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Animal behavioural responses to the environment ultimately affect their survival. Monitoring animal fine-scale behaviour may improve understanding of animal functional response to the environment and provide an important indicator of the welfare of both wild and domesticated species. In this study, we illustrate the application of collar-attached acceleration sensors for investigating reindeer fine-scale behaviour. Using data from 19 reindeer, we tested the supervised machine learning algorithms Random forests, Support vector machines, and hidden Markov models to classify reindeer behaviour into seven classes: grazing, browsing low from shrubs or browsing high from trees, inactivity, walking, trotting, and other behaviours. We implemented leave-one-subject-out cross-validation to assess generalizable results on new individuals. Our main results illustrated that hidden Markov models were able to classify collar-attached accelerometer data into all our pre-defined behaviours of reindeer with reasonable accuracy while Random forests and Support vector machines were biased towards dominant classes. Random forests using 5-s windows had the highest overall accuracy (85%), while hidden Markov models were able to best predict individual behaviours and handle rare behaviours such as trotting and browsing high. We conclude that hidden Markov models provide a useful tool to remotely monitor reindeer and potentially other large herbivore species behaviour. These methods will allow us to quantify fine-scale behavioural processes in relation to environmental events., (© 2022. The Author(s).)

This article presents a new method for modelling collective movement in continuous time with behavioural switching, motivated by simultaneous tracking of wild or semi-domesticated animals. Each individual in the group is at times attracted to a unobserved leading point. However, the behavioural state of each individual can switch between 'following' and 'independent'. The 'following' movement is modelled through a linear stochastic differential equation, while the 'independent' movement is modelled as Brownian motion. The movement of the leading point is modelled either as an Ornstein-Uhlenbeck (OU) process or as Brownian motion (BM), which makes the whole system a higher-dimensional Ornstein-Uhlenbeck process, possibly an intrinsic non-stationary version. An inhomogeneous Kalman filter Markov chain Monte Carlo algorithm is developed to estimate the diffusion and switching parameters and the behaviour states of each individual at a given time point. The method successfully recovers the true behavioural states in simulated data sets , and is also applied to model a group of simultaneously tracked reindeer (Rangifer tarandus)., (© 2020 The International Biometric Society.)

Environmental and ecosystem models can help to guide management of changing natural systems by projecting alternative future states under a common set of scenarios. Combining contrasting models into multi-model ensembles (MMEs) can improve the skill and reliability of projections, but associated uncertainty complicates communication of outputs, affecting both the effectiveness of management decisions and, sometimes, public trust in scientific evidence itself. Effective data visualisation can play a key role in accurately communicating such complex outcomes, but we lack an evidence base to enable us to design them to be visually appealing whilst also effectively communicating accurate information. To address this, we conducted a survey to identify the most effective methods for visually communicating the outputs of an ensemble of global climate models. We measured the accuracy, confidence, and ease with which the survey participants were able to interpret 10 visualisations depicting the same set of model outputs in different ways, as well as their preferences. Dot and box plots outperformed all other visualisations, heat maps and radar plots were comparatively ineffective, while our infographic scored highly for visual appeal but lacked information necessary for accurate interpretation. We provide a set of guidelines for visually communicating the outputs of MMEs across a wide range of research areas, aimed at maximising the impact of the visualisations, whilst minimizing the potential for misinterpretations, increasing the societal impact of the models and ensuring they are well-placed to support management in the future., (© 2021. The Author(s).)

Habitat selection models are used in ecology to link the spatial distribution of animals to environmental covariates and identify preferred habitats. The most widely used models of this type, resource selection functions, aim to capture the steady-state distribution of space use of the animal, but they assume independence between the observed locations of an animal. This is unrealistic when location data display temporal autocorrelation. The alternative approach of step selection functions embed habitat selection in a model of animal movement, to account for the autocorrelation. However, inferences from step selection functions depend on the underlying movement model, and they do not readily predict steady-state space use. We suggest an analogy between parameter updates and target distributions in Markov chain Monte Carlo (MCMC) algorithms, and step selection and steady-state distributions in movement ecology, leading to a step selection model with an explicit steady-state distribution. In this framework, we explain how maximum likelihood estimation can be used for simultaneous inference about movement and habitat selection. We describe the local Gibbs sampler, a novel rejection-free MCMC scheme, use it as the basis of a flexible class of animal movement models, and derive its likelihood function for several important special cases. In a simulation study, we verify that maximum likelihood estimation can recover all model parameters. We illustrate the application of the method with data from a zebra., (© 2019 The International Biometric Society.)

The two dominant approaches for the analysis of species-habitat associations in animals have been shown to reach divergent conclusions. Models fitted from the viewpoint of an individual (step selection functions), once scaled up, do not agree with models fitted from a population viewpoint (resource selection functions [RSFs]). We explain this fundamental incompatibility, and propose a solution by introducing to the animal movement field a novel use for the well-known family of Markov chain Monte Carlo (MCMC) algorithms. By design, the step selection rules of MCMC lead to a steady-state distribution that coincides with a given underlying function: the target distribution. We therefore propose an analogy between the movements of an animal and the movements of an MCMC sampler, to guarantee convergence of the step selection rules to the parameters underlying the population's utilization distribution. We introduce a rejection-free MCMC algorithm, the local Gibbs sampler, that better resembles real animal movement, and discuss the wide range of biological assumptions that it can accommodate. We illustrate our method with simulations on a known utilization distribution, and show theoretically and empirically that locations simulated from the local Gibbs sampler give rise to the correct RSF. Using simulated data, we demonstrate how this framework can be used to estimate resource selection and movement parameters., (© 2018 The Authors Ecology published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.)

Competing Interests: The authors have declared that no competing interests exist.

Understanding how, where, and when animals move is a central problem in marine ecology and conservation. Key to improving our knowledge about what drives animal movement is the rising deployment of telemetry devices on a range of free-roaming species. An increasingly popular way of gaining meaningful inference from an animal's recorded movements is the application of hidden Markov models (HMMs), which allow for the identification of latent behavioral states in the movement paths of individuals. However, the use of HMMs to explore the population-level consequences of movement is often limited by model complexity and insufficient sample sizes. Here, we introduce an alternative approach to current practices and provide evidence of how the inclusion of prior information in model structure can simplify the application of HMMs to multiple animal movement paths with two clear benefits: (a) consistent state allocation and (b) increases in effective sample size. To demonstrate the utility of our approach, we apply HMMs and adapted HMMs to over 100 multivariate movement paths consisting of conditionally dependent daily horizontal and vertical movements in two species of demersal fish: Atlantic cod ( Gadus morhua ; n  = 46) and European plaice ( Pleuronectes platessa ; n  = 61). We identify latent states corresponding to two main underlying behaviors: resident and migrating. As our analysis considers a relatively large sample size and states are allocated consistently, we use collective model output to investigate state-dependent spatiotemporal trends at the individual and population levels. In particular, we show how both species shift their movement behaviors on a seasonal basis and demonstrate population space use patterns that are consistent with previous individual-level studies. Tagging studies are increasingly being used to inform stock assessment models, spatial management strategies, and monitoring of marine fish populations. Our approach provides a promising way of adding value to tagging studies because inferences about movement behavior can be gained from a larger proportion of datasets, making tagging studies more relevant to management and more cost-effective.

Australia's iconic Great Barrier Reef (GBR) continues to suffer from repeated impacts of cyclones, coral bleaching, and outbreaks of the coral-eating crown-of-thorns starfish (COTS), losing much of its coral cover in the process. This raises the question of the ecosystem's systemic resilience and its ability to rebound after large-scale population loss. Here, we reveal that around 100 reefs of the GBR, or around 3%, have the ideal properties to facilitate recovery of disturbed areas, thereby imparting a level of systemic resilience and aiding its continued recovery. These reefs (1) are highly connected by ocean currents to the wider reef network, (2) have a relatively low risk of exposure to disturbances so that they are likely to provide replenishment when other reefs are depleted, and (3) have an ability to promote recovery of desirable species but are unlikely to either experience or spread COTS outbreaks. The great replenishment potential of these 'robust source reefs', which may supply 47% of the ecosystem in a single dispersal event, emerges from the interaction between oceanographic conditions and geographic location, a process that is likely to be repeated in other reef systems. Such natural resilience of reef systems will become increasingly important as the frequency of disturbances accelerates under climate change.

This article presents a new approach to modeling group animal movement in continuous time. The movement of a group of animals is modeled as a multivariate Ornstein Uhlenbeck diffusion process in a high-dimensional space. Each individual of the group is attracted to a leading point which is generally unobserved, and the movement of the leading point is also an Ornstein Uhlenbeck process attracted to an unknown attractor. The Ornstein Uhlenbeck bridge is applied to reconstruct the location of the leading point. All movement parameters are estimated using Markov chain Monte Carlo sampling, specifically a Metropolis Hastings algorithm. We apply the method to a small group of simultaneously tracked reindeer, Rangifer tarandus tarandus, showing that the method detects dependency in movement between individuals., (© 2016, The International Biometric Society.)

Reduced fishing pressure and weak predator-prey interactions within marine reserves can create trophic cascades that increase the number of grazing fishes and reduce the coverage of macroalgae on coral reefs. Here, we show that the impacts of reserves extend beyond trophic cascades and enhance the process of coral recruitment. Increased fish grazing, primarily driven by reduced fishing, was strongly negatively correlated with macroalgal cover and resulted in a 2-fold increase in the density of coral recruits within a Bahamian reef system. Our conclusions are robust because four alternative hypotheses that may generate a spurious correlation between grazing and coral recruitment were tested and rejected. Grazing appears to influence the density and community structure of coral recruits, but no detectable influence was found on the overall size-frequency distribution, community structure, or cover of corals. We interpret this absence of pattern in the adult coral community as symptomatic of the impact of a recent disturbance event that masks the recovery trajectories of individual reefs. Marine reserves are not a panacea for conservation but can facilitate the recovery of corals from disturbance and may help sustain the biodiversity of organisms that depend on a complex three-dimensional coral habitat.

Quantifying the beta diversity (species replacement along spatiotemporal gradients) of ecosystems is important for understanding and conserving patterns of biodiversity. However, virtually all studies of beta diversity focus on one-dimensional transects orientated along a specific environmental gradient that is defined a priori. By ignoring a second spatial dimension and the associated changes in species composition and environmental gradients, this approach may provide limited insight into the full pattern of beta diversity. Here, we use remotely sensed imagery to quantify beta diversity continuously, in two dimensions, and at multiple scales across an entire tropical marine seascape. We then show that beta diversity can be modeled (0.852 > or = r2 > or = 0.590) at spatial scales between 0.5 and 5.0 km2, using the environmental variables of mean and variance of depth and wave exposure. Beta diversity, quantified within a "window" of a given size, is positively correlated to the range of environmental conditions within that window. For example, beta diversity increases with increasing variance of depth. By analyzing such relationships across seascapes, this study provides a framework for a range of disparate coral reef literature including studies of zonation, diversity, and disturbance. Using supporting evidence from soft-bottom communities, we hypothesize that depth will be an important variable for modeling beta diversity in a range of marine systems. We discuss the implications of our results for the design of marine reserves.

Objective: Identifying the patterning of congenitally absent teeth will contribute to understanding the aetiology of hypodontia. The aim of this study was to investigate patterns of hypodontia in a group of young adults in Sheffield, UK involving specific tooth types, gender differences and maxilla:mandible and left:right correlations., Methods: The patients were 198 unrelated Caucasian young adults (86 males and 112 females) with non-syndromic hypodontia. Statistical methods included the multivariate techniques of cluster analysis and principal components analysis and associated display devices of circular dotplots and biplots. Autologistic regression was used to model the relationship of the presence or absence of a particular tooth to the status of other teeth., Results: The results revealed distinct patterns of dependence. Common patterns included either third molars and second premolars missing in all quadrants and/or combinations of these two tooth types and the incisors. The gender of the patient and the severity of hypodontia did not have a significant effect on patterns of tooth type absence. If a tooth was missing, the odds ratios that the same tooth type in the horizontally or vertically opposite quadrant was also missing were some 20 times higher than if the tooth was present. For diagonally opposite quadrants the dependence was much weaker., Conclusions: These statistical techniques are valuable for increasing understanding of hypodontia and identifying groups of patients for genetic studies.

Mangrove forests are one of the world's most threatened tropical ecosystems with global loss exceeding 35% (ref. 1). Juvenile coral reef fish often inhabit mangroves, but the importance of these nurseries to reef fish population dynamics has not been quantified. Indeed, mangroves might be expected to have negligible influence on reef fish communities: juvenile fish can inhabit alternative habitats and fish populations may be regulated by other limiting factors such as larval supply or fishing. Here we show that mangroves are unexpectedly important, serving as an intermediate nursery habitat that may increase the survivorship of young fish. Mangroves in the Caribbean strongly influence the community structure of fish on neighbouring coral reefs. In addition, the biomass of several commercially important species is more than doubled when adult habitat is connected to mangroves. The largest herbivorous fish in the Atlantic, Scarus guacamaia, has a functional dependency on mangroves and has suffered local extinction after mangrove removal. Current rates of mangrove deforestation are likely to have severe deleterious consequences for the ecosystem function, fisheries productivity and resilience of reefs. Conservation efforts should protect connected corridors of mangroves, seagrass beds and coral reefs.

The formation of a social group, such as the group of individuals sharing a territory, depends on the interaction between choices made by individuals to stay or disperse. The process can be modelled as a multi-player variant of the well-known War of Attrition in evolutionary game theory, as shown by Blackwell (1997; J. Theor. Biol.189, 175-181). In this paper, we extend the set of strategies defined there by allowing reappraisal during the game. We give a formal analysis of the evolutionarily stable strategy, where one exists, and illustrate it with an example based on badger (Meles meles) territoriality. The results predict that group size will be well adapted to, and very sensitive to, the precise conditions under which the game is played, and give an indication of the potential for parent-offspring conflict.

In a recent study, the ideas of Procrustes analysis were introduced to the study of tooth shape for teeth represented as configurations of 'landmarks' from digital images. This study aimed to establish how well the method could be expected to perform (in its standard form) when used on surfaces from a variety of tooth types and, in particular, how much impact inconsistencies in the positioning of landmarks would have on investigations of shape. Using four different operators' images and landmarks from 10 different surfaces from each of 20 patients, the consequences of location inconsistency are evaluated by calculating its effect on the recorded variation in Procrustes fits, obtained for each set of multiple representations. The proportion of variation in shape attributable to actual differences between patients, rather than other sources of error, ranged from only 36 to 65% for the five buccal-surfaces considered and was no more than 30% for any of the five occlusal surfaces. Further examination of these results indicated that consistent orientation differences before imaging might be a particular source of error in obtaining any occlusal-landmark data, as might location ambiguities around the edges of the teeth. Orientation effects were also suggested for the buccal-surfaces of the molar teeth. In contrast, the relatively flatter buccal-surfaces of the incisors and canines produced the most reliable data. Methods of analysis need to accommodate these problems if landmark data are to be used to describe variations in tooth shape. Different surfaces each present their own particular difficulties and so a variety of solutions may be required.

This article describes an inhomogeneous Poisson point process in the plane with an intensity function based on a Dirichlet tessellation process and a method for using observations on the point process to make fully Bayesian inferences about the underlying tessellation. The method is implemented using a Markov chain Monte Carlo approach. An application to modeling the territories of clans of badgers, Meles meles, is described.

Accurate quantification of variation in tooth shape is important in studies of dental development, which typically have involved measuring distances between subjectively identified landmarks, key points of correspondence on teeth. An established statistical framework now exists for the analysis of shape when objects are represented as configurations of landmark coordinates; allowing work with the full geometry of objects, which is otherwise lost. This approach was introduced here to the study of tooth morphology, demonstrating how after optimally matching shapes to account for the unwanted effects of location, scale and rotation, most standard descriptive and inferential statistical techniques can be adapted and applied successfully. The techniques are illustrated using a sample of buccal-surface images of central incisors from patients with hypodontia; a significant difference is found in mean buccal-surface shape (Hotelling's two-sample T(2)-test; P=0.004) when compared to a corresponding control group. Successful implementation of these methods depends on the accuracy and reliability with which the landmarks are collected; issues and problems to be addressed are discussed.

The choices made by juveniles, in territorial species, between dispersing and remaining in the natal territory, can be modelled as a simple multi-player evolutionary game, related to the well-known War of Attrition [Maynard Smith, J. (1974) J. theor. Biol. 47, 209-221; Haigh J. & Cannings, C. (1989) Acta Applicandae Mathematicae 14, 59-74]. The game is shown to have a unique evolutionarily stable strategy, involving a random choice between dispersing early in the game and staying indefinitely. An example is given, involving badgers (Meles meles), in which the key factor affecting the pay-off in the game is the possibility of inheriting the territory on the death of the current holders. The example indicates the sensitivity of the size of the group occupying the territory to the mortality rate among dispersers., (Copyright 1997 Academic Press Limited.)