Using recent knowledge of the relationship between bacterial fitness and metabolism, we build a simple metabolic model and test the effect of resource competition on polymorphism. Without making an a priori hypothesis on fitness functions, we show that stable polymorphic situations could be observed under high nutrient competition, and we propose a functional, metabolism-based explanation to the debated issue of polymorphism maintenance.

A Morphogenetic Model Accounting for Pollen Aperture Pattern in Flowering Plants.

Pollen grains are embeddded in an extremely resistant wall. Apertures are well defined places where the pollen wall is reduced or absent that permit pollen tube germination. Pollen grains are produced by meiosis and aperture number definition appears to be linked with the partition that follows meiosis and leads to the formation of a tetrad of four haploid microspores. In dicotyledonous plants, meiosis is simultaneous which means that cytokinesis occurs once the two nuclear divisions are completed. A syncitium with the four nuclei stemming from meiosis is formed and cytokinesis isolates simulataneously the four products of meiosis. We propose a theoretical morphogenetic model which takes into account part of the features of the ontogeny of the pollen grains. The nuclei are considered as attractors acting upon a morphogenetic substance distributed within the cytoplasm of the dividing cell. This leads to a partition of the volume of the cell in four domains that is similar to the observations of cytokinesis in the studied species. The most widespread pattern of aperture distribution in dicotyledonous plants (three apertures equidistributed on the pollen grain equator) can be explained by bipolar interactions between nuclei stemming from the second meiotic division, and observed variations on these patterns by disturbances of these interactions. In numerous plant species, several pollen grains differing in aperture number are produced by a single individual. The distribution of the different morphs within tetrads indicates that the four daughter cells can have different aperture number. The model provides an explanation for the duplication of one of the apertures of a three-aperture pollen grain leading to a four-aperture one and in parallel it gives an explanation for how heterogeneous tetrads can be formed.Copyright 1998 Academic Press

Dispersal and metapopulation viability in a heterogeneous landscape

Conditions of persistence or extinction of a metapopulation of a colonizing annual species are studied in a heterogeneous landscape, a mixture of two elementary landscapes. An elementary landscape is a landscape whose age-structure is described by only one transition matrix, giving the probability for a site to be disturbed, or to follow the process of succession. We first provide an analytical study of the range of dispersal rates that allow metapopulation persistence in an elementary landscape. Second, conditions for metapopulation persistence in a heterogeneous landscape are derived from results obtained in each elementary landscape. Three cases are distinguished. If the two ranges of dispersal rates defined in each elementary landscape overlap, the metapopulation persists in any mixture of the elementary landscapes. If these two dispersal rates ranges are non-overlapping, either the metapopulation goes extinct for some values of the proportion of the elementary landscapes, or two discontinuous ranges of dispersal rates allow the metapopulation persistence. The consequences of these results are discussed in terms of landscape management. In particular, it is shown that under some conditions, a rapid change in environment (from one elementary landscape to another one) might less often lead to metapopulation extinction than a slower change. Copyright 1999 Academic Press.

Phenotypic variation in Galerida larks in Morocco: the role of history and natural selection.

The relative influences of history, natural selection and hybridization in shaping phenotypic variation in closely related taxa is a crucial issue in current evolutionary biology. In this study, we used as a model two sibling but paradoxically highly variable species of larks (Galerida theklae and Galerida cristata) of Morocco to separate the impacts of these evolutionary forces. In the former species, variation is manifested mainly in colouration, while in the latter, variation also encompasses bill size and shape. Mitochondrial and nuclear DNA sequencing were used to identify the historical relationships among the subspecies and species. According to our analyses, G. cristata and G. theklae diverged about 3.7 million years ago (Ma), and we found no evidence for a role of hybridization in maintaining their similarity. In G. theklae, there was no further subdivision, while in G. cristata two major mtDNA groups were identified (divergence approximately 1.1 Ma). These two lineages are parapatric and regroup, respectively, the three short-billed subspecies [G. (cristata) cristata] and the two long-billed subspecies [G. (cristata) randonii]. Patterns of morphological variation were then contrasted to this pattern of neutral relationships: we found that G. (c.) cristata was morphologically more similar to G. theklae than to G. (c.) randonii. Overall, these results point towards the prominent role of (i) natural selection and/or phenotypic plasticity in adapting the plumage to local conditions and (ii) natural selection in combination with historical isolation in driving the divergence in size and bill morphology in the crested larks.

The evolutionary dynamics of selfish replicators: a two-level selection model.

The aim of the present paper is to study the evolutionary dynamics of selfish replicators in a constant genetic background. Selfish replicators are viewed as alleles at a single locus, having a pleiotropic effect. Infinitely many alleles are possible; they act on individual fitness and have various levels of ability to distort segregation. This results in a two-level process of selection, including inter-individual selection (effect on individual fitness) and intra-individual selection (ability to distort segregation). The model takes other parameters into account, such as dominance, inbreeding and inbreeding depression. The system can have two different behaviours. (1) In some cases, evolutionary cycles are possible. The cycles correspond to an alternation of phases with predominant inter-individual selection, corresponding to major-effect mutations, and phases with predominant intra-individual selection, corresponding to small-effect mutations. (2) For other values of the parameters, a synthetic fitness can be defined: this absolute allelic fitness is estimated as a function of one's fitness due to both inter-individual and intra-individual selection. During the course of evolution, the synthetic fitness increases. The optimisation of a synthetic fitness is the most general process. The optimised value is essentially homologous to the value optimised for resource allocation to male and female function in hermaphrodites (female function being homologous to the effect on individual fitness, and male function being homologous to distortion ability). The relative importance of both behaviours is discussed. It is argued that repeated sequences causing some human degenerative hereditary diseases may follow a two-step evolutionary process: a progressive increase in number of sequences accompanied by a decrease of the individual fitness would be followed by massive elimination of such sequences. But in general the optimisation of the synthetic fitness seems to be more likely.

Evolution of the plant mitochondrial genome: dynamics of duplication and deletion of sequences.

Several descriptive models have been proposed to explain the occurrence of deletion-duplication events in the plant mitochondrial genome. In order to investigate the dynamics of these events, we have simulated them using a computer model. The simulation shows that whatever the recombination rates between repeats, if a mitochondrial sequence becomes unnecessary for the proper function of mitochondria, this sequence can be deleted and another sequence can be duplicated in consequence. Furthermore, the model shows that the organization of the sequences with respect to the origin of replication has a great influence over the dynamics of the deletion-duplication events.

Molecular evolution of plant haemoglobin: two haemoglobin genes in Nymphaeaceae Euryale ferox.

We isolated and sequenced two haemoglobin genes from the early-branching angiosperm Euryale ferox (Nymphaeaceae). The two genes belong to the two known classes of plant haemoglobin. Their existence in Nymphaeaceae supports the theory that class 1 haemoglobin was ancestrally present in all angiosperms, and is evidence for class 2 haemoglobin being widely distributed. These sequences allowed us to unambiguously root the angiosperm haemoglobin phylogeny, and to corroborate the hypothesis that the class 1/class 2 duplication event occurred before the divergence between monocots and eudicots. We addressed the molecular evolution of plant haemoglobin by comparing the synonymous and nonsynonymous substitution rates in various groups of genes. Class 2 haemoglobin genes of legumes (functionally involved in a symbiosis with nitrogen-fixing bacteria) show a higher nonsynonymous substitution rate than class 1 (nonsymbiotic) haemoglobin genes. This suggests that a change in the selective forces applying to plant haemoglobins has occurred during the evolutionary history of this gene family, potentially in relation with the evolution of symbiosis.

Genome size, fluorochrome banding, and karyotype evolution in some Hypochoeris species.

Four South American and two European species of Hypochoeris (Asteraceae) were studied using fluorochrome banding, and genome size was determined by flow cytometry, in order to obtain information about microevolution in this genus and about its primary origin. Fluorochrome banding patterns showed GC-rich repeated sequences, particularly around the nucleolar organizer regions. Few differences appeared among the South American species. Nevertheless, determination of nuclear DNA content and base composition revealed significant differences among these species. The phylogenetic position of Hypochoeris robertia, which has the smallest DNA content, is discussed with regard to chromosome evolution in this genus.

Reducing the genome size of organelles favours gene transfer to the nucleus.

Endosymbiotic organelles exhibit strong genetic erosion during their evolution as a result of the loss of unnecessary genes and of gene transfer to the nucleus. The reasons for this erosion are much debated. Unidirectionality of DNA exchange between cell compartments could favour biased gene transfer, but selection might also act to favour nuclear localization of genes, for example, because organelles accumulate more mutations than do nuclei. Selection for rapid replication might be a general cause of organelle genome reduction. This selection also accounts for the compactness of organelle genomes.

A model for the evolution of high frequencies of males in an androdioecious plant based on a cross-compatibility advantage of males.

Lloyd's (1975) and Charlesworth & Charlesworth's (1978) phenotypic selection models for the maintenance of androdioecy predict that males (female-sterile individuals) must have an advantage in fertility (K) of at least two in order to invade a hermaphroditic population, and that their equilibrium frequency (x(eq)=(K - 2)/2(K - 1)) is always less than 0.5. In this paper, we develop a model in which male fertility is frequency-dependent, a situation not investigated in the previous models, to explore the conditions under which a high frequency of males (i.e. more than 50%) could be maintained at equilibrium. We demonstrate that a gametophytic self-incompatibility (GSI) locus linked to a nuclear sex determination locus can favour rare alleles through male function, by causing frequency-dependent selection. Thus, the spread of a female-sterility allele in a hermaphroditic population may be induced. In contrast with the previous models, our model can explain male frequencies greater than 50% in a functionally androdioecious species, as long as there is (i) dominance of female-sterility at the sex locus, and (ii) a few alleles at the self-incompatibility locus, even if the advantage in fertility of male phenotype is lower than two.

A model for antagonistic pleiotropic gene action for mortality and advanced age.

Association or linkage studies involving control and long-lived populations provide information on genes that influence longevity. However, the relationship between allele-specific differences in survival and the genetic structure of aging cohorts remains unclear. We model a heterogeneous cohort comprising several genotypes differing in age-specific mortality. In its most general form, without any specific assumption regarding the shape of mortality curves, the model permits derivation of a fundamental property underlying abrupt age-related changes in the composition of a cohort. The model is applied to sex-specific survival curves taken from period life tables, and Gompertz-Makeham mortality coefficients are calculated for the French population. Then, adjustments are performed under Gompertz-Makeham mortality functions for three genotypes composing a heterogeneous cohort, under the constraint of fitting the resultant mortality to the real French population mortality obtained from life tables. Multimodal curves and divergence after the 8th decade appear as recurrent features of the frequency trajectories. Finally, a fit to data previously obtained at the angiotensin-converting-enzyme locus is realized, explaining what had seemed to be paradoxical results-namely, that the frequency of a genotype known as a cardiovascular risk factor was increased in centenarians. Our results help explain the well-documented departure from Gompertz-Makeham mortality kinetics at older ages. The implications of our model are discussed in the context of known genetic effects on human longevity and age-related pathologies. Since antagonistic pleiotropy between early and late survival emerges as a general rule, extrapolating the effects measured for a gene in a particular age class to other ages could be misleading.

A method to determine the mean pollen dispersal of individual plants growing within a large pollen source.

Pollen dispersal has been recently focused on as a major issue in the risk assessment of transgenic crop plants. The shape of the pollen dispersal of individual plants is hard to determine since a very large number of plants must be monitored in order to track rare longdistance dispersal events. Conversely, studies using large plots as a pollen source provide a pollen distribution that depends on the shape of the source plot. We report here on a method based on the use of Fourier transforms by which the pollen dispersal of a single, average individual can be obtained from data using large plots as pollen sources, thus allowing the estimation of the probability of long-distance dispersal for single plants. This method is subsequently implemented on simulated data to test its susceptibility to random noise and edge effects. Its conditions of application and value for use in ecological studies, in particular risk assessment of the deliberate release of transgenic plants, are discussed.

Mutators and sex in bacteria: conflict between adaptive strategies.

Bacterial mutation rates can increase and produce genetic novelty, as shown by in vitro and in silico experiments. Despite the cost due to a heavy deleterious mutation load, mutator alleles, which increase the mutation rate, can spread in asexual populations during adaptation because they remain associated with the rare favorable mutations they generate. This indirect selection for a genetic system generating diversity (second-order selection) is expected to be highly sensitive to changes in the dynamics of adaptation. Here we show by a simulation approach that even rare genetic exchanges, such as bacterial conjugation or transformation, can dramatically reduce the selection of mutators. Moreover, drift or competition between the processes of mutation and recombination in the course of adaptation reveal how second-order selection is unable to optimize the rate of generation of novelty.

Heterochromatin study demonstrating the non-linearity of fluorometry useful for calculating genomic base composition.

A novel procedure for calculating base-pair frequencies in whole genomes is reported. This has been developed during a study of the role of heterochromatin in microevolution. Closely related species of the Crepis praemorsa complex have similar karyotypes but for their heterochromatin. The changes in relative AT frequency between species have been attributed to heterochromatin sequences by in situ banding of chromosomes with two base-specific fluorochromes. The absolute genome size of species, measured by cytofluorometry, correlated positively with increased karyotypic heterochromatin, as did the proportion of AT bases in the DNA. However, the determination of base content has called for a curvilinear interpretation of data obtained with two base-specific fluorochromes (bisbenzimide Hoechst 33342 and mithramycin), in contrast to the commonly assumed but erroneous direct relationship between fluorescence intensity and base content. Essentially, the fluorochromes' requirements for a sequence of certain base-pairs lead to the notion of Coefficients of Overspecificity: the result is a simple formula for calculating the AT proportion in a genome relative to a reference species from cytometric data, taking account of ligand binding statistics. These statistics and probabilities of oligonucleotide binding are essentially the same.

Role of mutator alleles in adaptive evolution.

Because most newly arising mutations are neutral or deleterious, it has been argued that the mutation rate has evolved to be as low as possible, limited only by the cost of error-avoidance and error-correction mechanisms. But up to one per cent of natural bacterial isolates are 'mutator' clones that have high mutation rates. We consider here whether high mutation rates might play an important role in adaptive evolution. Models of large, asexual, clonal populations adapting to a new environment show that strong mutator genes (such as those that increase mutation rates by 1,000-fold) can accelerate adaptation, even if the mutator gene remains at a very low frequency (for example, 10[-5]). Less potent mutators (10 to 100-fold increase) can become fixed in a fraction of finite populations. The parameters of the model have been set to values typical for Escherichia coli cultures, which behave in a manner similar to the model in long-term adaptation experiments.