Molecular evolution and polymorphism in a random environment

A model of multi-allelic selection in a random environment, the SAS-CFF model, is examined for compatability with allele frequency and genetic distance data acquired by electrophoresis. The symmetric version of the model tends to predict higher than observed levels of polymorphism unless substantial positive autocorrelations in the environment are postulated. The actual allele frequency configurations observed in nature are in rough agreement with those predicted by the SAS-CFF model. An approximate analysis of the transient properties of the SAS-CFF model shows that, in broad outline, the behavior is quite similar to that of the neutral model.     

Translocations and a balanced polymorphism in a Drosophila population

A Drosophila population cage initiated with equal numbers of two viable II–III translocation homozygotes rapidly evolved into a balanced polymorphism with the two translocations maintained throughout 25 generations at which time the experiment was terminated. The fertility of this population averaged 26%; a control population averaged 90%. The establishment of the polymorphism was interpreted with reference to the reduced viability of the two homozygotes such that their net fitness was considerably less than that of partially sterile double heterozygote. By the incorporation of specific values for the relative fitness of the three genotypes in a computer programme it was possible to simulate the polymorphism.     

Protected polymorphism in the two-locus haploid model with unpredictable fitnesses

 In an unpredictable environment, the distributions of alleles from which polymorphism can be maintained forever belong to a certain set, the C-viability kernel. Such a set is calculated in the two-locus haploid model, as well as the corresponding fitnesses at any time which make this maintenance possible. The dependence of the C-viability kernel on the set U of admissible fitnesses and on the recombination rate r is studied. Notably, the C-viability kernel varies rapidly in the neighborhood of equal fitness of AB and ab; it becomes empty when ab has a fitness below a certain function, which is delineated, of the recombination rate. The properties of the two-locus model under constraints, out of equilibrium and with unpredictable selection are thus presented. Received: 20 May 1999     

Evolution of balanced genetic polymorphism

Extreme genetic polymorphism maintained by balancing selection (so called because many alleles are maintained in a balance by a mechanism of rare allele advantage) is intimately associated with the important task of self/non-self-discrimination. Widely disparate self-recognition systems of plants, animals and fungi share several general features, including the maintenance of large numbers of alleles at relatively even frequency, and persistence of this variation over very long time periods. Because the evolutionary dynamics of balanced polymorphism are very different from those of neutral genetic variation, data on balanced polymorphism have been used as a novel source for inference of the history of populations. This review highlights the unique evolutionary properties of balanced genetic polymorphism, and the use of theoretical understanding in analysis and application of empirical data for inference of population history. However, a second goal of this review is to point out where current theory is incomplete. Recent observations suggest that entirely novel selective forces may act in concert with balancing selection, and these novel forces may be extremely potent in shaping genetic variation at self-recognition loci.     

The effect of hitch-hiking on genes linked to a balanced polymorphism in a subdivided population

The effect of multi-allelic balancing selection on nucleotide diversity at linked neutral sites was investigated by simulations of subdivided populations. The motivation is to understand the behaviour of self-recognition systems such as the MHC and plant self-incompatibility. For neutral sites, two types of subdivision are present: (1) into demes (connected by migration), and (2) into classes defined by different functional alleles at the selected locus (connected by recombination). Previous theoretical studies of each type of subdivision separately have shown that each increases diversity, and decreases the relative frequencies of low-frequency variants, at neutral sites or loci. We show here that the two types of subdivision act non-additively when sampling is at the whole population level, and that subdivision produces some non-intuitive results. For instance, in highly subdivided populations, genetic diversity at neutral sites may decrease with tighter linkage to a selected locus or site. Another conclusion is that, if there is population subdivision, balancing selection leads to decreased expected FST values for neutral sites linked to the selected locus. Finally, we show that the ability to detect balancing selection by its effects on linked variation, using tests such as Tajima's D, is reduced when genes in a subdivided population are sampled from the total population, rather than within demes.     

Evolution of coadaptation in a two-locus epistatic system

Although recent advances in genome biology have dramatically increased our understanding of the contribution of gene interactions to the development of complex phenotypes, we still lack general agreement on the process and mechanisms responsible for the evolution of epistatic systems. Even if genes in a species are indeed integrated into coadapted complexes of interacting components, simple additive evolution may eventually result in epistatic differentiation of populations. Consequently, the prevalence of epistatic gene action does not tell us anything about the role of epistatic selection in the history of population divergence. To elucidate the contribution of epistatic selection in the evolution of coadaptation, we investigate the fixation process of two mutations that interact synergistically to enhance fitness. We show by diffusion analysis and simulations that epistatic selection on cosegregating variants does not by itself promote the evolution of epistatic systems; rather, accumulation of neutral mutations may play a crucial role, creating an appropriate genetic milieu for adaptive evolution in the future generations.     

Molecular evolution of a primate-specific microRNA family

Lineage-specific microRNA (miRNA) families may contribute to developmental novelties during evolution. However, little is known about the origin and evolution of new miRNA families. We report evidence of an Alu-mediated rapid expansion of miRNA genes in a previously identified primate-specific miRNA family, drawn from sequencing and comparative analysis of 9 diverse primate species. Evolutionary analysis reveals similar divergence among miRNA copies whether they are within or between species, lineage-specific gain and loss of miRNAs, and gene pseudolization in multiple species. These observations support a birth-and-death process of miRNA genes in this family, implicating functional diversification during primate evolution. In addition, both secondary structure conservation and reduced single nucleotide polymorphisms density attest to functional constraint of this family in primates. Finally, we observed preferential expression of miRNAs in human placenta and fetal brain, suggesting a functional importance of this family for primate development.     

Tension versus ecological zones in a two-locus system

Previous theories show that tension and ecological zones are indistinguishable in terms of gene frequency clines. Here I analytically show that these two types of zones can be distinguished in terms of genetic statistics other than gene frequency. A two-locus cline model is examined with the assumptions of random mating, weak selection, no drift, no mutation, and multiplicative viabilities. The genetic statistics for distinguishing the two types of zones are the deviations of one- or two-locus genotypic frequencies from Hardy-Weinberg equilibrium (HWE) or from random association of gametes (RAG), and the deviations of additive and dominance variances from the values at HWE. These deviations have a discontinuous distribution in space and different extents of interruptions in the ecological zone with a sharp boundary, but exhibit a continuous distribution in the tension zone. Linkage disequilibrium enhances the difference between the deviations from HWE and from RAG for any two-locus genotypic frequency.     

Reinforcement of genetic coherence in a two-locus model

Background  

In order to maintain populations as units of reproduction and thus enable anagenetic evolution, genetic factors must exist which prevent continuing reproductive separation or enhance reproductive contact. This evolutionary principle is called genetic coherence and it marks the often ignored counterpart of cladistic evolution. Possibilities of the evolution of genetic coherence are studied with the help of a two-locus model with two alleles at each locus. The locus at which viability selection takes place is also the one that controls the fusion of gametes. The second locus acts on the first by modifying the control of the fusion probabilities. It thus acts as a mating modifier whereas the first locus plays the role of the object of selection and mating. Genetic coherence is enhanced by modifications which confer higher probabilities of fusion to heterotypic gametic combinations (resulting in heterozygous zygotes) at the object locus.     

Molecular movies... coming to a lecture near you

Scientific visualizations are powerful tools for communicating the intricacies of cellular and molecular structures and dynamics. There is a disconnect, however, between the research data sets we seek to represent and the kinds of animation that allow us to visualize and communicate them. Scientists are increasingly turning to 3D animation software borrowed from the entertainment industry to import, animate, and even create simulations of their data.     

The evolution of phally polymorphism

Phally polymorphism in snails offers an opportunity, hitherto neglected, to study the evolution of sexual polymorphism in animals. It is characterized by the co-occurrence in natural populations of regular (euphallic) individuals and aphallic individuals with no male copulatory organ. Both sexual morphs can self-fertilize but, when outcrossing, aphallic individuals can only play the female role. Using simple models, we investigated the influence of selling rate, inbreeding depression and allocation to female function on the evolution of aphally, assuming different kinds of inheritance of aphally. These models show that high selfing rates favour the maintenance of aphally and permit polymorphic situations at equilibrium for some sets of these parameters, except with cytoplasmic inheritance. We then review the empirical data sets on aphally, mainly available in the freshwater snail Bulinus truncatus , to evaluate the determination of aphally and the parameters of the models as well as the potential role of other factors, including polyploidy, parasitism, population structure and dynamics. In the light of both theoretical and empirical results, we propose likely scenarios for the evolution of aphally.