Longevity, early emergence and body size in a pollinating fig wasp - implications for stability in a fig-pollinator mutualism

1. Fig trees (Ficus) are pollinated only by agaonid wasps, whose larvae also gall fig ovules. Each ovule develops into either a seed (when pollinated) or a wasp (when an egg is also laid inside) but not both. 2. Ovipositing wasps (foundresses) favour ovules near the centre of the enclosed inflorescence (syconium or 'fig'), leaving ovules near the outer wall to develop into seeds. This spatial stratification of wasps and seeds ensures reproduction in both partners, and thereby enables mutualism persistence. However, the mechanism(s) responsible remain(s) unknown. 3. Theory shows that foundresses will search for increasingly rare inner ovules and ignore outer ovules, as long as ovipositing in outer ovules is sufficiently slow and/or if inner ovules confer greater fitness to wasps. The fig-pollinator mutualism can therefore be stabilized by strong time constraints on foundresses and by offspring fitness gradients over variation in ovule position. 4. Female fig wasps cannot leave their galls without male assistance. We found that females in outer ovules were unlikely to be released. Inner ovules thus have added value to foundresses, because their female offspring are more likely to mate and disperse. 5. For those offspring that did emerge, gall position (inner/outer) and body size did not influence the order in which female pollinators exited syconia, nor did early emerging wasps enjoy increased life spans. 6. We also found that the life spans of female wasps nearly doubled when given access to moisture. We suggest that conflict resolution in the fig-pollinator mutualism may thus be influenced by tropical seasonality, because wasps may be less able to over-exploit ovules in dry periods due to time constraints.

Body mass, territory size and life history tactics in a socially monogamous canid, the red fox Vulpes vulpes

Male-biased sexual size dimorphism is typical of polygynous mammals, where the degree of dimorphism in body mass is related to male intrasexual competition and the degree of polygyny. However, the importance of body mass in monogamous mammals is largely unknown. We investigated the effect of body mass on life-history parameters and territory size in the red fox (Vulpes vulpes), a socially monogamous canid with slight sexual dimorphism. Increased body size in males appeared to confer an advantage in territory acquisition and defense contests because heavier males held larger territories and exerted a greater boundary pressure on smaller neighbors. Heavier male foxes invested more effort in searching for extrapair matings by moving over a wider area and farther from their territories, leading to greater reproductive success. Males that sired cubs outside their own social group appeared to be heavier than males that only sired cubs within their social group or that were cuckolded, but our results should be treated with caution because sample sizes were small. Territory size, boundary pressure, and paternity success were not related to age of males. In comparison, body mass of females was not related to territory size, probability of breeding, litter size, or cub mass. Only age affected probability of breeding in females: younger females reproduced significantly less than did older females, although we did not measure individual nutritional status. Thus, body mass had a significant effect on life-history traits and territory size in a socially monogamous species comparable to that reported in polygynous males, even in the absence of large size dimorphism.

Extending Zelterman’s approach for robust estimation of population size to zero-truncated clustered data

Estimation of population size with missing zero-class is an important problem that is encountered in epidemiological assessment studies. Fitting a Poisson model to the observed data by the method of maximum likelihood and estimation of the population size based on this fit is an approach that has been widely used for this purpose. In practice, however, the Poisson assumption is seldom satisfied. Zelterman (1988) has proposed a robust estimator for unclustered data that works well in a wide class of distributions applicable for count data. In the work presented here, we extend this estimator to clustered data. The estimator requires fitting a zero-truncated homogeneous Poisson model by maximum likelihood and thereby using a Horvitz-Thompson estimator of population size. This was found to work well, when the data follow the hypothesized homogeneous Poisson model. However, when the true distribution deviates from the hypothesized model, the population size was found to be underestimated. In the search of a more robust estimator, we focused on three models that use all clusters with exactly one case, those clusters with exactly two cases and those with exactly three cases to estimate the probability of the zero-class and thereby use data collected on all the clusters in the Horvitz-Thompson estimator of population size. Loss in efficiency associated with gain in robustness was examined based on a simulation study. As a trade-off between gain in robustness and loss in efficiency, the model that uses data collected on clusters with at most three cases to estimate the probability of the zero-class was found to be preferred in general. In applications, we recommend obtaining estimates from all three models and making a choice considering the estimates from the three models, robustness and the loss in efficiency. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

ONeSAMP: a program to estimate effective population size using approximate Bayesian computation

The estimation of effective population size from one sample of genotypes has been problematic because most estimators have been proven imprecise or biased. We developed a web-based program, ONeSAMP that uses approximate Bayesian computation to estimate effective population size from a sample of microsatellite genotypes. ONeSAMP requires an input file of sampled individuals' microsatellite genotypes along with information about several sampling and biological parameters. ONeSAMP provides an estimate of effective population size, along with 95% credible limits. We illustrate the use of ONeSAMP with an example data set from a re-introduced population of ibex Capra ibex.

Bayesian sample size for exploratory clinical trials incorporating historical data

This paper presents a simple Bayesian approach to sample size determination in clinical trials. It is required that the trial should be large enough to ensure that the data collected will provide convincing evidence either that an experimental treatment is better than a control or that it fails to improve upon control by some clinically relevant difference. The method resembles standard frequentist formulations of the problem, and indeed in certain circumstances involving 'non-informative' prior information it leads to identical answers. In particular, unlike many Bayesian approaches to sample size determination, use is made of an alternative hypothesis that an experimental treatment is better than a control treatment by some specified magnitude. The approach is introduced in the context of testing whether a single stream of binary observations are consistent with a given success rate p(0). Next the case of comparing two independent streams of normally distributed responses is considered, first under the assumption that their common variance is known and then for unknown variance. Finally, the more general situation in which a large sample is to be collected and analysed according to the asymptotic properties of the score statistic is explored. Copyright (C) 2007 John Wiley & Sons, Ltd.

Origin of avian genome size and structure in non-avian dinosaurs

Avian genomes are small and streamlined compared with those of other amniotes by virtue of having fewer repetitive elements and less non-coding DNA(1,2). This condition has been suggested to represent a key adaptation for flight in birds, by reducing the metabolic costs associated with having large genome and cell sizes(3,4). However, the evolution of genome architecture in birds, or any other lineage, is difficult to study because genomic information is often absent for long-extinct relatives. Here we use a novel bayesian comparative method to show that bone-cell size correlates well with genome size in extant vertebrates, and hence use this relationship to estimate the genome sizes of 31 species of extinct dinosaur, including several species of extinct birds. Our results indicate that the small genomes typically associated with avian flight evolved in the saurischian dinosaur lineage between 230 and 250 million years ago, long before this lineage gave rise to the first birds. By comparison, ornithischian dinosaurs are inferred to have had much larger genomes, which were probably typical for ancestral Dinosauria. Using comparative genomic data, we estimate that genome-wide interspersed mobile elements, a class of repetitive DNA, comprised 5 - 12% of the total genome size in the saurischian dinosaur lineage, but was 7 - 19% of total genome size in ornithischian dinosaurs, suggesting that repetitive elements became less active in the saurischian lineage. These genomic characteristics should be added to the list of attributes previously considered avian but now thought to have arisen in non-avian dinosaurs, such as feathers(5), pulmonary innovations 6, and parental care and nesting

Effects of body size and lifestyle on evolution of mammal life histories

It has recently been proposed that life-history evolution is subject to a fundamental size-dependent constraint. This constraint limits the rate at which biomass can be produced so that production per unit of body mass is inevitably slower in larger organisms than in smaller ones. Here we derive predictions for how changes in body size and production rates evolve in different lifestyles subject to this constraint. Predictions are tested by using data on the mass of neonate tissue produced per adult per year in 637 placental mammal species and are generally supported. Compared with terrestrial insectivores with generalized primitive traits, mammals that have evolved more specialized lifestyles have divergent massspecific production rates: (i) increased in groups that specialize on abundant and reliable foods: grazing and browsing herbivores (artiodactyls, lagomorphs, perissoclactyls, and folivorous rodents) and flesh-eating marine mammals (pinnipeds, cetaceans); and (ii) decreased in groups that have lifestyles with reduced death rates: bats, primates, arboreal, fossorial, and desert rodents, bears, elephants, and rhinos. Convergent evolution of groups with similar lifestyles is common, so patterns of productivity across mammalian taxa reflect both ecology and phylogeny. The overall result is that groups with different lifestyles have parallel but offset relationships between production rate and body size. These results shed light on the evolution of the fast-slow life-history continuum, suggesting that variation occurs along two axes corresponding to body size and lifestyle.

The influence of winter oilseed rape (Brassica napus ssp oleifera var. biennis) canopy size on grass weed growth and grass weed seed return

Four experiments conducted over three seasons (2002-05) at the Crops Research Unit, University of Reading, investigated effects of canopy management of autumn sown oilseed rape (Brassica napus L. ssp. oleifera var. biennis (DC.) Metzg.) on competition with grass weeds. Emphasis was placed on the effect of the crop on the weeds. Rape canopy size was manipulated using sowing date, seed rate and the application of autumn fertilizer. Lolium multiflorum Lam., L. x boucheanum Kunth and Alopecurus myosuroides Huds. were sown as indicative grass weeds. The effects of sowing date, seed rate and autumn nitrogen on crop competitive ability were correlated with rape biomass and fractional interception of photosynthetically active radiation (PAR) by the rape floral layer, to the extent that by spring there was good evidence of crop: weed replacement. An increase in seed rate up to the highest plant densities tested increased both rape biomass and competitiveness, e.g. in 2002/3, L. multiflorum head density was reduced from 539 to 245 heads/m(2) and spikelet density from 13 170 to 5960 spikelets/m(2) when rape plant density was increased from 16 to 81 plants/m(2). Spikelets/head of Lolium spp. was little affected by rape seed rate, but the length of heads of A. myosuroides was reduced by 9 % when plant density was increased from 29-51 plants/m(2). Autumn nitrogen increased rape biomass and reduced L. multiflorum head density (415 and 336 heads/m(2) without and with autumn nitrogen, respectively) and spikelet density (9990 and 8220 spikelets/m(2) without and with autumn nitrogen, respectively). The number of spikelets/head was not significantly affected by autumn nitrogen. Early sowing could increase biomass and competitiveness, but poor crop establishment sometimes overrode the effect. Where crop and weed establishment was similar for both sowing dates, a 2-week delay (i.e. early September to mid-September) increased L. multiflorum head density from 226 to 633 heads/m(2) and spikelet density from 5780 to 15 060 spikelets/m(2).

Vertical distribution, size and composition of the weed seedbank under various tillage and herbicide treatments in a sequence of industrial crops

Investigations were conducted during the 2003, 2004 and 2005 growing seasons in northern Greece to evaluate effects of tillage regime (mouldboard plough, chisel plough and rotary tiller), cropping sequence (continuous cotton, cotton-sugar beet rotation and continuous tobacco) and herbicide treatment on weed seedbank dynamics. Amaranthus spp. and Portulaca oleracea were the most abundant species, ranging from 76% to 89% of total weed seeds found in 0-15 and 15-30 cm soil depths during the 3 years. With the mouldboard plough, 48% and 52% of the weed seedbank was found in the 0-15 and 15-30 cm soil horizons, while approximately 60% was concentrated in the upper 15 cm soil horizon for chisel plough and rotary tillage. Mouldboard ploughing significantly buried more Echinochloa crus-galli seeds in the 15-30 cm soil horizon compared with the other tillage regimes. Total seedbank (0-30 cm) of P. oleracea was significantly reduced in cotton-sugar beet rotation compared with cotton and tobacco monocultures, while the opposite occurred for E. crus-galli. Total seed densities of most annual broad-leaved weed species (Amaranthus spp., P. oleracea, Solanum nigrum) and E. crus-galli were lower in herbicide treated than in untreated plots. The results suggest that in light textured soils, conventional tillage with herbicide use gradually reduces seed density of small seeded weed species in the top 15 cm over several years. In contrast, crop rotation with the early established sugar beet favours spring-germinating grass weed species, but also prevents establishment of summer-germinating weed species by the early developing crop canopy.

Allelic size standards and reference genotypes to unify international cocoa (Theobroma cacao L.) microsatellite data

Standardisation of microsatellite allele profiles between laboratories is of fundamental importance to the transferability of genetic fingerprint data and the identification of clonal individuals held at multiple sites. Here we describe two methods of standardisation applied to the microsatellite fingerprinting of 429 Theobroma cacao L. trees representing 345 accessions held in the worlds largest Cocoa Intermediate Quarantine facility: the use of a partial allelic ladder through the production of 46 cloned and sequenced allelic standards (AJ748464 to AJ48509), and the use of standard genotypes selected to display a diverse allelic range. Until now a lack of accurate and transferable identification information has impeded efforts to genetically improve the cocoa crop. To address this need, a global initiative to fingerprint all international cocoa germplasm collections using a common set of 15 microsatellite markers is in progress. Data reported here have been deposited with the International Cocoa Germplasm Database and form the basis of a searchable resource for clonal identification. To our knowledge, this is the first quarantine facility to be completely genotyped using microsatellite markers for the purpose of quality control and clonal identification. Implications of the results for retrospective tracking of labelling errors are briefly explored.

The effect of potato variety mixtures on epidemics of late blight, in relation to plot size and level of resistance

Potatoes of a number of varieties of contrasting levels of resistance were planted in pure or mixed stands in four experiments over 3 years. Three experiments compared the late blight severity and progress in mixtures with that in pure stands. Disease on susceptible or moderately resistant varieties typical of those in commercial use was similar in mixtures and pure stands. In 2 of 3 years, there were slight reductions on cv. Sante, which is moderately susceptible, in mixture with cv. Cara, which is moderately resistant. Cara was unaffected by this mixture. Mixtures of an immune or near-immune partner with Cara or Sante substantially reduced disease on the latter. The effect of the size of plots of individual varieties or mixtures on blight severity was compared in two experiments. Larger plots had a greater area under the disease progress curve, but the average rate of disease progress was greater in smaller plots; this may be because most disease progress took place later, under more favourable conditions, in the smaller plots. In one experiment, two planting densities were used. Density had no effect on disease and did not interact with mixture effects. The overall conclusion is that, while mixtures of potato varieties may be desirable for other reasons, they do not offer any improvement on the average of the disease resistance of the components.

Effect of plant density and initial crown size on growth, development and yield in strawberry cultivars Elsanta and Bolero

The effects of density (plant spacing) and initial plant size on vegetative growth, flowering and fruiting were studied in the strawberry cultivars Elsanta and Bolero in their first and second years of cropping. The influence of these factors on light use and dry-matter partitioning was investigated. The size of planting material in 'Elsanta' and 'Bolero' slightly affected plant growth and yield, but this effect was not consistent and radiation use efficiency (RUE) and harvest index were unaltered. Plant spacing did not significantly affect the early stages of crop growth, but was important in determining growth and yield later in the season, this effect being more significant in the second year of cropping. Plant growth and yield per plant increased as plant spacing increased from 20 to 30 cm in both 'Elsanta' and 'Bolero', but the highest harvest index and yield per square metre were obtained at the closest spacing. Increased plant spacing also resulted in a greater leaf area and leaf area index. However, light was used less efficiently resulting in a lower RUE and lower harvest index (HI).

Detection and enumeration of sulphate-reducing bacteria in estuarine sediments by competitive PCR

The distribution of sulphate-reducing bacteria (SRB) in the sediments of the Colne River estuary, Essex, UK covering different saline concentrations of sediment porewater was investigated by the use of quantitative competitive PCR. Here, we show that a new PCR primer set and a new quantitative method using PCR are useful tools for the detection and the enumeration of SRB in natural environments. A PCR primer set selective for the dissimilatory sulphite reductase gene (dsr) of SRB was designed. PCR amplification using the single set of dsr-specific primers resulted in PCR products of the expected size from all 27 SRB strains tested, including Gram-negative and positive species. Sixty clones derived from sediment DNA using the primers were sequenced and all were closely related with the predicted dsr of SRB. These results indicate that PCR using the newly designed primer set are useful for the selective detection of SRB from a natural sample. This primer set was used to estimate cell numbers by dsr selective competitive PCR using a competitor, which was about 20% shorter than the targeted region of dsr. This procedure was applied to sediment samples from the River Colne estuary, Essex, UK together with simultaneous measurement of in situ rates of sulphate reduction. High densities of SRB ranging from 0.2 - 5.7 × 108 cells ml-1 wet sediment were estimated by the competitive PCR assuming that all SRB have a single copy of dsr. Using these estimates cell specific sulphate reduction rates of 10-17 to 10-15 mol of SO42- cell-1 day-1 were calculated, which is within the range of, or lower than, those previously reported for pure cultures of SRB. Our results show that the newly developed competitive PCR technique targeted to dsr is a powerful tool for rapid and reproducible estimation of SRB numbers in situ and is superior to the use of culture-dependent techniques.

Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation

We describe and evaluate a new estimator of the effective population size (N-e), a critical parameter in evolutionary and conservation biology. This new "SummStat" N-e. estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N-e. Simulations of a Wright-Fisher population with known N-e show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N-e values. We also address the paucity of information about the relative performance of N-e estimators by comparing the SUMMStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated rising initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and Ne less than or equal to 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N-e. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any, potentially informative summary statistic from Population genetic data.