1. Temporary migration - where individuals can leave and re-enter a sampled population - is a feature of many capture-mark-recapture (CMR) studies of mobile populations which, if unaccounted for, can lead to biased estimates of population capture probabilities and consequently biased estimates of population abundance.2. We present a method for incorporating radiotelemetry data within a CMR study to eliminate bias due to temporary migration using a Bayesian state-space model.3. Our results indicate that using a relatively small number of telemetry tags, it is possible to greatly reduce bias in estimates of capture probabilities using telemetry data to model transition probabilities in and out of the sampling area. In a capture-recapture data set for trout Cod in the Murray river, Australia, accounting for temporary migration led to overall higher estimates of capture probabilities than models assuming permanent or zero migration. Also, individual heterogeneity in detectability can be managed through explicit modelling. We show how accounting for temporary migration when estimating capture probabilities can be used to estimate the abundance and size distribution of a population as though it were closed.4. Our model provides a basis for more complex models that might integrate telemetry data into other CMR scenarios, thus allowing for greater precision in estimates of vital rates that might otherwise be biased by temporary migration. Our results highlight the importance of accounting for migration in survey design and parameter estimation, and the potential scope for supplementing large-scale CMR data sets with a subset of auxiliary data that provide information on processes that are hidden to primary sampling processes.

The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these 'protist' taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale mRNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean genera Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 73 ribosomal protein-coding genes were selected for phylogeny. After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts. Overall the tree was well resolved and supported, when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test. The deepest branches of the dinoflagellate tree can now be resolved with strong support, and provides a clearer view of the evolution of the distinctive traits of dinoflagellates.

Policy documents advocate that managers should keep their options open while planning to protect coastal ecosystems from climate-change impacts. However, the actual costs and benefits of maintaining flexibility remain largely unexplored, and alternative approaches for decision making under uncertainty may lead to better joint outcomes for conservation and other societal goals. For example, keeping options open for coastal ecosystems incurs opportunity costs for developers. We devised a decision framework that integrates these costs and benefits with probabilistic forecasts for the extent of sea-level rise to find a balance between coastal ecosystem protection and moderate coastal development. Here, we suggest that instead of keeping their options open managers should incorporate uncertain sea-level rise predictions into a decision-making framework that evaluates the benefits and costs of conservation and development. In our example, based on plausible scenarios for sea-level rise and assuming a risk-neutral decision maker, we found that substantial development could be accommodated with negligible loss of environmental assets. Characterization of the Pareto efficiency of conservation and development outcomes provides valuable insight into the intensity of trade-offs between development and conservation. However, additional work is required to improve understanding of the consequences of alternative spatial plans and the value judgments and risk preferences of decision makers and stakeholders. Minimizando el Costo de Mantener Opciones Abiertas para la Conservacion en un Clima CambianteResumen Los documentos de politica abogan que los administradores deben mantener sus opciones abiertas mientras planean proteger a los ecosistemas costeros de los impactos del cambio climatico. Sin embargo, el beneficio de mantener la flexibilidad permanece en su mayoria sin explorar y los acercamientos alternativos para la toma de decisiones bajo incertidumbre pueden llevar a mejores resultados conjuntos para la conservacion y otras metas sociales. Por ejemplo, mantener las opciones abiertas para los ecosistemas costeros incurre en costos de oportunidad para los desarrolladores. Disenamos un marco de trabajo de decision que integra estos costos con pronosticos de probabilidad para la extension del aumento en el nivel del mar para encontrar un balance entre la proteccion del ecosistema costero y el desarrollo costero moderado. Aqui sugerimos que en lugar de mantener sus opciones abiertas, los administradores deben incorporar predicciones inciertas del aumento en el nivel del mar en el marco de toma de decisiones que evalue los beneficios y los costos de la conservacion y el desarrollo. En nuestro ejemplo, basado en escenarios plausibles del aumento del nivel del mar y suponiendo que participa alguien que toma decisiones neutral al riesgo, encontramos que el desarrollo sustancial puede acomodarse con la perdida despreciable de bienes ambientales. La caracterizacion de la eficiencia de Pareto de la conservacion y los resultados del desarrollo proporcionaron una perspicacia valiosa para la intensidad de los equilibrios entre el desarrollo y la conservacion. Sin embargo, se requiere trabajo adicional para mejorar el entendimiento de las consecuencias de los planes espaciales alternativos y los juicios de valor y las preferencias de riesgo de los tomadores de decisiones y las partes interesadas.

Background and Aims The charophyte green algae (CGA) are thought to be the closest living relatives to the land plants, and ancestral CGA were unique in giving rise to the land plant lineage. The cell wall has been suggested to be a defining structure that enabled the green algal ancestor to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes.Methods Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs characterized in land plants. In addition, gene cloning was employed in two cases to answer important evolutionary questions.Key Results Genetic evidence was obtained indicating that many of the most important core cell wall polysaccharides have their evolutionary origins in the CGA, including cellulose, mannan, xyloglucan, xylan and pectin, as well as arabino-galactan protein. Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA species Coleochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA.Conclusions The results provide new insights into the evolution of cell walls and support the notion that the CGA were pre-adapted to life on land by virtue of the their cell wall biosynthetic capacity. These findings are highly significant for understanding plant cell wall evolution as they imply that some features of land plant cell walls evolved prior to the transition to land, rather than having evolved as a result of selection pressures inherent in this transition.

Time is of the essence in conservation biology. To secure the persistence of a species, we need to understand how to balance time spent among different management actions. A new and simple method to test the efficacy of a range of conservation actions is required. Thus, we devised a general theoretical framework to help determine whether to test a new action and when to cease a trial and revert to an existing action if the new action did not perform well. The framework involves constructing a general population model under the different management actions and specifying a management objective. By maximizing the management objective, we could generate an analytical solution that identifies the optimal timing of when to change management action. We applied the analytical solution to the case of the Christmas Island pipistrelle bat (Pipistrelle murrayi), a species for which captive breeding might have prevented its extinction. For this case, we used our model to determine whether to start a captive breeding program and when to stop a captive breeding program and revert to managing the species in the wild, given that the management goal is to maximize the chance of reaching a target wild population size. For the pipistrelle bat, captive breeding was to start immediately and it was desirable to place the species in captivity for the entire management period. The optimal time to revert to managing the species in the wild was driven by several key parameters, including the management goal, management time frame, and the growth rates of the population under different management actions. Knowing when to change management actions can help conservation managers' act in a timely fashion to avoid species extinction. Determinar Cuando Cambiar el Rumbo en las Acciones de ManejoResumen El tiempo es de suma importancia en la Biologia de la Conservacion. Para poder asegurar la persistencia de una especie necesitamos entender como equilibrar el tiempo utilizado en diferentes acciones de manejo. Se requiere un metodo novedoso y simple para evaluar la efectividad de una gama de acciones de conservacion. Por esto disenamos un marco de trabajo teorico y general para ayudar a determinar si se debe evaluar una accion nueva y cuando se debe detener una prueba y revertirla a una accion existente si la nueva accion no tuvo un buen desempeno. El marco de trabajo involucra construir un modelo poblacional general bajo las diferentes acciones de manejo y especificar un objetivo de manejo. Al maximizar el objetivo de manejo, podemos generar una solucion analitica que identifica la oportunidad optima de cuando cambiar la accion de manejo. Aplicamos la solucion analitica al caso del murcielago de la Isla Navidad (Pipistrelle murrayi), una especie para la cual la reproduccion en cautiverio puede haber prevenido su extincion. Para este caso, usamos nuestro modelo para determinar si iniciabamos un programa de reproduccion en cautiverio o cuando detendriamos un programa de reproduccion en cautiverio y revertiriamos al manejo en vida libre de la especie, dado que el objetivo de manejo es maximizar la posibilidad de obtener un tamano de poblacion silvestre determinado. Para el murcielago, la reproduccion en cautiverio empezaria de inmediato y lo deseado seria mantener a la especie en cautiverio durante el periodo de manejo. El tiempo optimo para revertirnos a manejar a la especie en vida libre fue conducido por varios parametros clave, incluidos el objetivo de manejo, el marco de tiempo del manejo y las tasas de crecimiento de la poblacion bajo diferentes acciones de manejo. El saber cuando cambiar las acciones de manejo puede ayudar a quienes manejan la conservacion a actuar oportunamente para evitar la extincion de una especie.

The microclimate experienced by organisms is determined by local weather conditions. Yet the environmental data available for predicting the effect of climate on the distribution and abundance of organisms are typically in the form of long-term average monthly climate measured at standardized heights above the ground.Here, we demonstrate how hourly microclimates can be modelled mechanistically over decades at the continental scale with biologically suitable accuracy.We extend the microclimate model of the software package niche mapper to capture spatial and temporal variation in soil thermal properties and integrate it with gridded soil and weather data for Australia at 0 center dot 05 degrees resolution.When tested against historical observations of soil temperature, the microclimate model predicted 85% of the variation in hourly soil temperature across 10years from the surface to 1m deep with an accuracy of 2-3 center dot 3 degrees C (c. 10% of the temperature range at a given depth) across an extremely climatically diverse range of sites.This capacity to accurately and mechanistically predict hourly local microclimates across continental scales creates new opportunities for understanding how organisms respond to changes in climate.

Chronic periodontitis has a polymicrobial biofilm aetiology and interactions between key bacterial species are strongly implicated as contributing to disease progression. Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia have all been implicated as playing roles in disease progression. P. gingivalis cell-surface-located protease/adhesins, the gingipains, have been suggested to be involved in its interactions with several other bacterial species. The aims of this study were to determine polymicrobial biofilm formation by P. gingivalis, T. denticola and T. forsythia, as well as the role of P. gingivalis gingipains in biofilm formation by using a gingipain null triple mutant. To determine homotypic and polymicrobial biofilm formation a flow cell system was employed and the biofilms imaged and quantified by fluorescent in situ hybridization using DNA species-specific probes and confocal scanning laser microscopy imaging. Of the three species, only P. gingivalis and T. denticola formed mature, homotypic biofilms, and a strong synergy was observed between P. gingivalis and T. denticola in polymicrobial biofilm formation. This synergy was demonstrated by significant increases in biovolume, average biofilm thickness and maximum biofilm thickness of both species. In addition there was a morphological change of T. denticola in polymicrobial biofilms when compared with homotypic biofilms, suggesting reduced motility in homotypic biofilms. P. gingivalis gingipains were shown to play an essential role in synergistic polymicrobial biofilm formation with T. denticola.