Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of Drosophila

Antagonistic host-parasite interactions can drive rapid adaptive evolution in genes of the immune system, and such arms races may be an important force shaping polymorphism in the genome. The RNA interference pathway gene Argonaute-2 (AGO2) is a key component of antiviral defense in Drosophila, and we have previously shown that genes in this pathway experience unusually high rates of adaptive substitution. Here we study patterns of genetic variation in a 100-kbp region around AGO2 in three different species of Drosophila. Our data suggest that recent independent selective sweeps in AGO2 have reduced genetic variation across a region of more than 50 kbp in Drosophila melanogaster, D. simulans, and D. yakuba, and we estimate that selection has fixed adaptive substitutions in this gene every 30-100 thousand years. The strongest signal of recent selection is evident in D. simulans, where we estimate that the most recent selective sweep involved an allele with a selective advantage of the order of 0.5-1% and occurred roughly 13-60 Kya. To evaluate the potential consequences of the recent substitutions on the structure and function of AGO2, we used fold-recognition and homology-based modeling to derive a structural model for the Drosophila protein, and this suggests that recent substitutions in D. simulans are overrepresented at the protein surface. In summary, our results show that selection by parasites can consistently target the same genes in multiple species, resulting in areas of the genome that have markedly reduced genetic diversity.     

Host-switching by a vertically transmitted rhabdovirus in Drosophila

A diverse range of endosymbionts are found within the cells of animals. As these endosymbionts are normally vertically transmitted, we might expect their evolutionary history to be dominated by host-fidelity and cospeciation with the host. However, studies of bacterial endosymbionts have shown that while this is true for some mutualists, parasites often move horizontally between host lineages over evolutionary timescales. For the first time, to our knowledge, we have investigated whether this is also the case for vertically transmitted viruses. Here, we describe four new sigma viruses, a group of vertically transmitted rhabdoviruses previously known in Drosophila. Using sequence data from these new viruses, and the previously described sigma viruses, we show that they have switched between hosts during their evolutionary history. Our results suggest that sigma virus infections may be short-lived in a given host lineage, so that their long-term persistence relies on rare horizontal transmission events between hosts.     

Prior reproduction and weather affect berry crops in central Ontario, Canada

Populations of many perennial plants intermittently produce large seed crops—a phenomenon referred to as mast seeding or masting. Masting may be a response to spatially correlated environmental conditions (the Moran effect), an adaptive reproductive strategy reflecting economies of scale, or a consequence of the internal resource budgets of individual plants. Fruit production by endozoochorous plants representing eight genera varied synchronously over much of central Ontario, Canada, 1998–2009. We tested for effects of weather and prior reproduction on fruit production by comparing AIC_c values among regression models fit to time series of fruit production scores and partitioning contributions by different predictors to multiple R ² into independent and joint contributions. Fruit production by mountain ash (Sorbus spp.), juneberry (Amelanchier spp.), dogwoods (Cornus spp.), nannyberry (Viburnum lentago), and possibly cherries (Prunus spp.) was inversely related to production in the previous year. These effects were independent of weather conditions, suggesting that intrinsic factors such as internal resource budgets or an adaptive strategy of variable reproductive output influenced fruit production. To our knowledge, this is the first evidence of masting in members of the genera Cornus, Viburnum, and Amelanchier, and in members of Prunus and Sorbus in North America. All species produced fewer fruits when weather conditions were dry, so the Moran effect could have synchronized fruit production both within and among species. Patterns and causes of variation in berry crops have implications for ecosystem dynamics, particularly in boreal and subArctic environments where berry crops are important wildlife foods.     

The age and evolution of an antiviral resistance mutation in Drosophila melanogaster

What selective processes underlie the evolution of parasites and their hosts? Arms-race models propose that new host-resistance mutations or parasite counter-adaptations arise and sweep to fixation. Frequency-dependent models propose that selection favours pathogens adapted to the most common host genotypes, conferring an advantage to rare host genotypes. Distinguishing between these models is empirically difficult. The maintenance of disease-resistance polymorphisms has been studied in detail in plants, but less so in animals, and rarely in natural populations. We have made a detailed study of genetic variation in host resistance in a natural animal population, Drosophila melanogaster, and its natural pathogen, the sigma virus. We confirm previous findings that a single (albeit complex) mutation in the gene ref(2)P confers resistance against sigma and show that this mutation has increased in frequency under positive selection. Previous studies suggested that ref(2)P polymorphism reflects the progress of a very recent selective sweep, and that in Europe during the 1980s, this was followed by a sweep of a sigma virus strain able to infect flies carrying this mutation. We find that the ref(2)P resistance mutation is considerably older than the recent spread of this viral strain and suggest that—possibly because it is recessive—the initial spread of the resistance mutation was very slow.     

Probing the molecular determinants of aniline dioxygenase substrate specificity by saturation mutagenesis

Aniline dioxygenase is a multicomponent Rieske nonheme-iron dioxygenase enzyme isolated from Acinetobacter sp. strain YAA. Saturation mutagenesis of the substrate-binding pocket residues, which were identified using a homology model of the alpha subunit of the terminal dioxygenase (AtdA3), was used to probe the molecular determinants of AtdA substrate specificity. The V205A mutation widened the substrate specificity of aniline dioxygenase to include 2-isopropylaniline, for which the wild-type enzyme has no activity. The V205A mutation also made 2-isopropylaniline a better substrate for the enzyme than 2,4-dimethylaniline, a native substrate of the wild-type enzyme. The I248L mutation improved the activity of aniline dioxygenase against aniline and 2,4-dimethylaniline approximately 1.7-fold and 2.1-fold, respectively. Thus, it is shown that the alpha subunit of the terminal dioxygenase indeed plays a part in the substrate specificity as well as the activity of aniline dioxygenase. Interestingly, the equivalent residues of V205 and I248 have not been previously reported to influence the substrate specificity of other Rieske dioxygenases. These results should facilitate future engineering of the enzyme for bioremediation and industrial applications.     

Correlations of plasma lipid metabolites with hibernation and lactation in wild black bears Ursus americanus

During the denning period, black bears (Ursus americanus) are capable of enduring several months without food. At the same time, female bears that are pregnant or lactating have an added metabolic stress. Based on laboratory studies, much of the energy required to support metabolism and lactation during denning in black bears comes from lipid reserves. These lipid reserves are mobilized and the most metabolically active lipid fraction in the blood are nonesterified fatty acids (NEFA). Therefore, we hypothesized that plasma NEFAs would be higher in denning relative to active bears and in lactating relative to non-lactating female bears. We further hypothesized that in bears with elevated plasma NEFA levels, other lipid-related parameters (e.g., ketone bodies, albumin, cholesterol, lipase) would also be elevated in the plasma. Denning bears had significantly increased NEFA levels in all classes (saturates, monoenes, and polyenes). A doubling of plasma NEFA levels and a 33% increase in albumin, the plasma fatty acid binding protein, in denning bears, resulted in NEFA/albumin ratios that were higher in denning bears (4:1) compared to those of active bears (3:1). Bears became relatively ketonemic with a 17-fold increase in D-beta-hydroxybutyrate levels during the denning period. Plasma cholesterol approximately doubled and lipase was ten-fold lower in denning relative to active bears. These findings indicate a strong correlation between plasma lipid metabolites and the denning period in a wild population of black bears.     

Natural selection drives extremely rapid evolution in antiviral RNAi genes

RNA interference (RNAi) is perhaps best known as a laboratory tool. However, RNAi-related pathways represent an antiviral component of innate immunity in both plants and animals. Since viruses can protect themselves by suppressing RNAi, interaction between RNA viruses and host RNAi may represent an ancient coevolutionary "arms race." This could lead to strong directional selection on RNAi genes, but to date their evolution has not been studied. By comparing DNA sequences from different species of Drosophila, we show that the rate of amino acid evolution is substantially elevated in genes related to antiviral RNAi function (Dcr2, R2D2, and Ago2). They are among the fastest evolving 3% of all Drosophila genes; they evolve significantly faster than other components of innate immunity and faster than paralogous genes that mediate "housekeeping" functions. Based on DNA polymorphism data from three species of Drosophila, McDonald-Kreitman tests showed that this rapid evolution is due to strong positive selection. Furthermore, Dcr2 and Ago2 display reduced genetic diversity, indicative of a recent selective sweep in both genes. Together, these data show rapid adaptive evolution of the antiviral RNAi pathway in Drosophila. This is a signature of host-pathogen arms races and implies that the ancient battle between RNA viruses and host antiviral RNAi genes is active and significant in shaping RNAi function.     

Optimization of slow-release fertilizer dosage for bioremediation of oil-contaminated beach sediment in a tropical environment

The optimization of fertilizer concentrations for stimulating bioremediation in contaminated marine substrates is desirable for minimizing both cost and environmental risks associated with eutrophication. In this study, the effect of various dosages of the slow-release fertilizer, Osmocote, in stimulating an indigenous microbial biomass in oil-contaminated beach sediments was investigated. The Osmocote used comprises water-soluble N–P–K at concentrations of 18, 4.8, and 8.3% w/w respectively, and dosages tested were in the range of 0–4.0% dry weight equivalent of sediment. The beach sediments were taken from a tropical foreshore environment and spiked with an Arabian light crude oil (ALCO) to achieve a petroleum hydrocarbon content of 4.4% w/w. The experiment was conducted in open microcosms irrigated with seawater over a 42-day period. It was found that all Osmocote-dosed sediments had a sustained nutrient release for at least 42 days. An addition of 0 8% Osmocote to the sediments was sufficient to maximize metabolic activity of the biomass, and the biodegradation of straight-chain alkanes (C₁₀–C₃₃). An Osmocote dosage of 1.5% resulted in optimal biodegradation of more recalcitrant branched-chain alkanes (i.e. pristane, and phytane).