Fitting complex population models by combining particle filters with Markov chain Monte Carlo

We show how a recent framework combining Markov chain Monte Carlo (MCMC) with particle filters (PFMCMC) may be used to estimate population state-space models. With the purpose of utilizing the strengths of each method, PFMCMC explores hidden states by particle filters, while process and observation parameters are estimated using an MCMC algorithm. PFMCMC is exemplified by analyzing time series data on a red kangaroo (Macropus rufus) population in New South Wales, Australia, using MCMC over model parameters based on an adaptive Metropolis-Hastings algorithm. We fit three population models to these data; a density-dependent logistic diffusion model with environmental variance, an unregulated stochastic exponential growth model, and a random-walk model. Bayes factors and posterior model probabilities show that there is little support for density dependence and that the random-walk model is the most parsimonious model. The particle filter Metropolis-Hastings algorithm is a brute-force method that may be used to fit a range of complex population models. Implementation is straightforward and less involved than standard MCMC for many models, and marginal densities for model selection can be obtained with little additional effort. The cost is mainly computational, resulting in long running times that may be improved by parallelizing the algorithm.     

Environmental policy evaluation in the EU: between learning,accountability, and political opportunities?

ABSTRACT

Policy evaluation has grown significantly in the EU environmental sector since the 1990s. In identifying and exploring the putative drivers behind its rise – a desire to learn, a quest for greater accountability, and a wish to manipulate political opportunity structures – new ground is broken by examining how and why the existing literatures on these drivers have largely studied them in isolation. The complementarities and potential tensions between the three drivers are then addressed in order to advance existing research, drawing on emerging empirical examples in climate policy, a very dynamic area of evaluation activity in the EU. The conclusions suggest that future studies should explore the interactions between the three drivers to open up new and exciting research opportunities in order to comprehend contemporary environmental policy and politics in the EU.     

In search of human-associated bacterial pathogens in Antarctic wildlife: report from six penguin colonies regularly visited by tourists

We investigated the potential role of Antarctic tourism in the introduction of human-associated pathogens into Antarctic wildlife. We collected and analyzed 233 fecal samples from eight bird species. The samples were collected at six localities on the Antarctic Peninsula, which often is visited by tourists. Every sample was investigated for pathogens of potential human origin: Campylobacter jejuni, Salmonella spp., and Yersina spp. None of these bacteria was found. Our data suggest that the tourism industry so far has achieved its goal of not introducing pathogens into the Antarctic region. There is, however, an urgent need to further investigate the situation in areas closer to permanent Antarctic settlements.     

Dynamics of Turbulence in Low-Speed Oscillating Bottom-Boundary Layers of Stratified Basins

This paper focuses on the impact of an oscillating low-speed current on the structure and dynamics of the bottom-boundary layer (BBL) in a small stratified basin. A set of high-resolution current profile measurements in combination with temperature-microstructure measurements were collected during a complete cycle of the internal oscillation (`seiching') in the BBL of Lake Alpnach, Switzerland. It was found that even a relatively long seiching period of 24 hours significantly changed the form of the near-bottom current profiles as well as the dynamics of the turbulent dissipation rate compared to the steady-state law-of-the-wall. A logarithmic fit to the measured current profiles starting at a distance of 0.5 m above the sediment led to inconsistent estimates of both friction velocity and roughness length. Moreover, a phase lag between the current and the turbulent dissipation of 1.5 hours and a persistent maximum in the current profile at a height of 2.5 to 3 m above the sediment were observed. The experimental findings were compared to the results of a k- turbulence model and showed good agreement in general. Specifically, the inconsistent logarithmic fitting results and the observed phase lag were reproduced well by the model.     

Microbial fuel cell-induced production of fungal laccase to degrade the anthraquinone dye Remazol Brilliant Blue R

Environmental Chemistry Letters - The anthraquinone dye Remazol Brilliant Blue R is largely used in the textile industry. However, its removal from wastewaters is costly and complex. Many methods...     

Influence of contaminant burial depth on the bioaccumulation of PCBs and PBDEs by two benthic invertebrates (Monoporeia affinis and Marenzelleria spp.)

The bioaccumulation of buried polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) added to specific depths in sediment (2.0-2.5, 5.0-5.5 and 10.0-10.5 cm) was studied in two infaunal species with similar feeding habits (surface deposit-feeders) but different bioturbation modes. The deep-burrowing polychaetes Marenzelleria spp. (Mz) displayed up to 36 times higher tissue concentrations of buried (spiked) contaminants than the surface-dwelling biodiffusing amphipod Monoporeia affinis. The differences in bioaccumulation were most pronounced for less hydrophobic contaminants due to the bioirrigating activity of Mz. Contaminants buried at shallow depths displayed higher accumulation than more deeply buried contaminants. In contrast, the bioaccumulation of unspiked (native) contaminants with a uniform vertical distribution in the sediment was similar between the species. For Mz, the BSAFs increased with increased K_OW for the uniformly distributed contaminants, but decreased for the buried contaminants, which indicates that the dominant uptake routes of the buried contaminants can differ from the uniformly distributed contaminants. The surface sediment concentration of buried contaminants increased in Mz treatments, showing that Mz bioturbation can remobilize historically buried contaminants to the biologically active surface layer and increase the exposure for surface-dwelling species.     

Multi-decadal changes in tundra environments and ecosystems: synthesis of the International Polar Year-Back to the Future project (IPY-BTF)

Understanding the responses of tundra systems to global change has global implications. Most tundra regions lack sustained environmental monitoring and one of the only ways to document multi-decadal change is to resample historic research sites. The International Polar Year (IPY) provided a unique opportunity for such research through the Back to the Future (BTF) project (IPY project #512). This article synthesizes the results from 13 papers within this Ambio Special Issue. Abiotic changes include glacial recession in the Altai Mountains, Russia; increased snow depth and hardness, permafrost warming, and increased growing season length in sub-arctic Sweden; drying of ponds in Greenland; increased nutrient availability in Alaskan tundra ponds, and warming at most locations studied. Biotic changes ranged from relatively minor plant community change at two sites in Greenland to moderate change in the Yukon, and to dramatic increases in shrub and tree density on Herschel Island, and in subarctic Sweden. The population of geese tripled at one site in northeast Greenland where biomass in non-grazed plots doubled. A model parameterized using results from a BTF study forecasts substantial declines in all snowbeds and increases in shrub tundra on Niwot Ridge, Colorado over the next century. In general, results support and provide improved capacities for validating experimental manipulation, remote sensing, and modeling studies.     

Exceptional responders in conservation

Conservation operates within complex systems with incomplete knowledge of the system and the interventions utilized. This frequently results in the inability to find generally applicable methods to alleviate threats to Earth's vanishing wildlife. One approach used in medicine and the social sciences has been to develop a deeper understanding of positive outliers. Where such outliers share similar characteristics, they may be considered exceptional responders. We devised a 4‐step framework for identifying exceptional responders in conservation: identification of the study system, identification of the response structure, identification of the threshold for exceptionalism, and identification of commonalities among outliers. Evaluation of exceptional responders provides additional information that is often ignored in randomized controlled trials and before–after control‐intervention experiments. Interrogating the contextual factors that contribute to an exceptional outcome allow exceptional responders to become valuable pieces of information leading to unexpected discoveries and novel hypotheses.     

Integral models for bubble,droplet, and multiphase plume dynamics in stratification and crossflow

We present the development and validation of a numerical modeling suite for bubble and droplet dynamics of multiphase plumes in the environment. This modeling suite includes real-fluid equations of state, Lagrangian particle tracking, and two different integral plume models: an Eulerian model for a double-plume integral model in quiescent stratification and a Lagrangian integral model for multiphase plumes in stratified crossflows. Here, we report a particle tracking algorithm for dispersed-phase particles within the Lagrangian integral plume model and a comprehensive validation of the Lagrangian plume model for single- and multiphase buoyant jets. The model utilizes literature values for all entrainment and spreading coefficients and has one remaining calibration parameter \( \kappa \), which reduces the buoyant force of dispersed phase particles as they approach the edge of a Lagrangian plume element, eventually separating from the plume as it bends over in a crossflow. We report the calibrated form \( \kappa = [(b - r) / b]^4 \), where b is the plume half-width, and r is the distance of a particle from the plume centerline. We apply the validated modeling suite to simulate two test cases of a subsea oil well blowout in a stratification-dominated crossflow. These tests confirm that errors from overlapping plume elements in the Lagrangian integral model during intrusion formation for a weak crossflow are negligible for predicting intrusion depth and the fate of oil droplets in the plume. The Lagrangian integral model has the added advantages of being able to account for entrainment from an arbitrary crossflow, predict the intrusion of small gas bubbles and oil droplets when appropriate, and track the pathways of individual bubbles and droplets after they separate from the main plume or intrusion layer.     

Testing the developmental stress hypothesis in canaries: consequences of nutritional stress on adult song phenotype and mate attractiveness

The complex songs of songbirds are thought to have evolved through sexual selection. Sexually selected signals must be associated with costs in order to ensure their honesty as indicator of male quality. Costs may relate to the development of the neural substrate underlying song learning, which develops already very early in life. Song may, therefore, serve as an indicator of the early developmental history. This nutritional stress hypothesis has initially been confirmed for a variety of species, but recent studies using zebra finches as a model species reported somewhat inconsistent effects, and the functional consequences of changes in adult song phenotype remain unclear. We tested the nutritional stress hypothesis in canaries by manipulating either the brood size or the food quality postfledging. The brood size manipulation had a significant effect on early development, and low food quality postfledging led to a transient reduction in body mass. However, we did not find evidence that any of the song traits measured reflected the early developmental conditions, which is in conflict with the nutritional stress hypothesis. Canaries may be less vulnerable to nutritional stress or are able to compensate stressful conditions during early development. However, if males compensated, this compensation may have come at a survival cost. Female mate choice decisions were independent of the developmental history of a male. Instead, females preferred males singing longer song bouts, a trait that may contain a heritable component.