Accounting for matching uncertainty in two stage capture–recapture experiments using photographic measurements of natural marks

We propose a Bayesian hierarchical modeling approach for estimating the size of a closed population from data obtained by identifying individuals through photographs of natural markings. We assume that noisy measurements of a set of distinctive features are available for each individual present in a photographic catalogue. To estimate the population size from two catalogues obtained during two different sampling occasions, we embed the standard two-stage $M_t$ capture–recapture model for closed population into a multivariate normal data matching model that identifies the common individuals across the catalogues. In addition to estimating the population size while accounting for the matching process uncertainty, this hierarchical modelling approach allows to identify the common individuals by using the information provided by the capture–recapture model. This way, our model also represents a novel and reliable tool able to reduce the amount of effort researchers have to expend in matching individuals. We illustrate and motivate the proposed approach via a real data set of photo-identification of narwhals. Moreover, we compare our method with a set of possible alternative approaches by using both the empirical data set and a simulation study.     

Definition and calculation of uncertainty in ecological process models

We present a method of multi-criteria assessment for the analysis of process model uncertainty that combines analysis of model structure, parameters and data requirements. There are three components in calculation and definition of uncertainty.

(1)

Assessment criteria: Uncertainty in a process model is reduced as the model can simultaneously simulate an increased number of assessment criteria selected to test specific aspects of the theory being investigated, and within acceptable limits set for those criteria. This reduces incomplete specification of the model—the characteristic that a model may explain some, but not all, of the observed features of a phenomenon. The calculation required is computation of the Pareto set which provides the list of simultaneously achieved criteria within specified ranges.     

Continuity and change: understanding livelihood shifts and adaptation in coastal Belize 1830–2012

This paper situates livelihood adaptations in two coastal villages within the broader context of Belize's colonial and post-colonial history and environmental processes of change. Through observations, qualitative interviews, and archival reviews, we explore the dynamics of livelihood change and analyse the diverse factors that have been influencing options and adaptation over time. The results reveal that both villages have undergone profound changes in livelihoods and productive activities on several occasions. While the villages' histories, geographies, and cultures are different, similarities in long-term trends include the transition from land-based to marine resources and the decline of small-scale agriculture. Our analysis illuminates the deep connections between local livelihoods and national as well as global political–economic processes, which favour extraction and export of natural resources throughout the period investigated, whereby resource access and market mechanisms create and constrict adaptation options for the villagers. Gradual environmental changes, such as erosion, and episodic events, such as hurricanes, have also influenced livelihood shifts and adaptations in combination with a wide range of political–economic factors. Despite the demonstrated importance of the influence of history and dimensions of political economy on contemporary adaptation options in the communities studied, the literature on climate change adaptation inadequately accounts for these factors. This paper adds new perspectives to current debates in climate change research by emphasising that longer temporal dimensions of livelihood change are important for understanding the current context for adaptation.     

Future agriculture with minimized phosphorus losses to waters: Research needs and direction

The series of papers in this issue of AMBIO represent technical presentations made at the 7th International Phosphorus Workshop (IPW7), held in September, 2013 in Uppsala, Sweden. At that meeting, the 150 delegates were involved in round table discussions on major, predetermined themes facing the management of agricultural phosphorus (P) for optimum production goals with minimal water quality impairment. The six themes were (1) P management in a changing world; (2) transport pathways of P from soil to water; (3) monitoring, modeling, and communication; (4) importance of manure and agricultural production systems for P management; (5) identification of appropriate mitigation measures for reduction of P loss; and (6) implementation of mitigation strategies to reduce P loss. This paper details the major challenges and research needs that were identified for each theme and identifies a future roadmap for catchment management that cost-effectively minimizes P loss from agricultural activities.     

Persistent organochlorine compounds in peregrine falcon (Falco peregrinus) eggs from South Greenland: levels and temporal changes between 1986 and 2003

Thirty-seven addled peregrine falcon eggs collected in South Greenland between 1986 and 2003 were analysed for their content of the organochlorine compounds polychlorinated biphenyls (PCBs), dichlorodiphenyl tricloroethane (DDT) and its degradation products, hexachlorocyclohexane (HCH) isomers and hexachlorobenzene (HCB). PCBs and DDT (including metabolites) were by far the most abundant OC groups, with median concentrations of 55 and 40 microg/g lw, respectively. The concentrations were high in an Arctic context, but similar to previously reported levels from Alaska and Norway and slightly lower than concentrations measured in eggs from industrialised regions. Geographical differences may be of importance, considering the migration of peregrine falcons and their prey. SigmaHCH and HCB had median concentrations of 0.39 and 0.17 microg/g lw, respectively. On average, DDE accounted for 97% of SigmaDDT, but was below critical levels for eggshell thinning. All compound groups showed a weak decreasing trend over the study period, which was statistically significant for HCB and close to being significant for SigmaHCH. The weak decrease of SigmaPCB and SigmaDDT is different from other time trend studies from Greenland, usually showing a more pronounced decrease in the beginning of the study period, followed by a certain stabilisation in recent years.     

Tissue distribution and neurotoxic effects of domoic acid in a prominent vector species, the northern anchovy Engraulis mordax

The planktivorous northern anchovy is a prominent vector of the phycotoxin domoic acid (DA) to organisms at higher trophic levels, including fish-eating seabirds and mammals. Although there are abundant data reporting DA-induced excitotoxic symptoms in higher vertebrates, to date there has been no reported evidence of neurotoxic effects in lower vertebrate vectors such as fish. To explain this apparent lack of toxicity, it has been suggested that DA may not reach the brain in anchovies and/or that fish are not as sensitive neurologically to DA. In the present study, intracoelomic (IC) injection of DA, at doses ranging from 1 to 14 μg DA g⁻¹ total fish weight, resulted in severe neurotoxic symptoms such as spinning, disorientation, inability to school, and mortality, indicating that anchovies are neurologically susceptible and that DA crosses the blood–brain barrier in fish. An ED₅₀ of 3.2 μg DA g⁻¹ total body weight was determined via IC injection of DA in 83 anchovies. Comparable intraperitoneal injection studies with mice, rats, and monkeys report similar DA-induced neurotoxic symptoms at doses near 3.2 μg DA g⁻¹, suggesting a similar neurologic sensitivity and mechanism of toxicity between anchovies and mammals. DA tissue distribution measurements from freshly collected field-exposed anchovies and orally gavaged anchovies indicate that DA uptake from the gastrointestinal tract does occur. Levels as high as 1,175 μg DA g⁻¹ were measured in anchovy viscera, while muscle and brain tissue DA levels were 3 orders of magnitude lower, indicating low but measurable DA uptake. Further evidence is needed to confirm that uptake is sufficient during field events to induce symptoms in anchovies. Our work provides the first reported evidence of neurotoxic symptoms in fish and suggests that anchovies may be affected by DA during toxic diatom blooms. If sufficient uptake occurs, DA-induced neurotoxic symptoms and mortality may make fish easier prey targets, thereby selecting for the highest toxin levels transferred, as well as providing a possible pathway for the transfer of DA to benthic communities. Received: 19 May 2000 / Accepted: 29 November 2000     

Dissolution and sorption of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT) residues from detonated mineral surfaces

Composition B (Comp B) is a commonly used military formulation composed of the toxic explosive compounds 2,4,6-trinitrotoluene (TNT), and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Numerous studies of the temporal fate of explosive compounds in soils, surface water and laboratory batch reactors have been conducted. However, most of these investigations relied on the application of explosive compounds to the media via aqueous addition and thus these studies do not provide information on the real world loading of explosive residues during detonation events. To address this we investigated the dissolution and sorption of TNT and RDX from Comp B residues loaded to pure mineral phases through controlled detonation. Mineral phases included nontronite, vermiculite, biotite and Ottawa sand (quartz with minor calcite). High Performance Liquid Chromatography and Attenuated Total Reflectance Fourier Transform Infrared spectroscopy were used to investigate the dissolution and sorption of TNT and RDX residues loaded onto the mineral surfaces. Detonation resulted in heterogeneous loading of TNT and RDX onto the mineral surfaces. Explosive compound residues dissolved rapidly (within 9 h) in all samples but maximum concentrations for TNT and RDX were not consistent over time due to precipitation from solution, sorption onto mineral surfaces, and/or chemical reactions between explosive compounds and mineral surfaces. We provide a conceptual model of the physical and chemical processes governing the fate of explosive compound residues in soil minerals controlled by sorption-desorption processes.     

Women's experiences with second trimester prenatal diagnosis

By means of questionnaires, 100 women were asked for their experiences concerning prenatal diagnosis. At four standardized stages of the pregnancy a questionnaire was filled in asking for: expectation, knowledge, attitude towards termination of the pregnancy in case of abnormal findings, reactions to the counselling and the obstetric treatment, interpretation of own risk, experiences since the normal test results were known and ideas to improve the treatment. With regard to the effect of pre-amniocentesis counselling it is concluded that the counselling had little impact on decision making; the counselling caused an increase of factual knowledge: somewhat more than half of the women who did not give a correct answer before counselling, indicated the right answer some time afterwards. Presumed differences in reaction patterns for a number of characteristics were not affirmed by the study; the reactions during the procedure of prenatal diagnosis seem to be highly individual and difficult to predict. In addition to the reactions of the 100 women described in this study, the responses to the first questionnaire of another 16 patients, declining amniocentesis after counselling, are presented.