A Bayesian state-space formulation of dynamic occupancy models

Species occurrence and its dynamic components, extinction and colonization probabilities, are focal quantities in biogeography and metapopulation biology, and for species conservation assessments. It has been increasingly appreciated that these parameters must be estimated separately from detection probability to avoid the biases induced by non-detection error. Hence, there is now considerable theoretical and practical interest in dynamic occupancy models that contain explicit representations of metapopulation dynamics such as extinction, colonization, and turnover as well as growth rates. We describe a hierarchical parameterization of these models that is analogous to the state-space formulation of models in time series, where the model is represented by two components, one for the partially observable occupancy process and another for the observations conditional on that process. This parameterization naturally allows estimation of all parameters of the conventional approach to occupancy models, but in addition, yields great flexibility and extensibility, e.g., to modeling heterogeneity or latent structure in model parameters. We also highlight the important distinction between population and finite sample inference; the latter yields much more precise estimates for the particular sample at hand. Finite sample estimates can easily be obtained using the state-space representation of the model but are difficult to obtain under the conventional approach of likelihood-based estimation. We use R and WinBUGS to apply the model to two examples. In a standard analysis for the European Crossbill in a large Swiss monitoring program, we fit a model with year-specific parameters. Estimates of the dynamic parameters varied greatly among years, highlighting the irruptive population dynamics of that species. In the second example, we analyze route occupancy of Cerulean Warblers in the North American Breeding Bird Survey (BBS) using a model allowing for site-specific heterogeneity in model parameters. The results indicate relatively low turnover and a stable distribution of Cerulean Warblers which is in contrast to analyses of counts of individuals from the same survey that indicate important declines. This discrepancy illustrates the inertia in occupancy relative to actual abundance. Furthermore, the model reveals a declining patch survival probability, and increasing turnover, toward the edge of the range of the species, which is consistent with metapopulation perspectives on the genesis of range edges. Given detection/non-detection data, dynamic occupancy models as described here have considerable potential for the study of distributions and range dynamics.     

Modelling aggregate exposure to pesticides from dietary and crop spray sources in UK residents

Environmental Science and Pollution Research - Human exposure to pesticide mixtures can occur from the diet and other sources. Realistic exposure and risk assessments should include multiple...     

Archetypical patterns and trajectories of land systems in Europe

Regional Environmental Change - Assessments of land-system change have dominantly focused on conversions among broad land-use categories, whereas intensity changes within these categories have...     

The reuse of reclaimed water for irrigation around the Mediterranean Rim: a step towards a more virtuous cycle?

Regional Environmental Change - Climate change and a growing population around the Mediterranean Rim are increasing the need for water and, consequently, the pressure on resources in terms of both...     

Bioaerosols concentrations in working areas in biomethanization facilities

This study sought to fill the gap in information about the type and the concentration of bioaerosols present in the air of biomethanization facilities (BF). Evaluation of bioaerosol composition and concentration was achieved in two biomethanization facilities located in Eastern Canada, during summer and winter. In order to have a thorough understanding of the studied environment, the methodology combined culture of bacteria and molds, qualitiative polymerase chain reaction (qPCR) for specific microorganisms, endotoxin quantification, and next-generation sequencing (NGS) for bacterial diversity. Results revealed that workers in biomethanization facilities are exposed to bioaerosols and pathogenic microorganisms similar to those found in composting plants. However, human exposure levels to bioaerosols are lower in BF than in composting plants. Despite these differences, use of personal protective equipment is recommended to lower the risks of health problems.

Implications: Biomethanization is a new technology used in eastern Canada for waste management. In the next few years, it is expected that there will be an expansion of facilities in response of tight governmental regulations. Workers in biomethanization facilities are exposed to various amounts of bioaerosols composed of some harmful microorganisms. Therefore, monitoring this occupational exposure could be an interesting tool for improving worker’s health.     

Policy Utopias for Nutrient Credit Trading Programs with Nonpoint Sources

A promising program to address water contamination from nutrients is water quality trading (WQT), whereby entities with high abatement costs purchase credits from entities with lower abatement costs. The concept has found some success with point source water pollution, but very few trades have occurred in over 50 programs in the United States (U.S.) that have focused on nonpoint sources (NPSs). To understand why success has been slow, we identified three environments needed for programs to succeed: physical, economic, and institutional. We estimate that only 5% of watersheds in the U.S. currently listed as nutrient impaired provide a viable physical environment for trading nitrogen; 13% are suitable for phosphorus. Economic and institutional challenges would shrink that domain even further. Therefore, we find places with the ideal physical, economic, and institutional environments necessary for feasible WQT programs are virtual policy utopias — rare places with ideal environments. Fortunately, a growing literature provides the tools necessary to identify where these policy utopias are and to expand that domain through a better understanding about how to manage WQT programs more effectively.     

Metal Extraction from Road Sediment using Different Strength Reagents: Impact on Anthropogenic Contaminant Signals

Washoff of road deposited sediment into storm drainsystems is one of the major contributors to nonpoint sourcepollution in urban fluvial networks. These sediments contain avariety of potentially toxic organic and inorganic contaminants.Road sediment from 13 locations in an urban (non-industrialized)drainage basin, and soil from 10 background (control) locationswere collected to assess total and labile fractions of Al, Co,Cu, Fe, Mn, Ni, Pb and Zn. Four digestions, of varying strength,were used to assess contaminant levels, these included: a totalfour-acid digestion, a microwave-assisted digestion withconcentrated nitric acid (USEPA Method 3051), a 0.5 M `cold' HCl,and a 0.05 M EDTA (pH 7). Road sediment data indicate that Al,Co, Fe, Mn and Ni were primarily lithogenic in origin, while Cu,Pb and Zn showed very significant anthropogenic signals, mostprobably from vehicle-related sources. Median Pb concentrationenrichment ratios for the EDTA extraction were about 42,indicating an extreme anthropogenic signal. The weak extractants(HCl and EDTA) are considered in this study to be superior intheir ability to characterize the degree of anthropogeniccontamination and should be utilized more widely in environmentalcontaminant studies.     

Mercury accumulation in fish species from the Persian Gulf and in human hair from fishermen

Total and methylmercury concentrations were assessed in muscle and liver of 141 fish samples from the northern part of the Persian Gulf. All fish samples belonged to five different species: grunt, flathead, greasy grouper, tiger-tooth croaker, and silver pomfret. In addition, Hg and methylmercury were analyzed in scalp hair of 19 fishermen living in the same coastal stations of the Persian Gulf and consuming several fish meals a week. Total mercury concentrations in fish muscle and liver ranged from 0.01 to 1.35 μg g^???1 w.w. and from 0.02 to 1.30 μg g^???1 w.w., respectively. In fish muscle, 3% of the Hg concentrations were higher than 0.5 μg g^???1 w.w., which corresponds to the maximum acceptable WHO level, while 9% were in the range of polluted fish (between 0.3 and 0.5 μg g^???1 w.w.). The highest mercury concentrations in fish muscle were observed in flathead fish at Abadan (average of 0.68 μ g g^???1 w.w.). Methylmercury fractions in fish muscle and liver amount to 34–99% (median 64%) and 24–70% (median 43%), respectively. The mean total Hg concentration in the fishermen’s scalp hair amounted to 2.9 ± 2.2 μ g g^???1, with 68% in the form of methylmercury. Ninety-five percent of the Hg levels in the fishermen’s hair were below 10 μ g g^???1, which is the WHO warning limit. In addition, relationships between the mercury levels in hair, on the one hand, and exposure-related factors such as Hg levels in specific fish species, regional differences, and number of fish meals, on the other hand, are discussed. It appears that a significant correlation for example exists between Hg levels human hair and fish muscle or human hair and age and that mean mercury levels in fish muscle and human hair decreased from western (Abadan) to eastern (Abbas port) coastal sites.     

Interspecific and geographical variations of trace metal concentrations in cephalopods from Tunisian waters

The concentrations of six metals (Ag, Cd, Cu, Hg, Pb, and Zn) were investigated and compared in three tissues (arms, digestive gland, and mantle) of three cephalopod species from the Tunisian waters: the common octopus (Octopus vulgaris), the common cuttlefish (Sepia officinalis), and the European squid (Loligo vulgaris). Whatever the species or the sites, the digestive gland displayed the highest concentrations of Ag, Cd, Cu, Pb, and Zn, highlighting its major role in their bioaccumulation and detoxification. This is also true for Hg but only for the digestive gland of O. vulgaris. Muscle from the arms and the mantle contained thus relatively low trace metal concentrations except for Hg in L. vulgaris and S. officinalis. Geographic comparison of metal concentrations in Tunisian cephalopods from three locations indicates that higher concentrations of Ag, Pb, and Hg were observed in cephalopods from northern and eastern coasts, whereas the highest Cd levels were detected in the southeastern, reflecting different conditions of exposure. Comparing the trace element concentrations between species, Ag, Cd, Cu, Hg, and Zn concentrations were the highest in the digestive gland of octopuses. This may be related to the differences in ecological features and swimming behavior among different cephalopod species. Effects of length and sex on metal levels were also considered, indicating a limited influence of sex on metal concentration.