The influence of phylogenetic uncertainty on the detection of positive Darwinian selection

The power of maximum likelihood tests of positive selection on protein-coding genes depends heavily on detecting and accounting for potential biases in the studied data set. Although the influence of transition:transversion and codon biases have been investigated in detail, little is known about how inaccuracy in the phylogeny used during the calculations affects the performance of these tests. In this study, 3 empirical data sets are analyzed using sets of simulated topologies corresponding to low, intermediate, and high levels of phylogenetic uncertainty. The detection of positive selection was largely unaffected by errors in the underlying phylogeny. However, the number of sites identified as being under positive selection tended to be overestimated.     

Media- and method-dependent variations in minimal inhibitory concentrations of antiplaque agents on oral bacteria

AIMS: To determine minimal inhibitory concentrations (MICs) and the percentage of nonsusceptible bacteria-- those still cultivable above a threshold concentration--in human supragingival dental plaque and saliva for antiplaque/antimicrobial agents including triclosan (TCS) and trichlorocarbanilide (TCC), and a new potential antimicrobial, 2-t-butyl-5-(4-t-butylphenyl)-phenol (DTBBP). METHODS AND RESULTS: Broth and agar dilution-based MIC tests were performed using 28 oral and nonoral bacterial strains representing 17 species. MICs for TCS were lowest and more than 100-fold lower than DTBBP (P < 0.0005) by both methods. MICs for TCS were lower in broth-based tests compared with TCC. The additions of defibrinated blood to agar and horse serum to broth increased MICs--in the case of TCS, 10- to 15-fold. Significantly higher proportions of nonsusceptible plaque and salivary bacteria were recovered from agar media containing DTBBP or TCC compared with TCS (P < 0.05). CONCLUSIONS: TCS is a more effective antimicrobial agent than either TCC or DTBBP as determined by in vitro testing. SIGNIFICANCE AND IMPACT OF THE STUDY: The utility of in vitro testing for antiplaque agents as a predictor of in vivo efficacy is affected by the methods used.     

An adaptive test for a subset of coefficients in a multivariate regression model

An adaptive multivariate test is proposed for a subset of regression coefficients in a linear model. This adaptive method uses the studentized deleted residuals to calculate an appropriate weight for each observation. The weights are then used to compute Wilk's lambda for the weighted model. The adaptive test is performed by permuting the independent variables corresponding to those parameters that are assumed to equal zero in the null hypothesis. The permuted variables are then weighted to obtain a permutation test statistic that is used to estimate the p-value. An example is presented of a multivariate regression that uses systolic and diastolic blood pressure as dependent variables with age and body mass index as independent variables. The simulation results show that the adaptive test maintains its size for the three multivariate error distributions that were used in the study. For normal error models the power of the adaptive test nearly equaled that of the non-adaptive test. For models that used non-normal errors the adaptive test was considerably more powerful than the traditional non-adaptive test.     

Host suitability and preference studies of Trichogramma cordubensis (Hymenoptera: Trichogrammatidae)

Studies of host suitability and preferences of Trichogramma cordubensis Vargas and Cabello (Hymenoptera: Trichogrammatidae) were performed with eggs of six Lepidoptera (Noctuidae) species: Thysanoplusia orichalcea Fabricius, Peridroma saucia (Hübner), Xestia c-nigrum L., Phlogophora meticulosa (L.), Noctua pronuba (L.), and N. atlantica (Warren). Host suitability was studied by analysing separately the effects of the attacked host species and the influence of the rearing host species on different biological parameters of T. cordubensis. Host preference was analysed by offering eggs of two host species simultaneously to a single female wasp without previous oviposition experience (dual-choice tests). Results show that P. saucia, followed by P. meticulosa were the least suitable hosts for T. cordubensis, since on these species the preimaginal development of the parasitoids was significantly longer and, the number of parasitized eggs as well the number of offspring per female were significantly lower. Contrarily, T. cordubensis parasitized at a higher rate the eggs of the endemic non-target species, N. atlantica. Dual choice tests showed that the option of the first host to be accepted by the wasp was random; however, the mean number of parasitized eggs differed significantly when two host species were offered simultaneously to T. cordubensis, always being the host species with heavier eggs the most parasitized.     

Tools and Techniques for the Assessment of Ecotoxicological Impacts of Contaminants in the Terrestrial Environment

Until recently, only a small number of standardized (mainly acute) tests with earthworms and plants were available for terrestrial risk assessment. However, during the last years various new methods (especially with chronic endpoints such as reproduction) were developed and standardized. Moreover, beyond structural aspects (e.g., the effect on individuals), the question of influences of chemicals on ecological soil functions like litter decomposition has been raised. Later, biological test methods were used in the area of Soil Quality Assessment, where an often unknown and complex contamination of a site-specific field soil has to be evaluated. Due to the variety of soils to be tested, the existing methods had to be adapted. This article briefly summarizes basic principles of method standardization before providing an overview of existing standardized tests for the compartment soil (mainly from Europe), focusing on zoological, plant, and functional methods. After presenting the main features of already standardized tests (in particular those used in soil quality assessment so far) the development of new tests for specific purposes, ideas for a battery of tests and a new, community-based approach assessing the biological quality of field soils are discussed.     

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.     

Recent population decline and selection shape diversity of taxol-related genes

Taxanes are defensive metabolites produced by Taxus species (yews) and used in anticancer therapies. Despite their medical interest, patterns of natural diversity in taxane-related genes are unknown. We examined variation at five main genes of Taxus baccata in the Iberian Peninsula, a region where unique yew genetic resources are endangered. We looked at several gene features and applied complementary neutrality tests, including diversity/divergence tests, tests solely based on site frequency spectrum (SFS) and Zeng's compound tests. To account for specific demography, microsatellite data were used to infer historical changes in population size based on an Approximate Bayesian Computation (ABC) approach. Polymorphism-divergence tests pointed to positive selection for genes TBT and TAT and balancing selection for DBAT. In addition, neutrality tests based on SFS found that while a recent reduction in population size may explain most statistics' values, selection may still be in action in genes TBT and DBAT, at least in some populations. Molecular signatures on taxol genes suggest the action of frequent selective waves with different direction or intensity, possibly related to varying adaptive pressures produced by the host-enemy co-evolution on defence-related genes. Such natural selection processes may have produced taxane variants still undiscovered.     

Testing Germination of Species for Hydroseeding Degraded Mediterranean Areas

The germination performance of native species and their suitability for a rapid erosion control are uncertain. Together with their relatively low commercial availability and high costs, these are still strong reasons preventing their common use in hydroseeding for restoration of Mediterranean degraded slopes, despite the increasing number of studies recommending it. In this study, 14 non‐native (commercial) and native herb and woody species were tested. Their germination performance was evaluated under laboratory (Petri dishes) and greenhouse conditions (seeds sown in target substrate). The results obtained were compared with the seedling densities in a Mediterranean quarry slope hydroseeded with the same species. In the laboratory, commercial species had a better germination performance than most native species, but this trend was not maintained in the greenhouse. Greenhouse tests were extended beyond spring and showed that many native species germinated better, or exclusively in autumn. Germination performance and success decreased, from laboratory to greenhouse and field conditions, for many species, but not for all. Relative to field performance, the predictive value of laboratory and greenhouse tests was poor, yet sowing on the target substrate under greenhouse conditions may be a better approach for certain native species. The main drawbacks revealed by native species in the present study included: (1) relatively slow germination; (2) seasonality; and (3) seed dormancy‐breaking requirements. The results suggest that these problems may be overcome through species selection, seed pre‐treatments, hydroseeding scheduling, and/or manipulation of seeding density and relative species proportion.     

Characterization and identification of virulent Klebsiella oxytoca isolated from abalone (Haliotis diversicolor supertexta) postlarvae with mass mortality in Fujian, China

An epidemic of mass mortality of abalone (Haliotis diversicolor supertexta) postlarvae aged 40 days or less has existed across south coast of China since the second half of 2002. Among 20 bacterial strains isolated from diseased abalone postlarvae on 2216E marine agar plates during an outbreak of postlarval disease in August 2005, a predominant strain (designated strain 20) was demonstrated to be virulent to postlarvae with an LD(50) value of 1.0x10(5) colony forming units (CFUml(-1)) on day 4, while the other 19 strains were either avirulent (16 strains) or weakly virulent (3 strains). The same bacterium could be re-isolated from postlarvae after bacterial challenge using 2216E marine agar plates. Preliminary toxicity tests of ECPs of strain 20 revealed that at 2.77mgproteinml(-1), crude ECPs completely liquefied postlarvae within 24h, leaving only shells. API 20E analysis identified strain 20 as Klebsiella oxytoca. 16S and ITS rDNA sequencing and phylogenetic analyses further confirmed this identification. Antibiotic susceptibility tests showed that strain 20 exhibited 94% of susceptibility to 16 various antibiotics tested and only showed resistance to streptomycin. Results of this work demonstrated that K. oxytoca is also linked to this epidemic in Fujian, China. This is considered to be the first report regarding K. oxytoca involved in the mass mortality of postlarval abalone in south China and the world.     

Scale-dependent niche axes of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are mutualistic with most species of plants and are known to influence plant community diversity and composition. To better understand natural plant communities and the ecological processes they control it is important to understand what determines the distribution and diversity of AMF. We tested three putative niche axes: plant species composition, disturbance history, and soil chemistry against AMF species composition to determine which axis correlated most strongly with a changing AMF community. Due to a scale dependency we were not able to absolutely rank their importance, but we did find that each correlated significantly with AMF community change at our site. Among soil properties, pH and NO₃ were found to be especially good predictors of AMF community change. In a similar analysis of the plant community we found that time since disturbance had by far the largest impact on community composition. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.