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Macroevolution simulated with autonomously replicating computer programs.

The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. The evolutionary outcome of selection acting on novel variation arising over long periods is therefore difficult to predict. The classical problem of this kind is whether 'replaying the tape of life' would invariably lead to the familiar organisms of the modern biota. Here we study the long-term behaviour of populations of autonomously replicating computer programs and find that the same type, introduced into the same simple environment, evolves on any given occasion along a unique trajectory towards one of many well-adapted end points.

Adaptation, Biological↗
PubMed2004

Organization of genetic variation in individuals of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal (AM) fungi (Glomeromycota) are thought to be the oldest group of asexual multicellular organisms. They colonize the roots of most land plants, where they facilitate mineral uptake from the soil in exchange for plant-assimilated carbon. Cells of AM fungi contain hundreds of nuclei. Unusual polymorphism of ribosomal DNA observed in individual spores of AM fungi inspired a hypothesis that heterokaryosis--that is, the coexistence of many dissimilar nuclei in cells--occurs throughout the AM fungal life history. Here we report a genetic approach to test the hypothesis of heterokaryosis in AM fungi. Our study of the transmission of polymorphic genetic markers in natural isolates of Glomus etunicatum, coupled with direct amplification of rDNA from microdissected nuclei by polymerase chain reaction, supports the alternative hypothesis of homokaryosis, in which nuclei populating AM fungal individuals are genetically uniform. Intrasporal rDNA polymorphism contained in each nucleus signals a relaxation of concerted evolution, a recombination-driven process that is responsible for homogenizing rDNA repeats. Polyploid organization of glomeromycotan genomes could accommodate intranuclear rDNA polymorphism and buffer these apparently asexual organisms against the effects of accumulating mutations.

Cell Nucleus↗
PubMed2006

Interference among deleterious mutations favours sex and recombination in finite populations.

Sex and recombination are widespread, but explaining these phenomena has been one of the most difficult problems in evolutionary biology. Recombination is advantageous when different individuals in a population carry different advantageous alleles. By bringing together advantageous alleles onto the same chromosome, recombination speeds up the process of adaptation and opposes the fixation of harmful mutations by means of Muller's ratchet. Nevertheless, adaptive substitutions favour sex and recombination only if the rate of adaptive mutation is high, and Muller's ratchet operates only in small or asexual populations. Here, by tracking the fate of modifier alleles that alter the frequency of sex and recombination, we show that background selection against deleterious mutant alleles provides a stochastic advantage to sex and recombination that increases with population size. The advantage arises because, with low levels of recombination, selection at other loci severely reduces the effective population size and genetic variance in fitness at a focal locus (the Hill-Robertson effect), making a population less able to respond to selection and to rid itself of deleterious mutations. Sex and recombination reveal the hidden genetic variance in fitness by combining chromosomes of intermediate fitness to create chromosomes that are relatively free of (or are loaded with) deleterious mutations. This increase in genetic variance within finite populations improves the response to selection and generates a substantial advantage to sex and recombination that is fairly insensitive to the form of epistatic interactions between deleterious alleles. The mechanism supported by our results offers a robust and broadly applicable explanation for the evolutionary advantage of recombination and can explain the spread of costly sex.

Alleles↗
PubMed2002

Playing for half the deck: the molecular biology of meiosis.

Meiosis reduces the number of chromosomes carried by a diploid organism by half, partitioning precisely one haploid genome into each gamete. The basic events of meiosis reflect three meiosis-specific processes: first, pairing and synapsis of homologous chromosomes; second, high-frequency, precisely controlled, reciprocal crossover; third, the regulation of sister-chromatid cohesion (SCC), such that during anaphase I, SCC is released along the chromosome arms, but not at the centromeres. The failure of any of these processes can result in aneuploidy or a failure of meiotic segregation.

Animals↗
PubMed2002

T helper 1-type immunity to trophoblast antigens in women with a history of recurrent pregnancy loss is associated with polymorphism of the IL1B promoter region.

Recurrent pregnancy loss (RPL) is a common disorder during early gestation. Recent evidence suggests that T helper 1 (Th1)-type immunity is associated with unsuccessful pregnancy especially in women with RPL of otherwise unknown etiology, while Th2-type immunity is associated with pregnancy success. Interleukin (IL)-1 may influence Th1/Th2 immune responsiveness and has been implicated in the establishment of successful pregnancy. In the present study, we investigated polymorphism of the IL-1beta gene (IL1B) in women with a history of RPL. Significant increases in the frequencies of IL1B promoter region variants IL1-511C and IL1B-31T were found in women with a history of RPL. Increased frequencies of these two variants and their homozygotes were found only in cases having evidence of Th1 immunity to trophoblast as determined by IFN-gamma production of peripheral blood mononuclear cells (PBMCs) stimulated with a trophoblast cell-line extract. Significantly higher IFN-gamma production by PBMCs in response to trophoblast correlated with variant IL1B-511C and its homozygocity in women with RPL. These results suggest that variants -511C and -31T in the IL1B promoter region confer risk for RPL associated with Th1 immunity to trophoblast antigens.

Abortion, Habitual↗
PubMed2002

Ontogenetic reaction norm for binary traits: the timing of phallus development in the snail Bulinus truncatus.

The ontogenetic trajectory of plastic binary traits may provide valuable insights into their evolutionary rate of change. In this paper, the timing of the plastic response of a temperature-dependent sexual polymorphism, aphally, is investigated in the freshwater snail Bulinus truncatus. Aphally is defined as the loss of the male copulatory organ in otherwise hermaphroditic animals. Individuals from two inbred lines were switched at various times during their early development between 25 and 30 degrees C, and their phally status ascertained, in order to evaluate the parameters characterising the ontogenetic reaction norm of aphally to temperature. A series of nested models including parameters for the onset, offset, and the intensity of the response to temperature were fitted to the data, allowing for a wide range of reaction norms. One genotype did not show any variation in aphally ratio with switching temperature, while a switch-point model (onset and offset corresponding to the same developmental point in time) best fitted the second genotype. The results suggest that the plasticity of aphally is expressed before eggs hatch. Their consequences on the evolution of aphally are discussed. More generally, the methodology proposed here can be used to analyse variation in ontogenetic parameters of discrete traits.

Animals↗
PubMed2002

Infection polymorphism and cytoplasmic incompatibility in Hymenoptera-Wolbachia associations.

Most cases of Wolbachia infection so far documented in haplodiploid Hymenoptera are associated with parthenogenesis induction. Only three examples of Wolbachia-mediated cytoplasmic incompatibility (CI) have been reported, resulting either in haploidisation of fertilised eggs, which develop into viable males, or in their death. To better document this variability, we studied two new Wolbachia-wasp associations involving Drosophila parasitoids. In Trichopria cf. drosophilae, individuals are infected by two different Wolbachia variants, populations are nearly totally infected, and Wolbachia induces incomplete CI resulting in death of the fertilised eggs. On the other hand, Pachycrepoideus dubius harbours only one bacterial variant, populations are polymorphic for infection, and Wolbachia has no detectable effect. These two cases show that the range of variation in Wolbachia's effects in Hymenoptera is as wide as in diploids, extending from complete CI to an undetectable effect. Cases so far studied show some parallel between the strength of incompatibility, the number of Wolbachia variants infecting each wasp, and the natural infection frequency. These empirical data support theoretical models predicting evolution of CI towards lower levels, resulting in the decline and ultimate loss of infection, and place multiple infections as being an important factor in the evolution of host-Wolbachia associations.

Animals↗
PubMed2003

Evidence for rare recombination at the gametophytic self-incompatibility locus.

The gametophytic self-incompatibility locus has been thought to be a nonrecombining genomic region. Inferences have been made, however, about the functional importance of different parts of the S-locus, based on differences in the levels of variability along the gene, and this is valid only if recombination occurs. It is thus important to test whether recombination occurs within and near the S-locus. Several recent attempts to test this have reached conflicting conclusions. In this study, we examine a large data set on sequence variation at the S-locus in several species with gametophytic self-incompatibility systems, in the Solanaceae, Rosaceae and Scrophulariaceae. We use the longest sequences available to test for recombination based on linkage disequilibrium between polymorphic sites in the S-locus. The relationship between linkage disequilibrium and physical distance between the sites suggests rare intragenic exchange in the evolutionary history of four species of Solanaceae and two species of Rosaceae.

Alleles↗
PubMed2004

Multiple CMS-restorer gene polymorphism in gynodioecious Plantago coronopus.

The mode of inheritance of the male sterility trait is crucial for understanding the evolutionary dynamics of the sexual system gynodioecy, which is the co-occurrence of female and hermaphrodite plants in natural populations. Both cytoplasmic (CMS) and nuclear (restorer) genes are known to be involved. Theoretical models usually assume a limited number of CMS genes with each a single restorer gene, while reality is more complex. In this study, it is shown that in the gynodioecious species Plantago coronopus two new CMS-restorer polymorphisms exist in addition to the two that were already known, which means four CMS-restorer systems at the species level. Furthermore, three CMS types were shown to co-occur within a single population. All new CMS types showed a multilocus system for male fertility restoration, in which both recessive and dominant restorer alleles occur. Our finding of more than two co-occurring CMS-restorer systems each with multiple restorer genes raises the question how this complex of male sterility systems is maintained in natural populations.

Crosses, Genetic↗
PubMed2006

The conversion of variance and the evolutionary potential of restricted recombination.

Genetic recombination is usually considered to facilitate adaptive evolution. However, recombination prevents the reliable cotransmission of interacting gene combinations and can disrupt complexes of coadapted genes. If interactions between genes have important fitness effects, restricted recombination may lead to evolutionary responses that are different from those predicted from a purely additive model and could even aid adaptation. Theory and data have demonstrated that phenomena that limit the effectiveness of recombination via increasing homozygosity, such as inbreeding and population subdivision and bottlenecks, can temporarily increase the additive genetic variance available to these populations. This effect has been attributed to the conversion of nonadditive to additive genetic variance. Analogously, phenomena such as chromosomal inversions and apomictic parthenogenesis that physically restrict recombination in part or all of the genome may also result in a release of additive variance. Here, we review and synthesize literature concerning the evolutionary potential of populations with effectively or physically restricted recombination. Our goal is to emphasize the common theme of increased short-term access to additive genetic variance in all of these situations and to motivate research directed towards a more complete characterization of the relevance of the conversion of variance to the evolutionary process.

Animals↗
PubMed2006

The genetic analysis of family structured inbreeding depression studies.

An important question emerging from theoretical studies of mating system evolution is whether the fitness of a randomly extracted, fully inbred genotype will exceed the mean of outbred individuals. We introduce two statistics (I(1) and I(2)) related to the probability of extracting a high line. I(1) and I(2) can be estimated from the family structured experimental designs typically used to estimate inbreeding depression (ID). Maximum likelihood procedures are developed from an explicit genetic model. These yield parameter estimates and provide the likelihoods necessary to test hypotheses, for example, whether population-level ID is nonzero. Finally, we describe a new publicly available computer program titled 'IDG' (Inbreeding Depression Genetics) to execute these procedures.

Analysis of Variance↗
PubMed2006

Effects of intra-gene fitness interactions on the benefit of sexual recombination.

Whereas spontaneous point mutation operates on nucleotides individually, sexual recombination manipulates the set of nucleotides within an allele as an essentially particulate unit. In principle, these two different scales of variation enable selection to follow fitness gradients in two different spaces: in nucleotide sequence space and allele sequence space respectively. Epistasis for fitness at these two scales, between nucleotides and between genes, may be qualitatively different and may significantly influence the advantage of mutation-based and recombination-based evolutionary trajectories respectively. We examine scenarios where the genetic sequence within a gene strongly influences the fitness effect of a mutation in that gene, whereas epistatic interactions between sites in different genes are weak or absent. We find that, in cases where beneficial alleles of a gene differ from one another at several nucleotide sites, sexual populations can exhibit enormous benefit compared with asexual populations: not only discovering fit genotypes faster than asexual populations, but also discovering high-fitness genotypes that are effectively not evolvable in asexual populations.

Animals↗