Using individual-based bioenergetic models to predict the aggregate effects of disturbance on populations: A case study with beaked whales and Navy sonar

Anthropogenic activities can lead to changes in animal behavior. Predicting population consequences of these behavioral changes requires integrating short-term individual responses into models that forecast population dynamics across multiple generations. This is especially challenging for long-lived animals, because of the different time scales involved. Beaked whales are a group of deep-diving odontocete whales that respond behaviorally when exposed to military mid-frequency active sonar (MFAS), but the effect of these nonlethal responses on beaked whale populations is unknown. Population consequences of aggregate exposure to MFAS was assessed for two beaked whale populations that are regularly present on U.S. Navy training ranges where MFAS is frequently used. Our approach integrates a wide range of data sources, including telemetry data, information on spatial variation in habitat quality, passive acoustic data on the temporal pattern of sonar use and its relationship to beaked whale foraging activity, into an individual-based model with a dynamic bioenergetic module that governs individual life history. The predicted effect of disturbance from MFAS on population abundance ranged between population extinction to a slight increase in population abundance. These effects were driven by the interaction between the temporal pattern of MFAS use, baseline movement patterns, the spatial distribution of prey, the nature of beaked whale behavioral response to MFAS and the top-down impact of whale foraging on prey abundance. Based on these findings, we provide recommendations for monitoring of marine mammal populations and highlight key uncertainties to help guide future directions for assessing population impacts of nonlethal disturbance for these and other long-lived animals.

Managing the effects of multiple stressors on wildlife populations in their ecosystems: developing a cumulative risk approach

Assessing cumulative effects of human activities on ecosystems is required by many jurisdictions, but current science cannot meet regulatory demands. Regulations define them as effect(s) of one human action combined with other actions. Here we argue for an approach that evaluates the cumulative risk of multiple stressors for protected wildlife populations within their ecosystems. Monitoring effects of each stressor is necessary but not sufficient to estimate how multiple stressors interact to affect wildlife populations. Examining the mechanistic pathways, from cellular to ecological, by which stressors affect individuals can help prioritize stressors and interpret how they interact. Our approach uses health indicators to accumulate the effects of stressors on individuals and to estimate changes in vital rates, driving population status. We advocate using methods well-established in human health and integrating them into ecosystem-based management to protect the health of commercially and culturally important wildlife populations and to protect against risk of extinction for threatened species. Our approach will improve abilities to conserve and manage ecosystems but will also demand significant increases in research and monitoring effort. We advocate for increased investment proportional to the economic scale of human activities in the Anthropocene and their pervasive effects on ecology and biodiversity.

Understanding the combined effects of multiple stressors: A new perspective on a longstanding challenge

Wildlife populations and their habitats are exposed to an expanding diversity and intensity of stressors caused by human activities, within the broader context of natural processes and increasing pressure from climate change. Estimating how these multiple stressors affect individuals, populations, and ecosystems is thus of growing importance. However, their combined effects often cannot be predicted reliably from the individual effects of each stressor, and we lack the mechanistic understanding and analytical tools to predict their joint outcomes. We review the science of multiple stressors and present a conceptual framework that captures and reconciles the variety of existing approaches for assessing combined effects. Specifically, we show that all approaches lie along a spectrum, reflecting increasing assumptions about the mechanisms that regulate the action of single stressors and their combined effects. An emphasis on mechanisms improves analytical precision and predictive power but could introduce bias if the underlying assumptions are incorrect. A purely empirical approach has less risk of bias but requires adequate data on the effects of the full range of anticipated combinations of stressor types and magnitudes. We illustrate how this spectrum can be formalised into specific analytical methods, using an example of North Atlantic right whales feeding on limited prey resources while simultaneously being affected by entanglement in fishing gear. In practice, case-specific management needs and data availability will guide the exploration of the stressor combinations of interest and the selection of a suitable trade-off between precision and bias. We argue that the primary goal for adaptive management should be to identify the most practical and effective ways to remove or reduce specific combinations of stressors, bringing the risk of adverse impacts on populations and ecosystems below acceptable thresholds.

Density dependence can obscure nonlethal effects of disturbance on life history of medium-sized cetaceans

Nonlethal disturbance of animals can cause behavioral and physiological changes that affect individual health status and vital rates, with potential consequences at the population level. Predicting these population effects remains a major challenge in ecology and conservation. Monitoring fitness-related traits may improve detection of upcoming population changes, but the extent to which individual traits are reliable indicators of disturbance exposure is not well understood, especially for populations regulated by density dependence. Here we study how density dependence affects a population’s response to disturbance and modifies the disturbance effects on individual health and vital rates. We extend an energy budget model for a medium-sized cetacean (the long-finned pilot whale Globicephala melas) to an individual-based population model in which whales feed on a self-replenishing prey base and disturbance leads to cessation of feeding. In this coupled predator-prey system, the whale population is regulated through prey depletion and the onset of yearly repeating disturbances on the whale population at carrying capacity decreased population density and increased prey availability due to reduced top-down control. In populations faced with multiple days of continuous disturbance each year, female whales that were lactating their first calf experienced increased mortality due to depletion of energy stores. However, increased prey availability led to compensatory effects and resulted in a subsequent improvement of mean female body condition, mean age at first reproduction and higher age-specific reproductive output. These results indicate that prey-mediated density dependence can mask negative effects of disturbance on fitness-related traits and vital rates, a result with implications for the monitoring and management of marine mammal populations.

Context-dependent variability in the predicted daily energetic costs of disturbance for blue whales

Assessing the long-term consequences of sub-lethal anthropogenic disturbance on wildlife populations requires integrating data on fine-scale individual behavior and physiology into spatially and temporally broader, population-level inference. A typical behavioral response to disturbance is the cessation of foraging, which can be translated into a common metric of energetic cost. However, this necessitates detailed empirical information on baseline movements, activity budgets, feeding rates and energy intake, as well as the probability of an individual responding to the disturbance-inducing stressor within different exposure contexts. Here, we integrated data from blue whales (Balaenoptera musculus) experimentally exposed to military active sonar signals with fine-scale measurements of baseline behavior over multiple days or weeks obtained from accelerometry loggers, telemetry tracking and prey sampling. Specifically, we developed daily simulations of movement, feeding behavior and exposure to localized sonar events of increasing duration and intensity and predicted the effects of this disturbance source on the daily energy intake of an individual. Activity budgets and movements were highly variable in space and time and among individuals, resulting in large variability in predicted energetic intake and costs. In half of our simulations, an individual's energy intake was unaffected by the simulated source. However, some individuals lost their entire daily energy intake under brief or weak exposure scenarios. Given this large variation, population-level models will have to assess the consequences of the entire distribution of energetic costs, rather than only consider single summary statistics. The shape of the exposure-response functions also strongly influenced predictions, reinforcing the need for contextually explicit experiments and improved mechanistic understanding of the processes driving behavioral and physiological responses to disturbance. This study presents a robust approach for integrating different types of empirical information to assess the effects of disturbance at spatio-temporal and ecological scales that are relevant to management and conservation.

The Epidemiological Framework for Biological Invasions (EFBI): an interdisciplinary foundation for the assessment of biosecurity threats

Emerging microparasite (e.g. viruses, bacteria, protozoa and fungi) epidemics and the introduction of non-native pests and weeds are major biosecurity threats worldwide. The likelihood of these threats is often estimated from probabilities of their entry, establishment, spread and ease of prevention. If ecosystems are considered equivalent to hosts, then compartment disease models should provide a useful framework for understanding the processes that underpin non-native species invasions. To enable greater cross-fertilisation between these two disciplines, the Epidemiological Framework for Biological Invasions (EFBI) is developed that classifies ecosystems in relation to their invasion status: Susceptible, Exposed, Infectious and Resistant. These states are linked by transitions relating to transmission, latency and recovery. This viewpoint differs markedly from the species-centric approaches often applied to non-native species. It allows generalisations from epidemiology, such as the force of infection, the basic reproductive ratio R0, super-spreaders, herd immunity, cordon sanitaire and ring vaccination, to be discussed in the novel context of non-native species and helps identify important gaps in the study of biological invasions. The EFBI approach highlights several limitations inherent in current approaches to the study of biological invasions including: (i) the variance in non-native abundance across ecosystems is rarely reported; (ii) field data rarely (if ever) distinguish source from sink ecosystems; (iii) estimates of the susceptibility of ecosystems to invasion seldom account for differences in exposure to non-native species; and (iv) assessments of ecosystem susceptibility often confuse the processes that underpin patterns of spread within -and between- ecosystems. Using the invasion of lakes as a model, the EFBI approach is shown to present a new biosecurity perspective that takes account of ecosystem status and complements demographic models to deliver clearer insights into the dynamics of biological invasions at the landscape scale. It will help to identify whether management of the susceptibility of ecosystems, of the number of vectors, or of the diversity of pathways (for movement between ecosystems) is the best way of limiting or reversing the population growth of a non-native species. The framework can be adapted to incorporate increasing levels of complexity and realism and to provide insights into how to monitor, map and manage biological invasions more effectively.

Propensity for Risk in Reproductive Strategy Affects Susceptibility to Anthropogenic Disturbance

AbstractAnimals initiate, interrupt, or invest resources in reproduction in light of their physiology and the environment. The energetic risks entailed in an individual's reproductive strategy can influence the ability to cope with additional stressors, such as anthropogenic climate change and disturbance. To explore the trade-offs between internal state, external resource availability, and reproduction, we applied state-dependent life-history theory (SDLHT) to a dynamic energy budget (DEB) model for long-finned pilot whales (Globicephala melas). We investigated the reproductive strategies emerging from the interplay between fitness maximization and propensity to take energetic risks, as well as the resulting susceptibility of individual vital rates to disturbance. Without disturbance, facultative reproductive behavior from SDLHT and fixed rules in the DEB model led to comparable individual fitness. However, under disturbance, the reproductive strategies emerging from SDLHT increased vulnerability to energetic risks, resulting in lower fitness than fixed rules. These fragile strategies might therefore be unlikely to evolve in the first place. Heterogeneous resource availability favored more cautious (and thus more robust) strategies, particularly when knowledge of resource variation was accurate. Our results demonstrate that the assumptions regarding the dynamic trade-offs underlying an individual's decision-making can have important consequences for predicting the effects of anthropogenic stressors on wildlife populations.

Bio-energetic modeling of medium-sized cetaceans shows high sensitivity to disturbance in seasons of low resource supply

Understanding the full scope of human impact on wildlife populations requires a framework to assess the population-level repercussions of nonlethal disturbance. The Population Consequences of Disturbance (PCoD) framework provides such an approach, by linking the effects of disturbance on the behavior and physiology of individuals to their population-level consequences. Bio-energetic models have been used as implementations of PCoD, as these integrate the behavioral and physiological state of an individual with the state of the environment, to mediate between disturbance and biological significant changes in vital rates (survival, growth, and reproduction). To assess which levels of disturbance lead to adverse effects on population growth rate requires a bio-energetic model that covers the complete life cycle of the organism under study. In a density-independent setting, the expected lifetime reproductive output of a single female can then be used to predict the level of disturbance that leads to population decline. Here, we present such a model for a medium-sized cetacean, the long-finned pilot whale (Globicephala melas). Disturbance is modeled as a yearly recurrent period of no resource feeding for the pilot whale female and her calf. Short periods of disturbance lead to the pre-weaned death of the first one or more calves of the young female. Higher disturbance levels also affect survival of calves produced later in the life of the female, in addition to degrading female survival. The level of disturbance that leads to a negative population growth rate strongly depends on the available resources in the environment. This has important repercussion for the timing of disturbance if resource availability fluctuates seasonally. The model predicts that pilot whales can tolerate on average three times longer periods of disturbance in seasons of high resource availability, compared to disturbance happening when resources are low. Although our model is specifically parameterized for pilot whales, it provides useful insights into the general consequences of nonlethal disturbance. If appropriate data on life history and energetics are available, it can be used to provide management advice for specific species or populations.

Understanding the population consequences of disturbance

Managing the nonlethal effects of disturbance on wildlife populations has been a long-term goal for decision makers, managers, and ecologists, and assessment of these effects is currently required by European Union and United States legislation. However, robust assessment of these effects is challenging. The management of human activities that have nonlethal effects on wildlife is a specific example of a fundamental ecological problem: how to understand the population-level consequences of changes in the behavior or physiology of individual animals that are caused by external stressors. In this study, we review recent applications of a conceptual framework for assessing and predicting these consequences for marine mammal populations. We explore the range of models that can be used to formalize the approach and we identify critical research gaps. We also provide a decision tree that can be used to select the most appropriate model structure given the available data. Synthesis and applications: The implementation of this framework has moved the focus of discussion of the management of nonlethal disturbances on marine mammal populations away from a rhetorical debate about defining negligible impact and toward a quantitative understanding of long-term population-level effects. Here we demonstrate the framework's general applicability to other marine and terrestrial systems and show how it can support integrated modeling of the proximate and ultimate mechanisms that regulate trait-mediated, indirect interactions in ecological communities, that is, the nonconsumptive effects of a predator or stressor on a species' behavior, physiology, or life history.

A simulation approach to assessing environmental risk of sound exposure to marine mammals

Intense underwater sounds caused by military sonar, seismic surveys, and pile driving can harm acoustically sensitive marine mammals. Many jurisdictions require such activities to undergo marine mammal impact assessments to guide mitigation. However, the ability to assess impacts in a rigorous, quantitative way is hindered by large knowledge gaps concerning hearing ability, sensitivity, and behavioral responses to noise exposure. We describe a simulation‐based framework, called SAFESIMM (Statistical Algorithms For Estimating the Sonar Influence on Marine Megafauna), that can be used to calculate the numbers of agents (animals) likely to be affected by intense underwater sounds. We illustrate the simulation framework using two species that are likely to be affected by marine renewable energy developments in UK waters: gray seal (Halichoerus grypus) and harbor porpoise (Phocoena phocoena). We investigate three sources of uncertainty: How sound energy is perceived by agents with differing hearing abilities; how agents move in response to noise (i.e., the strength and directionality of their evasive movements); and the way in which these responses may interact with longer term constraints on agent movement. The estimate of received sound exposure level (SEL) is influenced most strongly by the weighting function used to account for the specie's presumed hearing ability. Strongly directional movement away from the sound source can cause modest reductions (~5 dB) in SEL over the short term (periods of less than 10 days). Beyond 10 days, the way in which agents respond to noise exposure has little or no effect on SEL, unless their movements are constrained by natural boundaries. Most experimental studies of noise impacts have been short‐term. However, data are needed on long‐term effects because uncertainty about predicted SELs accumulates over time. Synthesis and applications. Simulation frameworks offer a powerful way to explore, understand, and estimate effects of cumulative sound exposure on marine mammals and to quantify associated levels of uncertainty. However, they can often require subjective decisions that have important consequences for management recommendations, and the basis for these decisions must be clearly described.

Effects of Model Formulation on Estimates of Health in Individual Right Whales (Eubalaena glacialis)

Right whales are vulnerable to many sources of anthropogenic disturbance including ship strikes, entanglement with fishing gear, and anthropogenic noise. The effect of these factors on individual health is unclear. A statistical model using photographic evidence of health was recently built to infer the true or hidden health of individual right whales. However, two important prior assumptions about the role of missing data and unexplained variance on the estimates were not previously assessed. Here we tested these factors by varying prior assumptions and model formulation. We found sensitivity to each assumption and used the output to make guidelines on future model formulation.

Lipids: From Chemical Structures, Biosynthesis, and Analyses to Industrial Applications

Lipids are one of the major subcellular components, and play numerous essential functions. As well as their physiological roles, oils stored in biomass are useful commodities for a variety of biotechnological applications including food, chemical feedstocks, and fuel. Due to their agronomic as well as economic and societal importance, lipids have historically been subjected to intensive studies. Major current efforts are to increase the energy density of cell biomass, and/or create designer oils suitable for specific applications. This chapter covers some basic aspects of what one needs to know about lipids: definition, structure, function, metabolism and focus is also given on the development of modern lipid analytical tools and major current engineering approaches for biotechnological applications. This introductory chapter is intended to serve as a primer for all subsequent chapters in this book outlining current development in specific areas of lipids and their metabolism.

Lipids: From Chemical Structures, Biosynthesis, and Analyses to Industrial Applications

Lipids are one of the major subcellular components, and play numerous essential functions. As well as their physiological roles, oils stored in biomass are useful commodities for a variety of biotechnological applications including food, chemical feedstocks, and fuel. Due to their agronomic as well as economic and societal importance, lipids have historically been subjected to intensive studies. Major current efforts are to increase the energy density of cell biomass, and/or create designer oils suitable for specific applications. This chapter covers some basic aspects of what one needs to know about lipids: definition, structure, function, metabolism and focus is also given on the development of modern lipid analytical tools and major current engineering approaches for biotechnological applications. This introductory chapter is intended to serve as a primer for all subsequent chapters in this book outlining current development in specific areas of lipids and their metabolism.

Predicting the effects of human developments on individual dolphins to understand potential long-term population consequences

Human activities that impact wildlife do not necessarily remove individuals from populations. They may also change individual behaviour in ways that have sublethal effects. This has driven interest in developing analytical tools that predict the population consequences of short-term behavioural responses. In this study, we incorporate empirical information on the ecology of a population of bottlenose dolphins into an individual-based model that predicts how individuals' behavioural dynamics arise from their underlying motivational states, as well as their interaction with boat traffic and dredging activities. We simulate the potential effects of proposed coastal developments on this population and predict that the operational phase may affect animals' motivational states. For such results to be relevant for management, the effects on individuals' vital rates also need to be quantified. We investigate whether the relationship between an individual's exposure and the survival of its calves can be directly estimated using a Bayesian multi-stage model for calf survival. The results suggest that any effect on calf survival is probably small and that a significant relationship could only be detected in large, closely studied populations. Our work can be used to guide management decisions, accelerate the consenting process for coastal and offshore developments and design targeted monitoring.

Modelling production per unit of food consumed in fish populations

The ratio of production-to-consumption (ρ) reflects how efficiently a population can transform ingested food into biomass. Usually this ratio is estimated by separately integrating cohort per-recruit production and consumption per unit of biomass. Estimates of ρ from cohort analysis differ from those that consider the whole population, because fish populations are usually composed of cohorts that differ in their relative abundance. Cohort models for ρ also assume a stable age-structure and a constant population size (stationary condition). This may preclude their application to harvested populations, in which variations in fishing mortality and recruitment will affect age-structure. In this paper, we propose a different framework for estimating (ρ) in which production and consumption are modelled simultaneously to produce a population estimator of ρ. Food consumption is inferred from the physiological concepts underpinning the generalised von Bertalanffy growth function (VBGF). This general framework allows the effects of different age-structures to be explored, with a stationary population as a special case. Three models with different complexities, depending mostly on what assumptions are made about age-structure, are explored. The full data model requires knowledge about food assimilation efficiency, parameters of the VBGF and the relative proportion of individuals at age a at time y (Py(a)). A simpler model, which requires less data, is based on the stationary assumption. Model results are compared with estimates from cohort models for ρ using simulated fish populations of different lifespans. The models proposed here were also applied to three fish populations that are targets of commercial fisheries in the south-east Pacific. Uncertainty in the estimation of ρ was evaluated using a resampling approach. Simulation showed that cohort and population models produce different estimates for ρ and those differences depend on lifespan, fishing mortality and recruitment variations. Results from the three case studies show that the population model gives similar estimates to those reported by empirical models in other fish species. This modelling framework allows ρ to be related directly to population length- or age-structure and thus has the potential to improve the biological realism of both population and ecosystem models.

Global population structure and demographic history of the grey seal

Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat availability and anthropogenic exploitation. We therefore analysed samples from over 1500 individuals collected from 22 colonies spanning the Western and Eastern Atlantic and the Baltic Sea regions, represented by 350 bp of the mitochondrial hypervariable region and up to nine microsatellites. Strong population structure was observed at both types of marker, and highly asymmetrical patterns of gene flow were also inferred, with the Orkney Islands being identified as a source of emigrants to other areas in the Eastern Atlantic. The Baltic and Eastern Atlantic regions were estimated to have diverged a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Sea. Approximate Bayesian computation also identified genetic signals consistent with postglacial population expansion across much of the species range, suggesting that grey seals are highly responsive to changes in habitat availability.

Applying distance sampling to fin whale calls recorded by single seismic instruments in the northeast Atlantic

Automated methods were developed to detect fin whale calls recorded by an array of ocean bottom seismometers (OBSs) deployed off the Portuguese coast between 2007 and 2008. Using recordings collected on a single day in January 2008, a standard seismological method for estimating earthquake location from single instruments, the three-component analysis, was used to estimate the relative azimuth, incidence angle, and horizontal range between each OBS and detected calls. A validation study using airgun shots, performed prior to the call analysis, indicated that the accuracy of the three-component analysis was satisfactory for this preliminary study. Point transect sampling using cue counts, a form of distance sampling, was then used to estimate the average probability of detecting a call via the array during the chosen day. This is a key step to estimating density or abundance of animals using passive acoustic data. The average probability of detection was estimated to be 0.313 (standard error: 0.033). However, fin whale density could not be estimated due to a lack of an appropriate estimate of cue (i.e., vocalization) rate. This study demonstrates the potential for using a sparse array of widely spaced, independently operating acoustic sensors, such as OBSs, for estimating cetacean density.

Estimating resource acquisition and at-sea body condition of a marine predator

1. Body condition plays a fundamental role in many ecological and evolutionary processes at a variety of scales and across a broad range of animal taxa. An understanding of how body condition changes at fine spatial and temporal scales as a result of interaction with the environment provides necessary information about how animals acquire resources. 2. However, comparatively little is known about intra- and interindividual variation of condition in marine systems. Where condition has been studied, changes typically are recorded at relatively coarse time-scales. By quantifying how fine-scale interaction with the environment influences condition, we can broaden our understanding of how animals acquire resources and allocate them to body stores. 3. Here we used a hierarchical Bayesian state-space model to estimate the body condition as measured by the size of an animal's lipid store in two closely related species of marine predator that occupy different hemispheres: northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The observation model linked drift dives to lipid stores. The process model quantified daily changes in lipid stores as a function of the physiological condition of the seal (lipid:lean tissue ratio, departure lipid and departure mass), its foraging location, two measures of behaviour and environmental covariates. 4. We found that physiological condition significantly impacted lipid gain at two time-scales - daily and at departure from the colony - that foraging location was significantly associated with lipid gain in both species of elephant seals and that long-term behavioural phase was associated with positive lipid gain in northern and southern elephant seals. In northern elephant seals, the occurrence of short-term behavioural states assumed to represent foraging were correlated with lipid gain. Lipid gain was a function of covariates in both species. Southern elephant seals performed fewer drift dives than northern elephant seals and gained lipids at a lower rate. 5. We have demonstrated a new way to obtain time series of body condition estimates for a marine predator at fine spatial and temporal scales. This modelling approach accounts for uncertainty at many levels and has the potential to integrate physiological and movement ecology of top predators. The observation model we used was specific to elephant seals, but the process model can readily be applied to other species, providing an opportunity to understand how animals respond to their environment at a fine spatial scale.

Heterogeneous properties of central lateral and parafascicular thalamic synapses in the striatum

To understand the principles of operation of the striatum it is critical to elucidate the properties of the main excitatory inputs from cortex and thalamus, as well as their ability to activate the main neurons of the striatum, the medium spiny neurons (MSNs). As the thalamostriatal projection is heterogeneous, we set out to isolate and study the thalamic afferent inputs to MSNs using small localized injections of adeno-associated virus carrying fusion genes for channelrhodopsin-2 and YFP, in either the rostral or caudal regions of the intralaminar thalamic nuclei (i.e. the central lateral or parafascicular nucleus). This enabled optical activation of specific thalamic afferents combined with whole-cell, patch-clamp recordings of MSNs and electrical stimulation of cortical afferents, in adult mice. We found that thalamostriatal synapses differ significantly in their peak amplitude responses, short-term dynamics and expression of ionotropic glutamate receptor subtypes. Our results suggest that central lateral synapses are most efficient in driving MSNs to depolarization, particularly those of the direct pathway, as they exhibit large amplitude responses, short-term facilitation and predominantly express postsynaptic AMPA receptors. In contrast, parafascicular synapses exhibit small amplitude responses, short-term depression and predominantly express postsynaptic NMDA receptors, suggesting a modulatory role, e.g. facilitating Ca(2+)-dependent processes. Indeed, pairing parafascicular, but not central lateral, presynaptic stimulation with action potentials in MSNs, leads to NMDA receptor- and Ca(2+)-dependent long-term depression at these synapses. We conclude that the main excitatory thalamostriatal afferents differ in many of their characteristics and suggest that they each contribute differentially to striatal information processing.

An investigation into utilising gestational body mass index as a screening tool for adverse birth outcomes and maternal morbidities in a group of pregnant women in Khayelitsha

OBJECTIVE

The aim of this study was to investigate the ability of the gestational body mass index (BMI) method to screen for adverse birth outcomes and maternal morbidities.

DESIGN

This was a substudy of a randomised controlled trial, the Philani Mentor Mothers' study.

SETTING AND SUBJECTS

The Philani Mentor Mothers' study took place in a peri-urban settlement, Khayelitsha, between 2009 and 2010. Pregnant women living in the area in 2009-2010 were recruited for the study.

OUTCOME MEASURES

Maternal anthropometry (height and weight) and gestational weeks were obtained at baseline to calculate the gestational BMI, which is maternal BMI adjusted for gestational age. Participants were classified into four gestational BMI categories: underweight, normal, overweight and obese. Birth outcomes and maternal morbidities were obtained from clinic cards after the births.

RESULTS

Pregnant women were recruited into the study (n = 1 058). Significant differences were found between the different gestational BMI categories and the following birth outcomes: maternal (p-value = 0.019), infant hospital stay (p-value = 0.03), infants staying for over 24 hours in hospital (p-value = 0.001), delivery mode (p-value = 0.001), birthweight (p-value = 0.006), birth length (p-value = 0.007), birth head circumference (p-value = 0.007) and pregnancy-induced hypertension (p-value = 0.001).

CONCLUSION

To the best of our knowledge, this is the first study that has used the gestational BMI method in a peri-urban South African pregnant population. Based on the findings that this method is able to identify unfavourable birth outcomes, it is recommended that it is implemented as a pilot study in selected rural, peri-urban and urban primary health clinics, and that its ease and effectiveness as a screening tool is evaluated. Appropriate medical and nutritional advice can then be given to pregnant women to improve both their own and their infants' birth-related outcomes and maternal morbidities.

(Meta)population dynamics of infectious diseases

The metapopulation concept provides a very powerful tool for analysing the persistence of spatially-disaggregated populations, in terms of a balance between local extinction and colonization. Exactly the same approach has been developed by epidemiologists, in order to understand patterns of diseases persistence. There is great scope for further cross-fertilization between areas. Recent work on the spatitemporal dynamics of measles illustrates that the large datasets and rich modelling literature on many infectious diseases offer great potential for developing and testing ideas about metapopulations.

NMR quantitation: influence of RF inhomogeneity

The NMR peak integral is ideally linearly dependent on the sine of excitation angle (θ), which has provided unsurpassed flexibility in quantitative NMR by allowing the use of a signal of any concentration as the internal concentration reference. Controlling the excitation angle is particularly critical for solvent proton concentration referencing to minimize the negative impact of radiation damping, and to reduce the risk of receiver gain compression. In practice, due to the influence of RF inhomogeneity for any given probe, the observed peak integral is not exactly proportional to sin θ. To evaluate the impact quantitatively, we introduce a RF inhomogeneity factor I(θ) as a function of the nominal pulse excitation angle and propose a simple calibration procedure. Alternatively, I(θ) can be calculated from the probe's RF profile, which can be readily obtained as a gradient image of an aqueous sample. Our results show that without consideration of I(θ), even for a probe with good RF homogeneity, up to 5% error can be introduced due to different excitation pulse angles used for the analyte and the reference. Hence, a simple calibration of I(θ) can eliminate such errors and allow an accurate description of the observed NMR signal's dependence on the excitation angle in quantitative analysis.

Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus)

Pathogen-driven balancing selection maintains high genetic diversity in many vertebrates, particularly in the major histocompatibility complex (MHC) immune system gene family, which is often associated with disease susceptibility. In large natural populations where subpopulations face different pathogen pressures, the MHC should show greater genetic differentiation within a species than neutral markers. We examined genetic diversity at the MHC-DQB locus and nine putatively neutral microsatellite markers in grey seals (Halichoerus grypus) from eight United Kingdom (UK) colonies, the Faeroe Islands and Sable Island, Canada. Five DQB alleles were identified in grey seals, which varied in prevalence across the grey seal range. Among the seal colonies, significant differences in DQB allele and haplotype frequencies and in average DQB heterozygosity were observed. Additionally, the DQB gene exhibited greater differentiation among colonies compared with neutral markers, yet a weaker pattern of isolation by distance (IBD). After correcting for the underlying IBD pattern, subpopulations breeding in similar habitats were more similar to one another in DQB allele frequencies than populations breeding in different habitats, but the same did not hold true for microsatellites, suggesting that habitat-specific pathogen pressure influences MHC evolution. Overall, the data are consistent with selection at MHC-DQB loci in grey seals with both varying selective pressures and geographic population structure appearing to influence the DQB genetic composition of breeding colonies.

Lipid classes and fatty acid patterns are altered in the brain of γ-synuclein null mutant mice

The well-documented link between α-synuclein and the pathology of common human neurodegenerative diseases has increased attention to the synuclein protein family. The involvement of α-synuclein in lipid metabolism in both normal and diseased nervous system has been shown by many research groups. However, the possible involvement of γ-synuclein, a closely-related member of the synuclein family, in these processes has hardly been addressed. In this study, the effect of γ-synuclein deficiency on the lipid composition and fatty acid patterns of individual lipids from two brain regions has been studied using a mouse model. The level of phosphatidylserine (PtdSer) was increased in the midbrain whereas no changes in the relative proportions of membrane polar lipids were observed in the cortex of γ-synuclein-deficient compared to wild-type (WT) mice. In addition, higher levels of docosahexaenoic acid were found in PtdSer and phosphatidylethanolamine (PtdEtn) from the cerebral cortex of γ-synuclein null mutant mice. These findings show that γ-synuclein deficiency leads to alterations in the lipid profile in brain tissues and suggest that this protein, like α-synuclein, might affect neuronal function via modulation of lipid metabolism.

The functional response of a generalist predator

BACKGROUND

Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species.

METHODOLOGY AND PRINCIPAL FINDINGS

Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a "predator pit" for one prey species only occurs when the availability of other prey species is low.

CONCLUSIONS AND SIGNIFICANCE

The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.

Comparison of the 1988 and 2002 phocine distemper epizootics in British harbour seal Phoca vitulina populations

In 1988 and 2002 dramatic and well-documented phocine distemper epizootics occurred in Europe. While their progression and impact were remarkably similar and consistent over much of Europe, mortality in the UK varied greatly between and within the 2 epizootics. We use antibody levels in blood samples to show that 51% (Bayesian 95% CI: 41 to 61%) of the individuals alive in 5 UK harbour seal populations at the end of the 1988 epizootic had been exposed to the virus, and that the equivalent figure after the 2002 outbreak was 22% (95% CI: 16 to 30%). Antibody prevalence was significantly higher in females than males after the 2002 epizootic. Combining these estimates with information on reductions in the numbers of animals observed hauled out during surveys of the Wash, Moray Firth, and Orkney populations and a simple epidemiological model, suggests that the differences between the 2 epizootics were primarily due to a 27% (95% CI: 8 to 43%) fall in R0, the basic reproductive rate of the virus. The large geographic variation in population effects observed within the UK during each epizootic appears to have been mainly due to differences in case mortality, with R0 being remarkably similar in all the populations investigated.

R: A quantitative measure of NMR signal receiving efficiency

Recognizing that the sensitivity of NMR is influenced by factors such as conductance and dielectric constant of the sample, we propose the receiving efficiency R to characterize how efficiently the NMR signal can be observed from a unit transverse magnetization in a sample under optimal probe tuning and matching conditions. Conveniently, the relative receiving efficiency can be defined as the ratio of the NMR signal induced by a unit transverse magnetization in a sample of interest and a reference solution. Based on the reciprocal relationship between excitation and observation in NMR, the relative receiving efficiency can be correlated with the 90 degrees pulse length (tau(90)). In the special case of perfect probe tuning (impedance matched to 50 Omega), R is inversely proportional to tau(90). Application of the NMR receiving efficiency in quantitative analysis potentially enables a single external concentration reference for almost any sample, eliminating the need to know its exact chemical composition or detailed electromagnetic properties.

Effect of irrigation on quality attributes of olive oil

Two irrigation treatments were applied to olive trees of the major commercial Cretan variety cv. Koroneiki, (a) irrigation with 0.4 evaporation class "A" pan and (b) rain-feed only, in two successive crop years to assess the effect of irrigation on olive oil quality. Olive fruits were harvested at their semiblack maturity stage. Data obtained indicated that irrigation increased fruit weight and oil content, but the standard quality indices (free fatty acids, peroxide value, K(232), and K(270)) of the oil were not affected significantly. However, irrigation affected some aspects of olive oil composition. There were changes in the proportions of polyunsaturated fatty acids (PUFAs), triacylglycerol molecular species, sterols, and aliphatic alcohols. Furthermore, the concentrations of the dialdehydic form of elenolic acid linked to 3,4-DHPEA (3,4-DHPEA-EDA) and the isomer of oleuropeine aglycon (3,4-DHPEA-EA) were higher in oils from non-irrigated trees. Tocopherol and total volatiles were higher in the oil produced from the non-irrigated trees. Such oil was graded more pungent when compared to oils produced from fruits of irrigated trees, although both oils were graded satisfactory by consumers.

Olive oil qualitative parameters after orchard irrigation with saline water

The effect of irrigation with saline water on oil quality was studied in the two olive ( Olea europaea L.) cultivars Koroneiki and Mastoidis, which are the main varieties grown extensively on the island of Crete. Plants (5 years old) were grown outdoors in containers, filled with freely drained light soil. Four treatments were applied, differing in the NaCl added to the irrigation water as follows: 0 (control) 50, 100, and 150 mM NaCl. Drip irrigation was applied regularly, during the dry season (from April to October). Plants in all treatments were irrigated when the soil-water potential reached -40 kPa at a depth of 30 cm. Data showed that increased NaCl levels in irrigation water resulted in a decrease in oil content in the fruits and an increase in total phenols and their secoiridoid derivatives in olive oils from harvested fruits. Furthermore, changes also took place in the composition of fatty acids and triacylglycerol molecular species. The extent of alterations was different for the two varieties and greater in cv. Koroneiki. This fitted with agronomic evidence that cv. Koroneiki is less saline-tolerant than cv. Mastoidis.

Passive acoustic detection of deep-diving beaked whales

Beaked whales can remain submerged for an hour or more and are difficult to sight when they come to the surface to breathe. Passive acoustic detection (PAD) not only complements traditional visual-based methods for detecting these species but also can be more effective because beaked whales produce clicks regularly to echolocate on prey during deep foraging dives. The effectiveness of PAD for beaked whales depends not only on the acoustic behavior and output of the animals but also on environmental conditions and the quality of the passive sonar implemented. A primary constraint on the range at which beaked whale clicks can be detected involves their high frequencies, which attenuate rapidly, resulting in limited ranges of detection, especially in adverse environmental conditions. Given current knowledge of source parameters and in good conditions, for example, with a wind speed of 2 ms, a receiver close to the surface should be able to detect acoustically Cuvier's beaked whales with a high probability at distances up to 0.7 km, provided the listening duration exceeds the deep dive interval, about 2.5 h on average. Detection ranges beyond 4 km are unlikely and would require low ambient noise or special sound propagation conditions.

Evaluating the influence of epidemiological parameters and host ecology on the spread of phocine distemper virus through populations of harbour seals

BACKGROUND

Outbreaks of phocine distemper virus (PDV) in Europe during 1988 and 2002 were responsible for the death of around 23,000 and 30,000 harbour seals, respectively. These epidemics, particularly the one in 2002, provided an unusual opportunity to estimate epidemic parameters for a wildlife disease. There were marked regional differences in the values of some parameters both within and between epidemics.

METHODOLOGY AND PRINCIPAL FINDINGS

We used an individual-based model of seal movement that allowed us to incorporate realistic representations of space, time and animal behaviour into a traditional epidemiological modelling framework. We explored the potential influence of a range of ecological (foraging trip duration, time of epidemic onset, population size) and epidemiological (length of infectious period, contact rate between infectious and susceptible individuals, case mortality) parameters on four readily-measurable epidemic characteristics (number of dead individuals, duration of epidemic, peak mortality date and prevalence) and on the probability that an epidemic would occur in a particular region. We analysed the outputs as if they were the results of a series of virtual experiments, using Generalised Linear Modelling. All six variables had a significant effect on the probability that an epidemic would be recognised as an unusual mortality event by human observers.

CONCLUSIONS

Regional and temporal variation in contact rate was the most likely cause of the observed differences between the two epidemics. This variation could be a consequence of differences in the way individuals divide their time between land and sea at different times of the year.