Combining bioenergetics and movement models to improve understanding of the population consequences of disturbance

Funding: Naval Facilities Engineering Systems Command EXWC - N3943019C2175.We developed dynamic bioenergetics models to investigate how behavioural responses to anthropogenic disturbance events might affect the population dynamics of three marine mammal species (harbour porpoise, grey seal and harbour seal) with contrasting life-history traits (capital versus income breeders) and movement behaviour (resident versus nomadic). We used these models to analyse how individual vital rates were affected by differences in the probability of disturbance and the duration of any behavioural response, while taking account of uncertainty in the model parameters and heterogeneity in behaviour. The outputs of individual movement models and telemetry data were then used to determine how the probability of exposure might vary among species, individuals, and geographical locations. We then demonstrate how these estimated probabilities of exposure can be translated into probabilities of disturbance. For illustrative purposes, we modelled the potential effects of a temporary decrease in energy assimilation associated with a series of disturbance events that might realistically occur during the construction of an offshore windfarm. Offspring starvation mortality was the vital rate that was most affected by these disturbance events. Monitoring of rate should be considered as standard practice so that populations responses can be detected as early as possible. Predicted effects on individual vital rates depended on the species' movement behaviour and the likely density of animals where the modelled construction activity was assumed to take place. The magnitude of these effects also depended critically on the assumed duration of the reduction in energy assimilation. No direct estimates of this variable are currently available, but we suggest some ways in which it could be estimated. The described approach could be extended to other species and activities, given sufficient information to parameterise the component models. However, we emphasise the need to account for among-individual heterogeneities and uncertainties in the values of the many model parameters.Publisher PDFPeer reviewe

Using habitat selection theories to predict the spatiotemporal distribution of migratory birds during stopover - a case study of pink-footed geese Anser brachyrhynchus

Th is study was part of MC ’ s PhD project funded by Aarhus University. Th e fi eldwork was supported by the Norwegian Research Council project MIGRAPOP.Understanding how animals select for habitat and foraging resources therein is a crucial component of basic and applied ecology. The selection process is typically influenced by a variety of environmental conditions including the spatial and temporal variation in the quantity and quality of food resources, predation or disturbance risks, and inter-and intraspecific competition. Indeed, some of the most commonly employed ecological theories used to describe how animals choose foraging sites are: nutrient intake maximisation, density-dependent habitat selection, central-place foraging, and predation risk effects. Even though these theories are not mutually exclusive, rarely are multiple theoretical models considered concomitantly to assess which theory, or combination thereof, best predicts observed changes in habitat selection over space and time. Here, we tested which of the above theories best-predicted habitat selection of Svalbard-breeding pink-footed geese at their main spring migration stopover site in mid-Norway by computing a series of resource selection functions (RSFs) and their predictive ability (k-fold cross validation scores). At this stopover site geese fuel intensively as a preparation for breeding and further migration. We found that the predation risk model and a combination of the density-dependent and central-place foraging models best-predicted habitat selection during stopover as geese selected for larger fields where predation risk is typically lower and selection for foraging sites changed as a function of both distance to the roost site (i.e. central-place) and changes in local density. In contrast to many other studies, the nutritional value of the available food resources did not appear to be a major limiting factor as geese used different food resources proportional to their availability. Our study shows that in an agricultural landscape where nutritional value of food resources is homogeneously high and resource availability changes rapidly; foraging behaviour of geese is largely a tradeoff between fast refuelling and disturbance/predator avoidance.Publisher PDFPeer reviewe

Density-dependent, central-place foraging in a grazing herbivore: competition and tradeoffs in time allocation near water

Optimal foraging theory addresses one of the core challenges of ecology: predicting the distribution and abundance of species. Tests of hypotheses of optimal foraging, however, often focus on a single conceptual model rather than drawing upon the collective body of theory, precluding generalization. Here we demonstrate links between two established theoretical frameworks predicting animal movements and resource use: central-place foraging and density-dependent habitat selection. Our goal is to better understand how the nature of critical, centrally placed resources like water (or minerals, breathing holes, breeding sites, etc.) might govern selection for food (energy) resources obtained elsewhere - a common situation for animals living in natural conditions. We empirically test our predictions using movement data from a large herbivore distributed along a gradient of water availability (feral horses, Sable Island, Canada, 2008–2013). Horses occupying western Sable Island obtain freshwater at ponds while in the east horses must drink at self-excavated wells (holes). We studied the implications of differential access to water (time needed for a horse to obtain water) on selection for vegetation associations. Consistent with predictions of density-dependent habitat selection, horses were reduced to using poorer-quality habitat (heathland) more than expected close to water (where densities were relatively high), but were free to select for higher-quality grasslands farther from water. Importantly, central-place foraging was clearly influenced by the type of water-source used (ponds vs. holes, the latter with greater time constraints on access). Horses with more freedom to travel (those using ponds) selected for grasslands at greater distances and continued to select grasslands at higher densities, whereas horses using water holes showed very strong density-dependence in how habitat could be selected. Knowledge of more than one theoretical framework may be required to explain observed variation in foraging behavior of animals where multiple constraints simultaneously influence resource selection

Characterization of the complete chloroplast genome of Pinus uliginosa (Neumann) from the Pinus mugo complex

Taxonomic status of endangered peat-bog pine, Pinus uliginosa (Neumann) classified within the Pinus mugo complex, still remains to be elucidated. Here we present a complete chloroplast genome of P. uliginosa, to aid resolve its complex systematical position. The total genome size was 119,877 bp in length and contained a total of 112 genes, including 73 protein-coding genes, 35 tRNAs, and four rRNAs. The most of genes occur as a single copy. Five tRNA genes were duplicated from two to four times. Eighteen genes contain one intron, with a single gene containing two introns. No large inverted repeats were identified. The overall G + C content of P. uliginosa chloroplast genome is 38.5%

Integrated modelling of Atlantic mackerel distribution patterns and movements : a template for dynamic impact assessments

The study was funded by Equinor (formerly Statoil).Modelling is important for impact assessments of anthropogenic pressures on wildlife. Models are particularly useful when dealing with complex dynamic systems (as pelagic ecosystems) where data are limited and if various ‘what if’ scenarios should be tested. The aim of this study was to produce and implement an integrated modelling approach, linking high resolution hydrodynamic models (HDM) of the marine environment with correlative species distribution models (SDM) and agent-based models (ABM), for describing the spatio-temporal distribution and movements of Atlantic mackerel (Scomber scombrus) in the Norwegian Sea. The SDM was fitted with scientific mackerel trawl data as response variables (collected in July and August 2006–2014) and temperature (from the HDM), water depth and time period as predictors of spatial distributions. The SDM was able to produce dynamic predictions of a similar order of magnitude as observed catch per unit effort (CPUE) as well as realistic large-scale distribution patterns, when tested on independent data (not included in the modelling). The ABM was calibrated, with normalized SDM predictions (habitat suitability as a proxy for food availability) and hydrodynamics as input and simulated on a single year (2013) for the period May–October, when the migratory mackerel is present in the study area. A pattern-oriented modelling (POM) approach was used to verify if the model reproduced multiple observed real-world patterns. The ABM produced similar patterns as observed regarding migration timing, growth and large scale geographic distribution. Fine scaled information on mackerel movement and behaviour is limited, which is also reflected in the results. More data and knowledge are therefore required to improve the patterns emerging from fine scaled processes. The potential of the model for assessing an impact of a single seismic survey (mimicking a real survey) was finally evaluated. The exercise allowed estimating the number of affected fish (within 50 km from the sound source) and potential changes in local migrations, with the specific assumed minimum sound pressure thresholds (resulting in a fleeing reaction by the mackerel) set to 165 dB re 1 μPa. The model framework was shown to be useful by allowing simulations of impact scenarios in a realistic and dynamic environment. The model can be further updated when data on fine scale movements of mackerel and most importantly when improved data on response behaviour to impacts of sound become available.PostprintPeer reviewe

From theory to practice in pattern?oriented modelling: identifying and using empirical patterns in predictive models

To robustly predict the effects of disturbance and ecosystem changes on species, it is necessary to produce structurally realistic models with high predictive power and flexibility. To ensure that these models reflect the natural conditions necessary for reliable prediction, models must be informed and tested using relevant empirical observations. Pattern?oriented modelling (POM) offers a systematic framework for employing empirical patterns throughout the modelling process and has been coupled with complex systems modelling, such as in agent?based models (ABMs). However, while the production of ABMs has been rising rapidly, the explicit use of POM has not increased. Challenges with identifying patterns and an absence of specific guidelines on how to implement empirical observations may limit the accessibility of POM and lead to the production of models which lack a systematic consideration of reality. This review serves to provide guidance on how to identify and apply patterns following a POM approach in ABMs (POM?ABMs), specifically addressing: where in the ecological hierarchy can we find patterns; what kinds of patterns are useful; how should simulations and observations be compared; and when in the modelling cycle are patterns used? The guidance and examples provided herein are intended to encourage the application of POM and inspire efficient identification and implementation of patterns for both new and experienced modellers alike. Additionally, by generalising patterns found especially useful for POM?ABM development, these guidelines provide practical help for the identification of data gaps and guide the collection of observations useful for the development and verification of predictive models. Improving the accessibility and explicitness of POM could facilitate the production of robust and structurally realistic models in the ecological community, contributing to the advancement of predictive ecology at large

Key questions in marine mammal bioenergetics

Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as ‘key’ questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations

Key questions in marine mammal bioenergetics

This work was funded by the Marine Mammal Commission (MMC19-173). The Office of Naval Research funded the bioenergetic workshop (N000142012392) that provided support for this work.Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as ‘key’ questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations.Publisher PDFPeer reviewe

Proteomics in food: Quality, safety, microbes, and allergens

Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumer's health. Customer's confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens