Generalized site occupancy models allowing for false positive and false negative errors

Site occupancy models have been developed that allow for imperfect species detection or "false negative" observations. Such models have become widely adopted in surveys of many taxa. The most fundamental assumption underlying these models is that "false positive" errors are not possible. That is, one cannot detect a species where it does not occur. However, such errors are possible in many sampling situations for a number of reasons, and even low false positive error rates can induce extreme bias in estimates of site occupancy when they are not accounted for. In this paper, we develop a model for site occupancy that allows for both false negative and false positive error rates. This model can be represented as a two-component finite mixture model and can be easily fitted using freely available software. We provide an analysis of avian survey data using the proposed model and present results of a brief simulation study evaluating the performance of the maximum-likelihood estimator and the naive estimator in the presence of false positive errors.     

Estimating species richness and accumulation by modeling species occurrence and detectability

A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.     

Mercury accumulation in soils and plants in the Almadén mining district, Spain: one of the most contaminated sites on Earth

Although mercury (Hg) mining in the Almadén district ceased in May 2002, the consequences of 2000 years of mining in the district has resulted in the dissemination of Hg into the surrounding environment where it poses an evident risk to biota and human health. This risk needs to be properly evaluated. The uptake of Hg has been found to be plant-specific. To establish the different manners in which plants absorb Hg, we carried out a survey of Hg levels in the soils and plants in the most representative habitats of this Mediterranean area and found that the Hg concentrations varied greatly and were dependent on the sample being tested (0.13–2,695 μg g⁻¹ Hg). For example, the root samples had concentrations ranging from 0.06 (Oenanthe crocata, Rumex induratus) to 1095 (Polypogon monspeliensis) μg g⁻¹ Hg, while in the leaf samples, the range was from 0.16 (Cyperus longus) to 1278 (Polypogon monspeliensis) μg g⁻¹ Hg. There are four well-differentiated patterns of Hg uptake: (1) the rate of uptake is constant, independent of Hg concentration in the soil (e.g., Pistacia lentiscus, Quercus rotundifolia); (2) after an initial linear relationship between uptake and soil concentration, no further increase in Hg_plant is observed (e.g., Asparagus acutifolius, Cistus ladanifer); (3) no increase in uptake is recorded until a threshold is surpassed, and thereafter a linear relationship between Hg_plant and Hg_soil is established (e.g., Rumex bucephalophorus, Cistus crispus); (4) there is no relationship between Hg_plant and Hg_soil (e.g., Oenanthe crocata and Cistus monspeliensis). Overall, the Hg concentrations found in plants from the Almadén district clearly reflect the importance of contamination processes throughout the study region.     

Perfluorinated chemicals in selected residents of the American continent

Perfluorinated chemicals (PFCs) are used in multiple consumer products. Perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), the most widely studied PFCs, may be potential developmental, reproductive, and systemic toxicants. Although PFCs seem to be ubiquitous contaminants found both in humans and animals, geographic differences may exist in human exposure patterns to PFCs. We measured 11 PFCs in 23 pooled serum samples collected in the United States from 1990 through 2002, and in serum samples collected in 2003 from 44 residents from Trujillo, Peru. PFOS and PFOA were detected in all the pooled samples; perfluorohexane sulfonic acid (PFHxS) was detected in 21. Median concentrations were 31.1 micrograms per liter (mug/l, PFOS), 11.6 microg/l (PFOA), and 2 microg/l (PFHxS). The 90th percentile concentrations of PFCs in the 44 Peruvian residents were 0.7 microg/l (PFOS), 0.1 microg/l (PFOA), and <0.3 microg/l (PFHxS). The frequencies of detection were 20% (PFOS), 25% (PFOA), and 9% (PFHxS). The frequent detection of selected PFCs in the pooled samples from the United States and the lack of clear concentration trends based on a year of collection suggest a sustained widespread exposure to these compounds among US residents, at least since the 1990s. By contrast, the much lower frequency of detection and concentration ranges of PFCs in Peru suggest a lower exposure of Peruvians to PFCs compared with North Americans. Genetic variability, diet, lifestyle, or a combination of all these may contribute to the different patterns of human exposure to PFCs in the United States and Peru.     

Pesticides and metabolites in cassava, eucalyptus, plum and cashew leaves and roots in relation to a point source in Kibaha, Tanzania

Leaves of Eucalyptus sp., Prunus domestica (plum), and Anacardium occidentale (cashew), as well as roots and leaves of Manihot esculenta (cassava) were used to study the local distribution of pesticides and metabolites from a point source, an old storage site at Vikuge farm in Tanzania. The GPC-cleaned extracts were analyzed by GC-ECD and GC/MS. Eleven organochlorine pesticide residues namely pentachloroanisole, p,p'-DDT, o,p'-DDT, p,p'-DDE, o,p'-DDE, p,p'-DDD, o,p'-DDD, alpha-HCH, beta-HCH, delta-HCH and epsilon-HCH were detected in the samples. The concentrations of total DDT were 818 ng/g fw in Eucalyptus sp., 16 ng/g fw in A. occidentale and 4 ng/g fw in P. domestica. In M. esculenta, total DDT ranged from 191 to 586 ng/g fw in roots and 7 to 425 ng/g fw in leaves. The concentrations of total HCH were up to 15 ng/g fw in Eucalyptus sp., while the concentrations of pentachloroanisole were up to 2 ng/g fw in leaves of M. esculenta. There are very strong positive correlations in the concentrations of the detected compounds, suggesting that they have a common source. The low DDE/DDT ratios (0.02-0.07) in all samples indicate input of non-degraded DDT from the source. The high alpha-HCH/gamma-HCH ratios in some samples (>3.1-10) indicate input of technical HCH. The concentrations of total DDT in cassava roots were either very close to, or greater than, the FAO/WHO limit, indicating risks and concern to public health.     

Modelling the extra and intracellular uptake and discharge of heavy metals in Fontinalis antipyretica transplanted along a heavy metal and pH contamination gradient

Samples of the aquatic bryophyte Fontinalis antipyretica Hedw. were transplanted to different sites with the aim of characterizing the kinetics of the uptake and discharge of heavy metals in the extra and intracellular compartments. The accumulation of metals in extracellular compartments, characterized by an initial rapid accumulation, then a gradual slowing down over time, fitted perfectly to a Michaelis-Menten model. The discharge of metals from the same compartment followed an inverse linear model or an inverse Michaelis-Menten model, depending on the metal. In intracellular sites both uptake and discharge occurred more slowly and progressively, following a linear model. We also observed that the acidity of the environment greatly affected metal accumulation in extracellular sites, even when the metals were present at relatively high concentrations, whereas the uptake of metals within cells was much less affected by pH.     

Arsenic chemistry in the rhizosphere of Pteris vittata L. and Nephrolepis exaltata L

This greenhouse experiment evaluated the influence of arsenic uptake by arsenic hyperaccumulator Pteris vittata L. and non-arsenic hyperaccumulator Nephrolepis exaltata L. on arsenic chemistry in bulk and rhizosphere soil. The plants were grown for 8 weeks in a rhizopot with a soil containing 105 mg kg(-1) arsenic. The soil arsenic was fractionated into five fractions with decreasing availability: non-specifically bound (N), specifically bound (S), amorphous hydrous-oxide bound (A), crystalline hydrous-oxide bound (C), and residual (R). P. vittata produced larger plant biomass (7.38 vs. 2.32 mg plant(-1)) and removed more arsenic (2.61 vs. 0.09 mg pot(-1) arsenic) than N. exaltata. Plant growth reduced water-soluble arsenic, and increased soil pH (P. vittata only) in the rhizosphere soil. P. vittata was more efficient than N. exaltata to access arsenic from all fractions (39-64% vs. 5-39% reduction). However, most of the arsenic taken up by both plants was from the A fraction (67-77%) in the rhizosphere soil, the most abundant (61.5%) instead of the most available (N fraction).     

Suitability of Crangonyx pseudogracilis (Crustacea: Amphipoda) as an Early Warning Indicator in the Multispecies Freshwater Biomonitor (9 pp)

Background Biological monitors are increasingly important in 'Biological Early Warning Systems' (BEWS) for monitoring water quality. This study examines the freshwater amphipod Crangonyx pseudogracilis as a potential new indicator species when used in the Multispecies Freshwater Biomonitor (MFB). The MFB is an online continuous biomonitor which uses impedance conversion to record behavioural responses of vertebrates and invertebrates. Methods Four experiments were undertaken to establish: (1) if the electrical field generated by the MFB affected the organisms' behaviour, (2) if defined behaviours and their response to a gradient of ammonium chloride could be detected by the MFB, (3) if there was variation in the behaviour of C. pseudogracilis over a diel cycle, and (4) if behaviour changed significantly in response to a pulse of ammonium chloride. Results and Discussion Results showed no significant effect of the MFB's current on behaviour of C. pseudogracilis. Four behaviours; swimming, walking, grooming and inactivity, were observed and identified in the MFB. In the MFB, each behaviour changed significantly in response to an increasing gradient of ammonium chloride exposure. The MFB also detected increases in nocturnal activity by C. pseudogracilis. The MFB also detected a significant increase in activity after a pulse of ammonium chloride. Conclusion The range of behaviours exhibited by Crangonyx pseudogracilis, together with its ease of culture, suggest future potential of this species as an indicator species for the Multispecies Freshwater Biomonitor. Recommendations and Perspective . Further testing is required over a range of toxicants and concentration gradients to establish threshold responses and the full compliment of behaviours that could be useful in online biomonitoring.     

Quality assured measurements of animal building emissions: gas concentrations

Comprehensive field studies were initiated in 2002 to measure emissions of ammonia (NH3), hydrogen sulfide (H2S), carbon dioxide (CO2), methane (CH4), nonmethane hydrocarbons (NMHC), particulate matter <10 microm in diameter, and total suspended particulate from swine and poultry production buildings in the United States. This paper focuses on the quasicontinuous gas concentration measurement at multiple locations among paired barns in seven states. Documented principles, used in air pollution monitoring at industrial sources, were applied in developing quality assurance (QA) project plans for these studies. Air was sampled from multiple locations with each gas analyzed with one high quality commercial gas analyzer that was located in an environmentally controlled on-farm instrument shelter. A nominal 4 L/min gas sampling system was designed and constructed with Teflon wetted surfaces, bypass pumping, and sample line flow and pressure sensors. Three-way solenoids were used to automatically switch between multiple gas sampling lines with > or =10 min sampling intervals. Inside and outside gas sampling probes were between 10 and 115 m away from the analyzers. Analyzers used chemiluminescence, fluorescence, photoacoustic infrared, and photoionization detectors for NH3, H2S, CO2, CH4, and NMHC, respectively. Data were collected using personal computer-based data acquisition hardware and software. This paper discusses the methodology of gas concentration measurements and the unique challenges that livestock barns pose for achieving desired accuracy and precision, data representativeness, comparability and completeness, and instrument calibration and maintenance.