Generalized estimators of avian abundance from count survey data

I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture-recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations) constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed

Traditional Korean islanders encounters with the British navy in the 1880s: The Port Hamilton Affair of 1885-1887

This article deals with the encounters between a traditional Korean rural and island population and western military forces when the British navy occupied Geomundo, an archipelago known to them as Port Hamilton, for 22 months between 1885 and 1887. The paper first outlines the sometimes painful process of East Asian countries being opened up to trade and outside influences in the 19th century, a process sometimes urged upon them by naval weapons in this era of gunboat diplomacy. This provides the setting for the Port Hamilton Affair itself when in preparation for possible war with Russia, a British naval squadron steamed into Port Hamilton and took it without reference to the local people or their national government. After brief reference to the political consequences of this action, the focus is then on what the records from the occupation and earlier investigations by the British, who had long coveted the islands’ strategic harbour, reveal about the life of the islanders. The article considers both their traditional life, from a time rather before western travel accounts were written about the Korean mainland, and how the islanders fared under the British

Estimadores generalizados de abundancia en aves a partir de datos de estudios de recuento

I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture–recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations) constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.En el presente estudio se analiza la modelación de la abundancia en aves mediante datos de recuento de aves, referenciados espacialmente y obtenidos a partir de protocolos comunes, como los de captura–recaptura, muestreo por observadores múltiples, muestreo por eliminación y recuentos de puntos simples. Las muestras de pequeño tamaño, así como el amplio número de parámetros, han propiciado numerosos análisis que no tienen en cuenta la indexación espacial de los datos y, por consiguiente, no proporcionan un tratamiento adecuado de la estructura espacial. En este trabajo se describe un marco general para la modelación de datos replicados en el espacio, que considera la abundancia local como un proceso aleatorio, todo ello basado en el punto de vista de que el conjunto de poblaciones locales referenciadas espacialmente (en los lugares de toma de muestras) constituye una metapoblación. De este modo, la atención puede centrarse en el desarrollo de un modelo para la variación en la abundancia local que sea independiente del protocolo de muestreo que se esté utilizando. La estructura del modelo metapoblacional, en combinación con el modelo de generación de datos, define un modelo jerárquico simple que puede analizarse mediante el empleo de métodos convencionales. El marco de modelación propuesto es de carácter general, en el sentido de que permite considerar amplias clases de modelos metapoblacionales, covariantes del nivel del emplazamiento sobre datos de detección, y la abundancia, pudiendo obtenerse estimaciones de abundancia y cantidades relacionadas para emplazamientos de muestreo, grupos de emplazamientos y emplazamientos no muestreados. A tal efecto, se incluyen dos breves ejemplos; el primero trata de los recuentos de puntos simples, mientras que el segundo se basa en los recuentos por extracción temporal. También se apunta la posibilidad de ampliar estos modelos a sistemas abiertos

Range verification for eye proton therapy based on proton-induced x-ray emissions from implanted metal markers.

Metal fiducial markers are often implanted on the back of the eye before proton therapy to improve target localization and reduce patient setup errors. We aim to detect characteristic x-ray emissions from metal targets during proton therapy to verify the treatment range accuracy. Initially gold was chosen for its biocompatibility properties. Proton-induced x-ray emissions (PIXE) from a 15 mm diameter gold marker were detected at different penetration depths of a 59 MeV proton beam at the CATANA proton facility at INFN-LNS (Italy). The Monte Carlo code Geant4 was used to reproduce the experiment and to investigate the effect of different size markers, materials, and the response to both mono-energetic and fully modulated beams. The intensity of the emitted x-rays decreases with decreasing proton energy and thus decreases with depth. If we assume the range to be the depth at which the dose is reduced to 10% of its maximum value and we define the residual range as the distance between the marker and the range of the beam, then the minimum residual range which can be detected with 95% confidence level is the depth at which the PIXE peak is equal to 1.96 σbkg, which is the standard variation of the background noise. With our system and experimental setup this value is 3 mm, when 20 GyE are delivered to a gold marker of 15 mm diameter. Results from silver are more promising. Even when a 5 mm diameter silver marker is placed at a depth equal to the range, the PIXE peak is 2.1 σbkg. Although these quantitative results are dependent on the experimental setup used in this research study, they demonstrate that the real-time analysis of the PIXE emitted by fiducial metal markers can be used to derive beam range. Further analysis are needed to demonstrate the feasibility of the technique in a clinical setup

The role of indirect genetic effects in the evolution of interacting reproductive behaviors in the burying beetle, Nicrophorus vespilloides

This is the final version. Available from Wiley via the DOI in this record.Data archiving:Data available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.9rk5f69.Social interactions can give rise to indirect genetic effects (IGEs), which occur when genes expressed in one individual affect the phenotype of another individual. The evolutionary dynamics of traits can be altered when there are IGEs. Sex often involves indirect effects arising from first order (current) or second order (prior) social interactions, yet IGEs are infrequently quantified for reproductive behaviors.Here, we use experimental populations of burying beetles that have experienced bidirectional selection on mating rate to test for social plasticity and IGEs associated with focal males mating with a female either without (first order effect) or with (second order effect) prior exposure to a competitor, and resource defense behavior (first order effect). Additive IGEs were detected for mating rate arising from (first order) interactions with females. For resource defense behavior, a standard variance partitioning analysis provided no evidence of additive genetic variance – either direct or indirect. However, behavior was predicted by focal size relative to that of the competitor, and size is also heritable. Assuming that behavior is causally dependent on relative size, this implies that both DGEs and IGEs do occur (and may potentially interact). The relative contribution of IGEs may differ among social behaviors related to mating which has consequences for the evolutionary trajectories of multivariate traits.Natural Environment Research Council (NERC

Spatial capture–recapture analysis of artificial cover board survey data reveals small scale spatial variation in slow-worm Anguis fragilis density

Vague and/or ad hoc definitions of the area sampled in monitoring efforts are common, and estimates of ecological state variables (e.g. distribution and abundance) can be sensitive to such specifications. The uncertainty in population metrics due to data deficiencies, vague definitions of space and lack of standardized protocols is a major challenge for monitoring, managing and conserving amphibian and reptile populations globally. This is especially true for the slow-worm (Anguis fragilis), a cryptic and fossorial legless lizard; uncertainty about spatial variation in density has hindered conservation efforts (e.g. in translocation projects). Spatial capture–recapture (SCR) methods can be used to estimate density while simultaneously and explicitly accounting for space and individual movement. We use SCR to analyse mark–recapture data of the slow-worm that were collected using artificial cover objects (ACO). Detectability varied among ACO grids and through the season. Estimates of slow-worm density varied across ACO grids (13, 45 and 46 individuals ha−1, respectively). The estimated 95% home range size of slow-worms was 0.38 ha. Our estimates provide valuable information about slow-worm spatial ecology that can be used to inform future conservation management