A terrestrial gamma-ray flash and ionospheric ultraviolet emissions powered by lightning.

Terrestrial gamma-ray flashes (TGFs) are transient gamma-ray emissions from thunderstorms, generated by electrons accelerated to relativistic energies in electric fields. Elves are ultraviolet and optical emissions excited in the lower ionosphere by electromagnetic waves radiated from lightning current pulses. We observed a TGF and an associated elve using the Atmosphere-Space Interactions Monitor on the International Space Station. The TGF occurred at the onset of a lightning current pulse that generated an elve, in the early stage of a lightning flash. Our measurements suggest that the current onset is fast and has a high amplitude-a prerequisite for elves-and that the TGF is generated in the electric fields associated with the lightning leader.

Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species.

In a genome alignment of five individuals of the ascomycete fungus Zymoseptoria pseudotritici, a close relative of the wheat pathogen Z. tritici (synonym Mycosphaerella graminicola), we observed peculiar diversity patterns. Long regions up to 100 kb without variation alternate with similarly long regions of high variability. The variable segments in the genome alignment are organized into two main haplotype groups that have diverged ∼3% from each other. The genome patterns in Z. pseudotritici are consistent with a hybrid speciation event resulting from a cross between two divergent haploid individuals. The resulting hybrids formed the new species without backcrossing to the parents. We observe no variation in 54% of the genome in the five individuals and estimate a complete loss of variation for at least 30% of the genome in the entire species. A strong population bottleneck following the hybridization event caused this loss of variation. Variable segments in the Z. pseudotritici genome exhibit the two haplotypes contributed by the parental individuals. From our previously estimated recombination map of Z. tritici and the size distribution of variable chromosome blocks untouched by recombination we estimate that the hybridization occurred ∼380 sexual generations ago. We show that the amount of lost variation is explained by genetic drift during the bottleneck and by natural selection, as evidenced by the correlation of presence/absence of variation with gene density and recombination rate. The successful spread of this unique reproductively isolated pathogen highlights the strong potential of hybridization in the emergence of pathogen species with sexual reproduction.

Environment-sensitive epigenetics and the heritability of complex diseases.

Genome-wide association studies have thus far failed to explain the observed heritability of complex human diseases. This is referred to as the "missing heritability" problem. However, these analyses have usually neglected to consider a role for epigenetic variation, which has been associated with many human diseases. We extend models of epigenetic inheritance to investigate whether environment-sensitive epigenetic modifications of DNA might explain observed patterns of familial aggregation. We find that variation in epigenetic state and environmental state can result in highly heritable phenotypes through a combination of epigenetic and environmental inheritance. These two inheritance processes together can produce familial covariances significantly higher than those predicted by models of purely epigenetic inheritance and similar to those expected from genetic effects. The results suggest that epigenetic variation, inherited both directly and through shared environmental effects, may make a key contribution to the missing heritability.

Selection at work in self-incompatible Arabidopsis lyrata. II. Spatial distribution of S haplotypes in Iceland.

We survey the distribution of haplotypes at the self-incompatibility (SI) locus of Arabidopsis lyrata (Brassicaceae) at 12 locations spread over the species' natural distribution in Iceland. Previous investigations of the system have identified 34 functionally different S haplotypes maintained by frequency-dependent selection and arranged them into four classes of dominance in their phenotypic expression. On the basis of this model of dominance and the island model of population subdivision, we compare the distribution of S haplotypes with that expected from population genetic theory. We observe 18 different S haplotypes, recessive haplotypes being more common than dominant ones, and dominant ones being shared by fewer populations. As expected, differentiation, although significant, is very low at the S locus even over distances of up to 300 km. The frequency of the most recessive haplotype is slightly larger than expected for a panmictic population, but consistent with a subdivided population with the observed differentiation. Frequencies in nature reflect effects of segregation distortion previously observed in controlled crosses. The dynamics of the S-locus variation are, however, well represented by a 12-island model and our simplified model of dominance interactions.

Selection at work in self-incompatible Arabidopsis lyrata: mating patterns in a natural population.

Identification and characterization of the self-incompatibility genes in Brassicaceae species now allow typing of self-incompatibility haplotypes in natural populations. In this study we sampled and mapped all 88 individuals in a small population of Arabidopsis lyrata from Iceland. The self-incompatibility haplotypes at the SRK gene were typed for all the plants and some of their progeny and used to investigate the realized mating patterns in the population. The observed frequencies of haplotypes were found to change considerably from the parent generation to the offspring generation around their deterministic equilibria as determined from the known dominance relations among haplotypes. We provide direct evidence that the incompatibility system discriminates against matings among adjacent individuals. Multiple paternity is very common, causing mate availability among progeny of a single mother to be much larger than expected for single paternity.

Influenza drift and epidemic size: the race between generating and escaping immunity.

Influenza in humans is characterised by strongly annual dynamics and antigenic evolution leading to partial escape from prior host immunity. The variability of new epidemic strains depends on the amount of virus currently circulating. In this paper, the amount of antigenic variation produced each year is dependent on the epidemic size. Our model reduces to a one-dimensional map and a full mathematical analysis is presented. This simple system suggests some basic principles which may be more generally applicable. In particular, for diseases with antigenic drift, vaccination may be doubly beneficial. Not only does it protect the population through classical herd immunity, but the overall case reduction reduces the chance of new variants being produced; hence, subsequent epidemics may be milder as a result of this positive feedback. Also, a disease with a high innate rate of antigenic variation will always be able to invade a susceptible population, whereas a disease with less potential for variation may require several introduction events to become endemic.

A codon-based model of host-specific selection in parasites, with an application to the influenza A virus.

Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model that attempts to include these effects by allowing the position-specific substitution process to change in conjunction with a host change event. Following maximum-likelihood parameter estimation, we employ an empirical Bayesian procedure to identify candidate sites potentially involved in host-specific adaptation. We discuss the applicability of the model to the more general problem of ascertaining whether the selective regime differs in two groups of related organisms. The utility of the model is illustrated on a data set of nucleoprotein sequences from the influenza A virus obtained from avian and human hosts.

MATE AVAILABILITY AND FECUNDITY SELECTION IN MULTI-ALLELIC SELF-INCOMPATIBILITY SYSTEMS IN PLANTS.

We investigate mate availability in different models of multiallelic self-incompatibility systems in mutation-selection-drift balance in finite populations. Substantial differences among self-incompatibility systems occur in average mate availability, and in variances of mate availability among individual plants. These differences are most pronounced in small populations in which low mate availability may reduce seed set in some types of sporophytic self-incompatibility. In cases where the pollination system causes a restriction in the number of pollen genotypes available to an individual plant, the fecundity of that plant depends on the availability of compatible pollen, which is determined by its genotype at the incompatibility locus. This leads to an additional component of selection acting on self-incompatibility systems, which we term "fecundity selection." Fecundity selection increases the number of alleles maintained in finite populations and increases mate availability in small populations. The strength of fecundity selection is dependent on the type of self-incompatibility. In some cases, fecundity selection markedly alters the equilibrium dynamics of self-incompatibility alleles. We discuss the population genetic consequences of mate availability and fecundity selection in the contexts of conservation management of self-incompatible plant species and experimental investigations on self-incompatibility in natural populations.

THE SELECTION BARRIER BETWEEN POPULATIONS SUBJECT TO STABILIZING SELECTION.

The introgression of genes carried by a small group of immigrants is studied. The recipient and the donor populations differ at several autosomal loci subject to weak selection, and two allelic forms of each gene are considered. Fitness variation is determined by additive allelic effects, by dominance effects, and by two-locus additive-by-additive epistatic interaction of the effects of the alleles. The fate of the group of immigrants is quantified by the selection barrier that describes the cumulative mean fitness of the hybrids and hybrid descendants relative to the fitness of the resident population. The monomorphic and the polymorphic loci of the recipient population contribute differently to the selection barrier. If the genetic difference between recipient and donor population is small, then the contribution of the monomorphic loci is dominated by a positive term dependent on the difference in gene frequencies. The contribution of the polymorphic loci depends only on the difference of the leading order in the pairwise linkage disequilibria between the two populations. This contribution may be positive or negative; and, thus, polymorphic loci may either contribute to the barrier or inflate the introgression.

Periodic orbit quantization of the anisotropic Kepler problem.

The periodic orbit quantization on the anisotropic Kepler problem is tested. By computing the stability and action of some 2000 of the shortest periodic orbits, the eigenvalue spectrum of the anisotropic Kepler problem is calculated. The aim is to test the following claims for calculating the quantum spectrum of classically chaotic systems: (1) Curvature expansions of quantum mechanical zeta functions offer the best semiclassical estimates; (2) the real part of the cycle expansions of quantum mechanical zeta functions cut at appropriate cycle length offer the best estimates; (3) cycle expansions are superfluous; and (4) only a small subset of cycles (irreducible cycles) suffices for good estimates for the eigenvalues. No evidence is found to support any of the four claims.