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.     

Adding infection to injury: synergistic effects of predation and parasitism on amphibian malformations

We explored the importance of interactions between parasite infection and predation in driving an emerging phenomenon of conservation importance: amphibian limb malformations. We suggest that injury resulting from intraspecific predation in combination with trematode infection contributes to the frequency and severity of malformations in salamanders. By integrating field surveys and experiments, we evaluated the individual and combined effects of conspecific attack and parasite (Ribeiroia ondatrae) infection on limb development of long-toed salamanders (Ambystoma macrodactylum). In the absence of Ribeiroia, abnormalities involved missing digits, feet, or limbs and were similar to those produced by cannibalistic attack in experimental trials. At field sites that supported Ribeiroia, malformations were dominated by extra limbs and digits. Correspondingly, laboratory exposure of larval salamanders to Ribeiroia cercariae over a 30-day period induced high frequencies of malformations, including extra digits, extra limbs, cutaneous fusion, and micromelia. However, salamander limbs exposed to both injury and infection exhibited 3-5 times more abnormalities than those exposed to either factor alone. Infection also caused significant delays in limb regeneration and time-to-metamorphosis. Taken together, these results help to explain malformation patterns observed in natural salamander populations while emphasizing the importance of interactions between parasitism and predation in driving disease.     

Photocatalytic oxidation of soot by P25 TiO2 films

The photomineralisation of soot by P25 titania films is studied using FT-IR and the process shown to involve the oxidation of carbon to CO2 exclusively. The efficiency of this process is low, however, with a formal quantum efficiency of 1.1 x 10(-4) molecules of carbon oxidized per incident photon of UVA light. The cause of this low efficiency is attributed largely to the less than intimate contact between the fibrous soot layer and the surface of the photocatalyst.     

Evaluation of diffusive gradients in thin film (DGT) samplers for measuring contaminants in the Antarctic marine environment

This work has been the first application of DGT samplers for measuring metals in water and sediment porewater in the Antarctic environment, and whilst DGT water sampling was restricted to quantification of Cd, Fe and Ni, preconcentration using Empore chelating disks provided results for an additional nine elements (Sn, Pb, Al, Cr, Mn, Co, Cu, Zn, As). Although higher concentrations were measured for some metals (Cd, Ni, Pb) using the Empore technique, most likely due to particulate-bound or colloidal species becoming entrapped in the Empore chelating disks, heavy metal concentrations in the impacted Brown Bay were found to be comparable with the non-impacted O'Brien Bay. Sediment porewater sampling using DGT also indicated little difference between Brown Bay and O'Brien Bay for many metals (Cd, Al, Cr, Co, Ni, Cu), however, greater amounts of Pb, Mn, Fe and As were accumulated in DGT probes deployed in Brown Bay compared with O'Brien Bay, and a higher accumulation of Sn was observed in Brown Bay inner than any of the other three sites sampled. Comparison of DGT derived porewater concentrations with actual porewater concentrations showed limited resupply of Cd, Pb, Al, Cr, Mn, Co, Ni, Cu, Zn and As from the solid phase to porewater, with these metals appearing to be strongly bound to the sediment, however, resupply of Fe and Sn was apparent. Based upon our observations here, we suggest that Sn, and to a lesser extent Pb, are critical contaminants.     

Global pilot study for persistent organic pollutants (POPs) using PUF disk passive air samplers

Polyurethane foam (PUF) disks were deployed at global background sites, to test logistical issues associated with a global monitoring network for persistent organic pollutants (POPs). alpha-HCH, exhibited relatively high and uniform concentrations (17-150 pg/m3) at temperate and arctic sites with elevated concentrations associated with trans-Pacific inflow. Concentrations were much lower (<5 pg/m3) in Bermuda, Chile and Cape Grim. Concentrations for gamma-HCH, the main component of lindane, were spatially similar to the alpha-HCH pattern but lower in magnitude (typically, <10 pg/m3). Chlordane concentrations (sum of cis-chlordane, trans-chlordane and trans-nonachlor) were also low (<10 pg/m3). Dieldrin concentrations were in the range 2-25 pg/m3 at most sites but elevated in Bermuda. Back trajectories suggest that advection from Africa and the US may contribute. Endosulfan, a popular current-use pesticide, exhibited highest concentrations ranging from tens to hundreds of pg/m3. There was good agreement between duplicate samplers at each site and PUF disk-derived air concentrations agreed with high volume data. Few logistical/analytical problems were encountered in this pilot study.     

Titration Curves: A Useful Instrument for Assessing the Buffer Systems of Acidic Mining Waters (10 pp)

Background, Aims and Scope The acidification of mine waters is generally caused by metal sulfide oxidation, related to mining activities. These waters are characterized by low pH and high acidity due to strong buffering systems. The standard acidity parameter, the Base Neutralization Capacity (BNC) is determined by endpoint titration, and reflects a cumulative parameter of both hydrogen ions and all buffering systems, but does not give information on the individual buffer systems. We demonstrate that a detailed interpretation of titration curves can provide information about the strength of the buffering systems. The buffering systems are of importance for environmental studies and treatment of acidic mining waters. Methods Titrations were carried out by means of an automatic titrator using acidic mining waters from Germany and Canada. The curves were interpreted, compared with each other, to endpoint titration results and to elemental concentrations contained therein. Results and Discussion The titration curves were highly reproducible, and contained information about the strength of the buffer systems present. Interpretations are given, and the classification and comparison of acidic mining waters, by the nature and strength of their buffering systems derived from titration curves are discussed. The BNC-values calculated from the curves were more precise than the ones determined by the standard endpoint titration method. Due to the complex buffer mechanisms in acidic mining waters, the calculation of major metal concentrations from the shape of the titration curve resulted in estimates, which should not be confused with precise elemental analysis results. Conclusion Titration curves provide an inexpensive, valuable and versatile tool, by which to obtain sophisticated information of the acidity in acidic water. The information about the strength of the present buffer systems can help to understand and document the complex nature of acidic mining water buffer systems. Finally, the interpretation of titration curves could help to improve treatment measurements and the ecological understanding of these acidic waters.     

Comparing the usability and reliability of a generic and a domain-specific medical error taxonomy

Medical error taxonomies are used to report and analyse patient safety incidents. Medical error taxonomies can be generic or domain-specific. In comparing generic and domain-specific medical error taxonomies, the literature compares the information both type of taxonomies classify. There is little evidence the taxonomies have been compared in terms of usability and reliability. Twenty nurses and 21 pharmacists participated in a study comparing the usability and reliability of a generic medical error taxonomy and a medication error taxonomy. The medical error taxonomies utilized were the Patient Safety Event Taxonomy and the NCC MERP Taxonomy of Medication Error. The study found no significant difference in the usability ratings of both taxonomies. The taxonomies required different amount of time to classify patient safety incidents and had significantly different reliability levels. The reliability of the NCC MERP Taxonomy of Medication Error was significantly different when used by nurses and pharmacists. The taxonomy was also preferred by the majority of participants. Some recommendations are made about the design of future medical error taxonomies.     

Detecting deterrence from patrol data

The threat posed to protected areas by the illegal killing of wildlife is countered principally by ranger patrols that aim to detect and deter potential offenders. Deterring poaching is a fundamental conservation objective, but its achievement is difficult to identify, especially when the prime source of information comes in the form of the patrols’ own records, which inevitably contain biases. The most common metric of deterrence is a plot of illegal activities detected per unit of patrol effort (CPUE) against patrol effort (CPUE-E). We devised a simple, mechanistic model of law breaking and law enforcement in which we simulated deterrence alongside exogenous changes in the frequency of offences under different temporal patterns of enforcement effort. The CPUE-E plots were not reliable indicators of deterrence. However, plots of change in CPUE over change in effort (ΔCPUE-ΔE) reliably identified deterrence, regardless of the temporal distribution of effort or any exogenous change in illegal activity levels as long as the time lag between patrol effort and subsequent behavioral change among offenders was approximately known. The ΔCPUE-ΔE plots offered a robust, simple metric for monitoring patrol effectiveness; were no more conceptually complicated than the basic CPUE-E plots; and required no specialist knowledge or software to produce. Our findings demonstrate the need to account for temporal autocorrelation in patrol data and to consider appropriate (and poaching-activity-specific) intervals for aggregation. They also reveal important gaps in understanding of deterrence in this context, especially the mechanisms by which it occurs. In practical applications, we recommend the use of ΔCPUE-ΔE plots in preference to other basic metrics and advise that deterrence should be suspected only if there is a clear negative slope. Distinct types of illegal activity should not be grouped together for analysis, especially if the signs of their occurrence have different persistence times in the environment.     

Bird conservation and the land sharing-sparing continuum in farmland-dominated landscapes of lowland England

Empirical evidence from many regions suggests that most species would be least negatively affected if human food demand were met through high-yield agricultural production and conservation of nonfarm ecosystems (land sparing), rather than through wildlife-friendly farming over a larger area (land sharing). However, repeated glaciation and a long history of agriculture may lead to different results in regions such as western Europe. We compared the consequences of land sparing and land sharing on breeding bird species in 2 lowland regions of England, The Fens, with 101 species, and Salisbury Plain, with 83. We derived density–yield responses for each species and then estimated regional population size under regional food production strategies, including land sharing and land sparing, a range of intermediate strategies, and a novel mixed strategy. In both regions, more species achieved maximum regional population size under land sparing than land sharing. In The Fens, the majority of birds were loser species (estimated to have smaller populations under all food production strategies than in the preagricultural baseline scenario), whereas in Salisbury Plain the majority were winners (smaller populations in the preagricultural baseline scenario). Loser species overwhelmingly achieved maximum regional population size under land sparing, whereas winner species achieved maximum regional population size under either land sharing or an intermediate strategy, highlighting the importance of defining which groups of species are the target of conservation. A novel 3-compartment strategy (combining high-yield farming, natural habitat, and low-yield farming) often performed better than either land sharing or land sparing. Our results support intermediate or 3-compartment land-sparing strategies to maximize bird populations across lowland agricultural landscapes. To deliver conservation outcomes, any shift toward land sparing must, however, ensure yield increases are sustainable in the long term, do not entail increased negative effects on surrounding areas, and are linked to allocation of land for nature.