Quantile-based permutation thresholds for quantitative trait Loci hotspots

Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key importance. One approach, randomly allocating observed QTL across the genomic locations separately by trait, implicitly assumes all traits are uncorrelated. Recently, an empirical test for QTL hotspots was proposed on the basis of the number of traits that exceed a predetermined LOD value, such as the standard permutation LOD threshold. The permutation null distribution of the maximum number of traits across all genomic locations preserves the correlation structure among the phenotypes, avoiding the detection of spurious hotspots due to nongenetic correlation induced by uncontrolled environmental factors and unmeasured variables. However, by considering only the number of traits above a threshold, without accounting for the magnitude of the LOD scores, relevant information is lost. In particular, biologically interesting hotspots composed of a moderate to small number of traits with strong LOD scores may be neglected as nonsignificant. In this article we propose a quantile-based permutation approach that simultaneously accounts for the number and the LOD scores of traits within the hotspots. By considering a sliding scale of mapping thresholds, our method can assess the statistical significance of both small and large hotspots. Although the proposed approach can be applied to any type of heritable high-volume "omic" data set, we restrict our attention to expression (e)QTL analysis. We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set.     

Local tissue temperature increase of a generic implant compared to the basic restrictions defined in safety guidelines

The objective of this study was to investigate if persons with implantable medical devices are intrinsically protected by the current electromagnetic safety guidelines. For inter-laboratory comparisons, the U.S. Food and Drug Administration has defined a generic implant as consisting of an insulated wire with noninsulated tips, simulating active implants composed of a metallic case, and insulated wires with electric contacts at the tip. In this study, we determined the amplitude of the uniform electric fields induced in body tissues that cause a local increase in the tissue temperature by 1 °C in the presence of this generic implant for a wide range of frequencies and wire lengths. The field amplitudes were compared to the basic restrictions of the current exposure guidelines for both occupational and uncontrolled exposure. Results showed that a 1 °C temperature increase in the tissues around the tips of the generic implant can be reached for field strengths much smaller than 1% of those in the basic restrictions. The simulated results were validated by experimental evaluations. The impact of perfusion was investigated and was found to lead to a reduction in the local temperature peak by only 1.6-3 times. Additional simulations inside an inhomogeneous anatomical model were performed to ascertain whether similar heating as in the generic model was observed. The significant temperature elevations due to the presence of a generic implant indicate that demonstrating compliance with the basic restrictions might not be sufficient for persons with implants. Special considerations may be required, especially in the case of novel, emerging technologies that feature strong near-fields at frequencies below 10 MHz (e.g., wireless power-transfer systems).     

Common and rare plant species respond differently to fertilisation and competition, whether they are alien or native

Plant traits associated with alien invasiveness may also distinguish rare from common native species. To test this, we grew 23 native (9 common, 14 rare) and 18 alien (8 common, 10 rare) herbaceous species in Switzerland from six plant families under nutrient-addition and competition treatments. Alien and common species achieved greater biomass than native and rare species did overall respectively. Across alien and native origins, common species increased total biomass more strongly in response to nutrient addition than rare species did and this difference was not confounded by habitat dissimilarities. There was a weak tendency for common species to survive competition better than rare species, which was also independent of origin. Overall, our study suggests that common alien and native plant species are not fundamentally different in their responses to nutrient addition and competition.     

Shallow-soil endemics: adaptive advantages and constraints of a specialized root-system morphology

Worldwide, many rare plant species occur in shallow-soil, drought-prone environments. For most of these species, the adaptations required to be successful in their own habitats, as well as their possible consequences for establishment and persistence in others, are unknown. Here, two rare Hakea (Proteaceae) species confined to shallow-soil communities in mediterranean-climate south-western Australia were compared with four congeners commonly occurring on deeper soils. Seedlings were grown for 7 months in a glasshouse in individual 1.8 x 0.2-m containers, to allow for unconstrained root development. In addition, a reciprocal transplant experiment was carried out. The rare Hakea species differed consistently from their common congeners in their spatial root placement. They invested more in deep roots and explored the bottom of the containers much more quickly. In the reciprocal transplant experiment they showed increased survival in their own habitat, but not in others. This research suggests that shallow-soil endemics have a specialized root system that allows them to explore a large rock surface area, thereby presumably increasing their chance to locate cracks in the underlying rock. However, this root-system morphology may be maladaptive on deeper soils, providing a possible explanation for the restricted distribution of many shallow-soil endemics.     

Effect of waterlogging on regeneration in the dwarf birch (<Emphasis Type="Italic">Betula nana</Emphasis>)

The aim of this study was to determine the effect of waterlogging on annual regeneration in the dwarf birch (Betula nana L.), and to determine which demographic factors are responsible for the absence of B. nana in the waterlogged parts of a peat-bog. Growth parameters and demographic data were collected from 2001 to 2003 at four sites in the Linje peat bog in the Chełmno Lake District in northern Poland. Three of the sites represented waterlogged open bog communities. The fourth site served as the reference. The density of first-year ramets, annual shoot growth, and the proportion of flowering shoots was significantly lower at the waterlogged sites than at the reference site. No seedlings were found during the course of the study, even though flowering and fruit production took place at the reference site. The flowering shoots were mainly between nine and thirteen years old. Ramets in this age range were found only at the reference site due to high mortality in mature ramets at the waterlogged sites. Mean ramet height was significantly lower at the waterlogged sites than at the reference site, and was strongly correlated with mean ramet age. The distribution of B. nana in peat bogs is limited primarily by two demographic factors: the high mortality rate in older ramets, and the low rate of vegetative reproduction. Another contribution factor is that the proportion of older fertile ramets is low. The effects of fluctuations in the water table on distribution of B. nana are also discussed.     

Plant attributes determining the regional abundance of weeds on central European arable land

Aim Several recent studies have aimed to identify the biological, ecological and distributional attributes that determine the regional abundance of plant species. Here we aim to assess the relationships between regional abundance and species attributes in weeds on arable land. Location Czech Republic, central Europe. Methods The relationships between regional abundance and species attributes were studied with a data set of 381 weed species occurring on arable land in the Czech Republic. Regional species abundances were estimated from their occurrence frequency in vegetation plots distributed across the country. Using regression tree models, abundance was related to the biological traits, ecological indicator values, geographical distribution and habitat range of species. The models were calculated for the entire country and separately for weeds in cereals, root crops, lowlands and uplands. The effects of phylogenetic relatedness among species on their regional abundance were quantified and compared with the effects of species attributes. Results The results were similar for the whole data set and its particular subsets. Phylogeny explained 11.2–14.9% and species attributes 16.1–56.9% of the variation in regional abundance of weed species. Removal of the phylogenetic signal did not result in important changes in the effects of particular attributes. The most abundant species were those flowering in pre‐spring and early spring, adapted to low temperatures, relatively shade tolerant and with high nutrient requirements. The high regional abundance of these species positively correlated with their broad geographical (often circumpolar) distribution and broad habitat ranges. Main conclusions The regional abundance of weeds can, to some extent, be explained by their attributes. The most important attributes are those that enable weeds to grow and reproduce in the cool season when there is limited competition with crop plants, and those that are adaptations to growth in dense vegetation stands and highly productive habitats.     

Breeding system and population genetics of the vulnerable plant Dillwynia tenuifolia (Fabaceae)

Dillwynia tenuifolia Sieber ex DC. is a vulnerable species endemic to the Sydney region in Australia. This investigation focused on the breeding system and genetic structuring of the species in locations encompassing its entire geographical range. A field pollination experiment showed that D. tenuifolia produced fruit from both self‐ and cross‐pollination events, and thus has a facultative breeding system. Fruiting success from self‐ pollination was approximately half that observed from cross‐pollination. The genetic structure of D. tenuifolia populations was investigated by using allozyme electrophoresis. A survey of 16 loci revealed a high level of genetic variation with approximately two‐thirds of the loci being polymorphic and a mean of 1.84 alleles per loci. The genotype frequencies deviated from the Hardy–Weinberg equilibrium, with the observed level of heterozygosity significantly less than expected. The inbreeding coefficient was 0.31. There was very little divergence between populations (F_ST = 0.04) but the fixation indices were high within populations. Spatial autocorrelation, using Moran’s I, showed that neighbouring plants were closely related (I > 0.4). The genetic neighbourhood and effective population size in the species were estimated at one location as 1.1 ha and 10⁴ plants, respectively.