Using ecological niche modelling to infer past, present and future environmental suitability for Leiopelma hochstetteri, an endangered New Zealand native frog

Leiopelma hochstetteri is an endangered New Zealand frog now confined to isolated populations scattered across the North Island. A better understanding of its past, current and predicted future environmental suitability will contribute to its conservation which is in jeopardy due to human activities, feral predators, disease and climate change. Here we use ecological niche modelling with all known occurrence data (N = 1708) and six determinant environmental variables to elucidate current, pre-human and future environmental suitability of this species. Comparison among independent runs, subfossil records and a clamping method allow validation of models. Many areas identified as currently suitable do not host any known populations. This apparent discrepancy could be explained by several non exclusive hypotheses: the areas have not been adequately surveyed and undiscovered populations still remain, the model is over simplistic; the species` sensitivity to fragmentation and small population size; biotic interactions; historical events. An additional outcome is that apparently suitable, but frog-less areas could be targeted for future translocations. Surprisingly, pre-human conditions do not differ markedly highlighting the possibility that the range of the species was broadly fragmented before human arrival. Nevertheless, some populations, particularly on the west of the North Island may have disappeared as a result of human mediated habitat modification. Future conditions are marked with higher temperatures, which are predicted to be favourable to the species. However, such virtual gain in suitable range will probably not benefit the species given the highly fragmented nature of existing habitat and the low dispersal ability of this species. (C) 2010 Elsevier Ltd. All rights reserved.

Replacement of the arginine biosynthesis operon in Xanthomonadales by ateral gene transfer

The role of lateral gene transfer (LGT) in prokaryotes has been shown to rapidly change the genome content, providing new gene tools for environmental adaptation. Features related to pathogenesis and resistance to strong selective conditions have been widely shown to be products of gene transfer between bacteria. The genomes of the gamma-proteobacteria from the genus Xanthomonas, composed mainly of phytopathogens, have potential genomic islands that may represent imprints of such evolutionary processes. In this work, the evolution of genes involved in the pathway responsible for arginine biosynthesis in Xanthomonadales was investigated, and several lines of evidence point to the foreign origin of the arg genes clustered within a potential operon. Their presence inside a potential genomic island, bordered by a tRNA gene, the unusual ranking of sequence similarity, and the atypical phylogenies indicate that the metabolic pathway for arginine biosynthesis was acquired through LGT in the Xanthomonadales group. Moreover, although homologues were also found in Bacteroidetes (Flavobacteria group), for many of the genes analyzed close homologues are detected in different life domains (Eukarya and Archaea), indicating that the source of these arg genes may have been outside the Bacteria clade. The possibility of replacement of a complete primary metabolic pathway by LGT events supports the selfish operon hypothesis and may occur only under very special environmental conditions. Such rare events reveal part of the history of these interesting mosaic Xanthomonadales genomes, disclosing the importance of gene transfer modifying primary metabolism pathways and extending the scenario for bacterial genome evolution.

Using non-homogeneous Poisson models with multiple change-points to estimate the number of ozone exceedances in Mexico City

In this paper, we consider some non-homogeneous Poisson models to estimate the probability that an air quality standard is exceeded a given number of times in a time interval of interest. We assume that the number of exceedances occurs according to a non-homogeneous Poisson process (NHPP). This Poisson process has rate function lambda(t), t >= 0, which depends on some parameters that must be estimated. We take into account two cases of rate functions: the Weibull and the Goel-Okumoto. We consider models with and without change-points. When the presence of change-points is assumed, we may have the presence of either one, two or three change-points, depending of the data set. The parameters of the rate functions are estimated using a Gibbs sampling algorithm. Results are applied to ozone data provided by the Mexico City monitoring network. In a first instance, we assume that there are no change-points present. Depending on the adjustment of the model, we assume the presence of either one, two or three change-points. Copyright (C) 2009 John Wiley & Sons, Ltd.

Estimating the number of ozone peaks in Mexico City using a non-homogeneous Poisson model

In this paper, we consider the problem of estimating the number of times an air quality standard is exceeded in a given period of time. A non-homogeneous Poisson model is proposed to analyse this issue. The rate at which the Poisson events occur is given by a rate function lambda(t), t >= 0. This rate function also depends on some parameters that need to be estimated. Two forms of lambda(t), t >= 0 are considered. One of them is of the Weibull form and the other is of the exponentiated-Weibull form. The parameters estimation is made using a Bayesian formulation based on the Gibbs sampling algorithm. The assignation of the prior distributions for the parameters is made in two stages. In the first stage, non-informative prior distributions are considered. Using the information provided by the first stage, more informative prior distributions are used in the second one. The theoretical development is applied to data provided by the monitoring network of Mexico City. The rate function that best fit the data varies according to the region of the city and/or threshold that is considered. In some cases the best fit is the Weibull form and in other cases the best option is the exponentiated-Weibull. Copyright (C) 2007 John Wiley & Sons, Ltd.

Using stochastic volatility models to analyse weekly ozone averages in Mexico City

In this paper we make use of some stochastic volatility models to analyse the behaviour of a weekly ozone average measurements series. The models considered here have been used previously in problems related to financial time series. Two models are considered and their parameters are estimated using a Bayesian approach based on Markov chain Monte Carlo (MCMC) methods. Both models are applied to the data provided by the monitoring network of the Metropolitan Area of Mexico City. The selection of the best model for that specific data set is performed using the Deviance Information Criterion and the Conditional Predictive Ordinate method.

Predator-prey models: an application for the plankton dynamics of lake Geneva

In this paper we present a hierarchical Bayesian analysis for a predator-prey model applied to ecology considering the use of Markov Chain Monte Carlo methods. We consider the introduction of a random effect in the model and the presence of a covariate vector. An application to ecology is considered using a data set related to the plankton dynamics of lake Geneva for the year 1990. We also discuss some aspects of discrimination of the proposed models.

Study of environmental burden of lead in children using teeth as bioindicator

The south region of Sao Paulo city hosts the Guarapiranga dam, responsible for water supply to 25% of the city population. Their surroundings have been subject to intense and irregular occupation by people from very low socioeconomics classes. Measurements undertaken on sediment and particulate materials in the dam revealed concentrations of lead. copper, zinc and cadmium above internationally accepted limits. Epidemiological and toxicological studies undertaken by the World Health Organization in individuals exhibiting lead concentrations in blood, near or below the maximum recommended (10 mu g dl(-1)), surprisingly revealed that toxic effects are more intense in individuals belonging to low socioeconomics classes. Motivated by these facts, we aimed at the investigation of chronic incorporation of lead. as well as the use of our BIOKINETICS code, which is based on an accepted ICRP biokinetics model for lead, in order to extrapolate the results from teeth to other organs. The focus of our data taking was children from poor families, living in a small, restrict and allegedly contaminated area in Sao Paulo city. Thus, a total of 74 human teeth were collected. The average concentration of lead in teeth of children 5 to 10 years old was determined by means of a high-resolution inductively coupled plasma mass spectrometer (ICP-MS). For standardization of the measurements, an animal bone certified material (H-Animal Bone), from the International Atomic Energy Agency, was analyzed. The amount of lead in children living in the surroundings of the dam, was approximately 40% higher than those from the control region, and the average lead concentration was equal to 1.3 mu g g(-1) approximately. Grouping the results in terms of gender, tooth type and condition, it was concluded that a carious molar of boys is a much more efficient contamination pathway for lead, resulting in concentrations 70% higher than in the control region. We also inferred the average concentrations of lead in other organs of these children, by making use of our BIOKINETIC code. (C) 2008 Elsevier Ltd. All rights reserved.

Characterization of organic matter in sediment cores of the Todos os Santos Bay, Bahia, Brazil, by elemental analysis and (13)C NMR

The impact of human activity on the sediments of Todos os Santos Bay in Brazil was evaluated by elemental analysis and (13)C Nuclear Magnetic Resonance ((13)C NMR). This article reports a study of six sediment cores collected at different depths and regions of Todos os Santos Bay. The elemental profiles of cores collected on the eastern side of Frades Island suggest an abrupt change in the sedimentation regime. Auto-regressive Integrated Moving Average (ARIMA) analysis corroborates this result. The range of depths of the cores corresponds to about 50 years ago, coinciding with the implantation of major onshore industrial projects in the region. Principal Component Analysis of the (13)C NMR spectra clearly differentiates sediment samples closer to the Subae estuary, which have high contents of terrestrial organic matter, from those closer to a local oil refinery. The results presented in this article illustrate several important aspects of environmental impact of human activity on this bay. (C) 2011 Elsevier Ltd. All rights reserved.

Bimodal extension based on the skew-normal distribution with application to pollen data

This paper considers an extension to the skew-normal model through the inclusion of an additional parameter which can lead to both uni- and bi-modal distributions. The paper presents various basic properties of this family of distributions and provides a stochastic representation which is useful for obtaining theoretical properties and to simulate from the distribution. Moreover, the singularity of the Fisher information matrix is investigated and maximum likelihood estimation for a random sample with no covariates is considered. The main motivation is thus to avoid using mixtures in fitting bimodal data as these are well known to be complicated to deal with, particularly because of identifiability problems. Data-based illustrations show that such model can be useful. Copyright (C) 2009 John Wiley & Sons, Ltd.

Generalized Birnbaum-Saunders distributions applied to air pollutant concentration

The generalized Birnbaum-Saunders (GBS) distribution is a new class of positively skewed models with lighter and heavier tails than the traditional Birnbaum-Saunders (BS) distribution, which is largely applied to study lifetimes. However, the theoretical argument and the interesting properties of the GBS model have made its application possible beyond the lifetime analysis. The aim of this paper is to present the GBS distribution as a useful model for describing pollution data and deriving its positive and negative moments. Based on these moments, we develop estimation and goodness-of-fit methods. Also, some properties of the proposed estimators useful for developing asymptotic inference are presented. Finally, an application with real data from Environmental Sciences is given to illustrate the methodology developed. This example shows that the empirical fit of the GBS distribution to the data is very good. Thus, the GBS model is appropriate for describing air pollutant concentration data, which produces better results than the lognormal model when the administrative target is determined for abating air pollution. Copyright (c) 2007 John Wiley & Sons, Ltd.

A preliminary characterization of the mutagenicity of atmospheric particulate matter collected during sugar cane harvesting using the Salmonella/microsome microsuspension assay

During sugar cane harvesting season, which occurs from May to November of each year, the crops are burnt, cut, and transported to the mills. There are reports showing that mutagenic activity and PAH content increase during harvesting season in some areas of Sao Paulo State in comparison with nonharvesting periods. The objective of this work was to preliminarily characterize the mutagenic activity of the total organic extracts as well as corresponding organic fractions of airborne particulate matter (PM) collected twice from two cities, Araraquara (ARQ) and Piracicaba (PRB), during sugar cane harvesting season using the Salmonella/microsome microssuspension assay. One sample collected in Sao Paulo metropolitan area was also included. The mutagenicity of the total extracts ranged from 55 to 320 revertants per cubic meter without the addition of S9 and from not detected to 57 revertants per cubic meter in the presence of S9 in areas with sugar cane plantations. Of the three fractions analyzed, the most polar ones (nitro and oxy) were the most potent. A comparison of the response of TA98 with YG1041 and the increased potencies without S9 indicated that nitro compounds are causing the observed effect. More studies are necessary to verify the sources of the mutagenic activity such as burning of vegetal biomass and combustion of heavy duty vehicles used to transport the sugar cane to the mills. The Salmonella/microsome assay can be an important tool to monitor the atmosphere for mutagenicity during sugar cane harvesting season.

State Senate Environmental Performance 2007-2009

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A broad-spectrum mer operon in a multi-drug resistant strain of the fish pathogen, Aeromonas salmonicida

Aeromonas salmonicida AS03, a potential fish pathogen, was isolated from Atlantic salmon, Salmo salar, in 2003. This strain was found to be resistant to ≥1000 mM HgCl2 and ≥32 mM phenylmercuric acetate as well as multiple antimicrobials. Mercury (Hg) and antibiotic resistance genes are often located on the same mobile genetic elements, so the genetic determinants of both resistances and the possibility of horizontal gene transfer were examined. Specific PCR primers were used to amplify and sequence distinctive regions of the mer operon. A. salmonicida AS03 was found to have a pDU1358-like broad-spectrum mer operon, containing merB as well as merA, merD, merP, merR and merT, most similar to Klebsiella pneumonaie plasmid pRMH760. To our knowledge, the mer operon has never before been documented in Aeromonas spp. PCR and gene sequencing were used to identify class 1 integron associated antibiotic resistance determinants and the Tet A tetracycline resistance gene. The transposase and resolvase genes of Tn1696 were identified through PCR and sequencing with Tn21 specific PCR primers. We provide phenotypic and genotypic evidence that the mer operon, the aforementioned antibiotic resistances, and the Tn1696 transposition module are located on a single plasmid or conjugative transposon that can be transferred to E. coli DH5α through conjugation in the presence of low level Hg and absence of any antibiotic selective pressure. Additionally, the presence of low-level Hg or chloramphenicol in the mating media was found to stimulate conjugation, significantly increasing the transfer frequency of conjugation above the transfer frequency measured with mating media lacking both antibiotics and Hg. This research demonstrates that mercury indirectly selects for the dissemination of the antibiotic resistance genes of A. salmonicida AS03.

Enforcement in environmental law: an economic analysis of citizen suits

Previous to 1970, state and federal agencies held exclusive enforcement responsibilities over the violation of pollution control standards. However, recognizing that the government had neither the time nor resources to provide full enforcement, Congress created citizen suits. Citizen suits, first amended to the Clean Air Act in 1970, authorize citizens to act as private attorney generals and to sue polluters for violating the terms of their operating permits. Since that time, Congress has included citizen suits in 13 other federal statutes. The citizen suit phenomenon is sufficiently new that little is known about it. However, we do know that citizen suits have increased rapidly since the early 1980's. Between 1982 and 1986 the number of citizen suits jumped from 41 to 266. Obviously, they are becoming a widely used method of enforcing the environmental statutes. This paper will provide a detailed description, analysis and evaluation of citizen suits. It will begin with an introduction and will then move on to provide some historic and descriptive background on such issues as how citizen suit powers are delegated, what limitations are placed on the citizens, what parties are on each side of the suit, what citizens can enforce against, and the types of remedies available. The following section of the paper will provide an economic analysis of citizen suits. It will begin with a discussion of non-profit organizations, especially non-profit environmental organizations, detailing the economic factors which instigate their creation and activities. Three models will be developed to investigate the evolution and effects of citizen suits. The first model will provide an analysis of the demand for citizen suits from the point of view of a potential litigator showing how varying remedies, limitations and reimbursement procedures can effect both the level and types of activities undertaken. The second model shows how firm behavior could be expected to respond to citizen suits. Finally, a third model will look specifically at the issue of efficiency to determine whether the introduction of citizen enforcement leads to greater or lesser economic efficiency in pollution control. The database on which the analysis rests consists of 1205 cases compiled by the author. For the purposes of this project this list of citizen suit cases and their attributes were computerized and used to test a series of hypotheses derived from three original economic models. The database includes information regarding plaintiffs, defendants date notice and/or complaint was filed and statutes involved in the claim. The analysis focuses on six federal environmental statutes (Clean Water Act} Resource Conservation and Recovery Act, Comprehensive Environmental Response Compensation and Liability Act, Clean Air Act, Toxic Substances Control Act, and Safe Drinking Water Act) because the majority of citizen suits have occurred under these statutes.

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.