Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability

A number of recent works have introduced statistical methods for detecting genetic loci that affect phenotypic variability, which we refer to as variability-controlling quantitative trait loci (vQTL). These are genetic variants whose allelic state predicts how much phenotype values will vary about their expected means. Such loci are of great potential interest in both human and non-human genetic studies, one reason being that a detected vQTL could represent a previously undetected interaction with other genes or environmental factors. The simultaneous publication of these new methods in different journals has in many cases precluded opportunity for comparison. We survey some of these methods, the respective trade-offs they imply, and the connections between them. The methods fall into three main groups: classical non-parametric, fully parametric, and semi-parametric two-stage approximations. Choosing between alternatives involves balancing the need for robustness, flexibility, and speed. For each method, we identify important assumptions and limitations, including those of practical importance, such as their scope for including covariates and random effects. We show in simulations that both parametric methods and their semi-parametric approximations can give elevated false positive rates when they ignore mean-variance relationships intrinsic to the data generation process. We conclude that choice of method depends on the trait distribution, the need to include non-genetic covariates, and the population size and structure, coupled with a critical evaluation of how these fit with the assumptions of the statistical model.

Stochastic Assessment Of Environmental Flows In Semiarid Environments

The regimen of environmental flows (EF) must be included as terms of environmental demand in the management of water resources. Even though there are numerous methods for the computation of EF, the criteria applied at different steps in the calculation process are quite subjective whereas the results are fixed values that must be meet by water planners. This study presents a friendly-user tool for the assessment of the probability of compliance of a certain EF scenario with the natural regimen in a semiarid area in southern Spain. 250 replications of a 25-yr period of different hydrological variables (rainfall, minimum and maximum flows, ...) were obtained at the study site from the combination of Monte Carlo technique and local hydrological relationships. Several assumptions are made such as the independence of annual rainfall from year to year and the variability of occurrence of the meteorological agents, mainly precipitation as the main source of uncertainty. Inputs to the tool are easily selected from a first menu and comprise measured rainfall data, EF values and the hydrological relationships for at least a 20-yr period. The outputs are the probabilities of compliance of the different components of the EF for the study period. From this, local optimization can be applied to establish EF components with a certain level of compliance in the study period. Different options for graphic output and analysis of results are included in terms of graphs and tables in several formats. This methodology turned out to be a useful tool for the implementation of an uncertainty analysis within the scope of environmental flows in water management and allowed the simulation of the impacts of several water resource development scenarios in the study site.

Genetic parameters and environmental effects on temperament score and reproductive traits of Nellore cattle

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic variability of residual variance of production traits in Nellore beef cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

PCR primed with minisatellite core sequences yields species-specific patterns and assessment of population variability in fishes of the genus Brycon

Minisatellite core sequences were used as single primers in polymerase chain reaction (PCR) to amplify genomic DNA in a way similar to the random amplified polymorphic DNA methodology. This technique, known as Directed Amplification of Minisatellite-region DNA, was applied in order to differentiate three neotropical fish species (Brycon orbignyanus, B. microlepis and B. lundii ) and to detect possible genetic variations among samples of the threatened species, B. lundii , collected in two regions with distinct environmental conditions in the area of influence of a hydroelectric dam. Most primers generated species-specific banding patterns and high levels of intraspecific polymorphism. The genetic variation observed between the two sampling regions of B. lundii was also high enough to suggest the presence of distinct stocks of this species along the same river basin. The results demonstrated that minisatellite core sequences are potentially useful as single primers in PCR to assist in species and population identification. The observed genetic stock differentiation in B. lundii associated with ecological and demographic data constitute a crucial task to develop efficient conservation strategies in order to preserve the genetic diversity of this endangered fish species.

Intraspecific variability of flavonoid glycosides and styrylpyrones from leaves of Cryptocarya mandioccana Meisner (Lauraceae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Changes in optical properties caused by UV-irradiation of aquatic humic substances from the amazon river basin: Seasonal variability evaluation

Aquatic humic substances (AHS) isolated from two characteristic seasons of the Negro river, winter and summer corresponding to floody and dry periods, were structurally characterized by (13)C nuclear magnetic ressonance. Subsequently, AHS aqueous solutions were irradiated with a polychromatic lamp (290-475 nm) and monitored by its total organic carbon (TOC) content, ultraviolet-visible (UV-vis) absorbance, fluorescence and Fourier transformed infrared spectroscopy (FTIR). As a result, a photobleaching upto 80% after irradiation of 48 h was observed. Conformational rearrangements and formation of low molecular complexity structures were formed during the irradiation, as deduced from the pH decrement and the fluorescence shifting to lower wavelengths. Additionally a significant mineralization with the formation of CO(2), CO, and inorganic carbon compounds was registered, as assumed by TOC losses of up to 70%. The differences in photodegradation between samples expressed by photobleaching efficiency were enhanced in the summer sample and related to its elevated aromatic content. Aromatic structures are assumed to have high autosensitization capacity effects mediated by the free radical generation from quinone and phenolic moieties.

Short-term variability of copepod abundance in Jurumirim Reservoir, São Paulo, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effects of daily changes in environmental factors on the abundance and richness of Odonata

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Intraspecific variability in the basal metabolic rate: Testing the food habits hypothesis

Several competing hypotheses attempt to explain how environmental conditions affect mass-independent basal metabolic rate (BMR) in mammals. One of the most inclusive and yet debatable hypotheses is the one that associates BMR with food habits, including habitat productivity. These effects have been widely investigated at the interspecific level under the assumption that for any given species all traits are fixed. Consequently, the variation among individuals is largely ignored. Intraspecific analysis of physiological traits has the potential to compensate for many of the pitfalls associated with interspecific analyses and, thus, to be a useful approach for evaluating hypotheses regarding metabolic adaptation. In this study, we investigated the effects of food quality, availability, and predictability on the BMR of the leaf-eared mouse Phyllotis darwini. BMR was measured on freshly caught animals from the field, since they experience natural seasonal variations in environmental factors ( and, hence, variations in habitat productivity) and diet quality. BMR was significantly correlated with the proportion of dietary plants and seeds. In addition, BMR was significantly correlated with monthly habitat productivity. Path analysis indicated that, in our study, habitat productivity was responsible for the observed changes in BMR, while diet per se had no effect on this variable.

Polymorphisms of DNA repair genes XRCC1 and XRCC3, interaction with environmental exposure and risk of chronic gastritis and grastic cancer

Aim: To evaluate the association between polymorphisms XRCC1 Arg194Trp and Arg399Gln and XRCC3 Thr241Met and the risk for chronic gastritis and gastric cancer, in a Southeastern Brazilian population. Methods: Genotyping by PCR-RFLP was carried out on 202 patients with chronic gastritis (CG) and 160 patients with gastric cancer (GC), matched to 202 (C1) and 150 (C2) controls, respectively. Results: No differences were observed among the studied groups with regard to the genotype distribution of XRCC1 codons 194 and 399 and of XRCC3 codon 241. However, the combined analyses of the three variant alleles (194Trp, 399Gln and 241Met) showed an increased risk for chronic gastritis when compared to the GC group. Moreover, an interaction between the polymorphic alleles and demographic and environmental factors was observed in the CG and GC groups. XRCC1 194Trp was associated with smoking in the CG group, while the variant alleles XRCC1 399Gln and XRCC3 241Met were related with gender, smoking, drinking and H pylori infection in the CG and GC groups. Conclusion: Our results showed no evidence of a rela-tionship between the polymorphisms XRCC1 Arg194Trp and Arg399Gln and XRCC3 Thr241Met and the risk of chronic gastritis and gastric cancer in the Brazilian population, but the combined effect of these variants may interact to increase the risk for chronic gastritis, considered a premalignant lesion. Our data also indicate a gene-environment interaction in the susceptibility to chronic gastritis and gastric cancer. © 2005 The WJG Press and Elsevier Inc. All rights reserved.

Regional hydroclimatic variability and Brazil's 2001 energy crisis

Purpose - This paper seeks to address the issue of persistent and widespread drought conditions during 2000 and 2001, which were the apparent cause of the decline of water levels in the reservoirs of Brazilian hydroelectric power plants. Design/methodology/approach - This issue is addressed here through a case study of the hydroclimatology of the Paraíba river basin, in Southeast Brazil, home to four large multi-purpose operational reservoirs. Findings - The data analysis shows that neither changes in the frequency nor magnitude of extreme hydrological events (droughts and floods) nor in annual rainfall amounts can be detected from the existing climate record. The explanation is consistent with the fact that the terrestrial water and energy cycles are tightly, and non-linearly, coupled through evapotranspiration. Research limitations/implications - Therefore small change in the seasonality of rainfall can have a significant impact on the basin's overall hydrologic regime, and thus on the availability of water resources. Originality/value - Often, adaptation and resilience to climate variability are discussed in the context of catastrophic events such as floods and droughts. This study suggests that a different type of impacts, those associated with subtle, yet persistent changes of seasonality in the terrestrial water cycle, cannot be ignored in studies of long-term sustainability of water resources. © Emerald Group Publishing Limited.

Loss of Genetic Variability Induced by Agroecosystems: Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) as a Case Study

Four species of green lacewings occur in Brazil, of which Chrysoperla externa (Hagen) (Neuroptera: Chrysopidae) exhibits the widest geographical distribution. Chrysoperla externa is a predatory insect that is potentially useful as a biological control agent of agricultural pests. Studies on the genetic diversity of lacewing populations are essential to reduce the environmental and economic harm that may be caused by organisms with a low ability to adapt to the adverse and/or different environmental conditions to which they are exposed. We used the cytochrome oxidase I mitochondrial gene as a molecular marker to investigate the genetic diversity of green lacewing species collected from native and agroecosystem environments. Populations derived from native areas showed higher rates of genetic variability compared to populations from agroecosystems. Demographic changes in the form of population expansion were observed in agroecosystems, whereas populations in the native environment appeared stable over time. A statistical analysis showed significant genetic structure between each of the sampled groups, combined with its complete absence within each group, corroborating each group's identity. We infer that the loss of variability exhibited by populations from the agroecosystems is the result of genetic drift by means of the founder effect, a similar effect that has been observed in other introduced populations. Agroecosystems might therefore function as exotic areas for green lacewings, even when these areas are within the normal range of the species. © 2012 Sociedade Entomológica do Brasil.

Spatial variability structure of soil CO2 emission and soil attributes in a sugarcane area

Soil CO2 emission (F-CO2) is influenced by chemical, physical and biological factors that affect the production of CO2 in the soil and its transport to the atmosphere. F-CO2 varies in time and space depending on environmental conditions, including the management of the agricultural area. The aim of this study was to investigate the spatial variability structure of F-CO2 and soil attributes in a mechanically harvested sugarcane area (green harvest) using fractal dimension (D-F) derived from isotropic variograms at different scales (fractograms). F-CO2 showed an overall average of 1.51 mu mol CO2 m(-2) s(-1) and correlated significantly (P < 0.05) with soil physical attributes, such as soil bulk density, air-filled pore space, macroporosity and microporosity. Topologically significant DF values were obtained from the characterization of F-CO2 at medium and large scales (above 20 m), with values of 2.92 and 2.90, respectively. The variations in D-F with scales indicate that the spatial variability structure of F-CO2 was similar to that observed for soil temperature and total pore volume and was the inverse of that observed for other soil attributes, such as soil moisture, soil bulk density, microporosity, air-filled pore space, silt and clay content, pH, available phosphorus and the sum of bases. Thus, the spatial variability structure of F-CO2 presented a significant relationship with the spatial variability structure for most soil attributes, indicating the possibility of using fractograms as a tool to better describe the spatial dependence of variables along the scale. (C) 2014 Elsevier B.V. All rights reserved.

Reproductive variability of the Amazon River prawn, Macrobrachium amazonicum (Caridea, Palaemonidae): influence of life cycle on egg production

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)