Statistical modelling of individual animal movement: an overview of key methods and a discussion of practical challenges

Tracking the Ghosts of the Himalayas: Snow Leopard Conservation Insights From Satellite Collar Data

This study presents the first movement analysis of snow leopards (Panthera uncia) using satellite telemetry data, focusing on the northeastern Himalayas of Nepal. By examining GPS-based satellite collar data between 2013 and 2017 from five collared snow leopards (effectively three individuals), the research uncovered distinct movement patterns, activity budgeting and home range utilisation from one adult male and two sub adult females. Hidden Markov models (HMMs) revealed three behavioural states based on the movement patterns-slow (indicative of resting), moderate and fast (associated with travelling) and demonstrated that the time of day influenced their behavioural state. While adult males exhibited behaviour focused on moderately active states, juvenile females presented behaviour focused on highly active states. Home ranges, estimated over a 5-21 month tracking period, were larger than those observed in previously studied snow leopards and included crossings of international boundaries from Nepal into China and India. These relatively large home ranges may be attributed to the rugged terrain and scarce resources within the study area. This research suggested that movement patterns and home range sizes might differ between male and female snow leopards, which may indicate different ecological needs and resource-use techniques. Furthermore, this study provides reliable information on snow leopards from the telemetry data and links it to conservation implications in northeastern Nepal to ensure their long-term survival, promote coexistence and foster cross-border collaboration.

How to account for behavioral states in step-selection analysis: a model comparison

Step-selection models are widely used to study animals' fine-scale habitat selection based on movement data. Resource preferences and movement patterns, however, often depend on the animal's unobserved behavioral states, such as resting or foraging. As this is ignored in standard (integrated) step-selection analyses (SSA, iSSA), different approaches have emerged to account for such states in the analysis. The performance of these approaches and the consequences of ignoring the states in step-selection analysis, however, have rarely been quantified. We evaluate the recent idea of combining iSSAs with hidden Markov models (HMMs), which allows for a joint estimation of the unobserved behavioral states and the associated state-dependent habitat selection. Besides theoretical considerations, we use an extensive simulation study and a case study on fine-scale interactions of simultaneously tracked bank voles (Myodes glareolus) to compare this HMM-iSSA empirically to both the standard and a widely used classification-based iSSA (i.e., a two-step approach based on a separate prior state classification). Moreover, to facilitate its use, we implemented the basic HMM-iSSA approach in the R package HMMiSSA available on GitHub.

Bat Motion can be Described by Leap Frogging

We present models of bat motion derived from radio-tracking data collected over 14 nights. The data presents an initial dispersal period and a return to roost period. Although a simple diffusion model fits the initial dispersal motion we show that simple convection cannot provide a description of the bats returning to their roost. By extending our model to include non-autonomous parameters, or a leap frogging form of motion, where bats on the exterior move back first, we find we are able to accurately capture the bat's motion. We discuss ways of distinguishing between the two movement descriptions and, finally, consider how the different motion descriptions would impact a bat's hunting strategy.

Crabs ride the tide: incoming tides promote foraging of Giant Mud Crab (Scylla serrata)

BACKGROUND

Effective fisheries management of mobile species relies on robust knowledge of animal behaviour and habitat-use. Indices of behaviour can be useful for interpreting catch-per-unit-effort data which acts as a proxy for relative abundance. Information about habitat-use can inform stocking release strategies or the design of marine protected areas. The Giant Mud Crab (Scylla serrata; Family: Portunidae) is a swimming estuarine crab that supports significant fisheries harvest throughout the Indo-West Pacific, but little is known about the fine-scale movement and behaviour of this species.

METHODS

We tagged 18 adult Giant Mud Crab with accelerometer-equipped acoustic tags to track their fine-scale movement using a hyperbolic positioning system, alongside high temporal resolution environmental data (e.g., water temperature), in a temperate south-east Australian estuary. A hidden Markov model was used to classify movement (i.e., step length, turning angle) and acceleration data into discrete behaviours, while also considering the possibility of individual variation in behavioural dynamics. We then investigated the influence of environmental covariates on these behaviours based on previously published observations.

RESULTS

We fitted a model with two well-distinguished behavioural states describing periods of inactivity and foraging, and found no evidence of individual variation in behavioural dynamics. Inactive periods were most common (79% of time), and foraging was most likely during low, incoming tides; while inactivity was more likely as the high tide receded. Model selection removed time (hour) of day and water temperature (°C) as covariates, suggesting that they do not influence Giant Mud Crab behavioural dynamics at the temporal scale investigated.

CONCLUSIONS

Our study is the first to quantitatively link fine-scale movement and behaviour of Giant Mud Crab to environmental variation. Our results suggest Giant Mud Crab are a predominantly sessile species, and support their status as an opportunistic scavenger. We demonstrate a relationship between the tidal cycle and foraging that is likely to minimize predation risk while maximizing energetic efficiency. These results may explain why tidal covariates influence catch rates in swimming crabs, and provide a foundation for standardisation and interpretation of catch-per-unit-effort data-a commonly used metric in fisheries science.

Using quantile regression and relative entropy to assess the period of anomalous behavior of marine mammals following tagging

Tagging of animals induces a variable stress response which following release will obscure natural behavior. It is of scientific relevance to establish methods that assess recovery from such behavioral perturbation and generalize well to a broad range of animals, while maintaining model transparency. We propose two methods that allow for subdivision of animals based on covariates, and illustrate their use onN = 20 narwhals (Monodon monoceros) andN = 4 bowhead whales (Balaena mysticetus), captured and instrumented with Acousonde™ behavioral tags, but with a framework that easily generalizes to other marine animals and sampling units. The narwhals were divided into two groups based on handling time, short (t < 58 min) and long (t ≥ 58 min), to measure the effect on recovery. Proxies for energy expenditure (VeDBA) and rapid movement (jerk) were derived from accelerometer data. Diving profiles were characterized using two metrics (target depth and dive duration) derived from depth data. For accelerometer data, recovery was estimated using quantile regression (QR) on the log-transformed response, whereas depth data were addressed using relative entropy (RE) between hourly distributions of dive duration (partitioned into three target depth ranges) and the long-term average distribution. Quantile regression was used to address location-based behavior to accommodate distributional shifts anticipated in aquatic locomotion. For all narwhals, we found fast recovery in the tail of the distribution (<3 h) compared with a variable recovery at the median (∼1-10 h) and with a significant difference between groups separated by handling time. Estimates of bowhead whale recovery times showed fast median recovery (<3 h) and slow recovery at the tail (>6 h), but were affected by substantial uncertainty. For the diving profiles, as characterized by the component pair (target depth, dive duration), the recovery was slower (narwhals-long:t < 16 h; narwhals-short:t < 10 h; bowhead whales: <9 h) and with a difference between narwhals with short vs long handling times. Using simple statistical concepts, we have presented two transparent and general methods for analyzing high-resolution time series data from marine animals, addressing energy expenditure, activity, and diving behavior, and which allows for comparison between groups of animals based on well-defined covariates.

Scaling up and down: movement ecology for microorganisms

Movement is critical for the fitness of organisms, both large and small. It dictates how individuals acquire resources, evade predators, exchange genetic material, and respond to stressful environments. Movement also influences ecological and evolutionary dynamics at higher organizational levels, such as populations and communities. However, the links between individual motility and the processes that generate and maintain microbial diversity are poorly understood. Movement ecology is a framework linking the physiological and behavioral properties of individuals to movement patterns across scales of space, time, and biological organization. By synthesizing insights from cell biology, ecology, and evolution, we expand theory from movement ecology to predict the causes and consequences of microbial movements.

Bee species perform distinct foraging behaviors that are best described by different movement models

In insect-pollinated plants, the foraging behavior of pollinators affects their pattern of movement. If distinct bee species vary in their foraging behaviors, different models may best describe their movement. In this study, we quantified and compared the fine scale movement of three bee species foraging on patches of Medicago sativa. Bee movement was described using distances and directions traveled between consecutive racemes. Bumble bees and honey bees traveled shorter distances after visiting many flowers on a raceme, while the distance traveled by leafcutting bees was independent of flower number. Transition matrices and vectors were calculated for bumble bees and honey bees to reflect their directionality of movement within foraging bouts; leafcutting bees were as likely to move in any direction. Bee species varied in their foraging behaviors, and for each bee species, we tested four movement models that differed in how distances and directions were selected, and identified the model that best explained the movement data. The fine-scale, within-patch movement of bees could not always be explained by a random movement model, and a general model of movement could not be applied to all bee species.

Evidence for a consistent use of external cues by marine fish larvae for orientation

The larval stage is the main dispersive process of most marine teleost species. The degree to which larval behavior controls dispersal has been a subject of debate. Here, we apply a cross-species meta-analysis, focusing on the fundamental question of whether larval fish use external cues for directional movement (i.e., directed movement). Under the assumption that directed movement results in straighter paths (i.e., higher mean vector lengths) compared to undirected, we compare observed patterns to those expected under undirected pattern of Correlated Random Walk (CRW). We find that the bulk of larvae exhibit higher mean vector lengths than those expected under CRW, suggesting the use of external cues for directional movement. We discuss special cases which diverge from our assumptions. Our results highlight the potential contribution of orientation to larval dispersal outcomes. This finding can improve the accuracy of larval dispersal models, and promote a sustainable management of marine resources.

Drivers of polar bear behavior and the possible effects of prey availability on foraging strategy

BACKGROUND

Change in behavior is one of the earliest responses to variation in habitat suitability. It is therefore important to understand the conditions that promote different behaviors, particularly in areas undergoing environmental change. Animal movement is tightly linked to behavior and remote tracking can be used to study ethology when direct observation is not possible.

METHODS

We used movement data from 14 polar bears (Ursus maritimus) in Hudson Bay, Canada, during the foraging season (January-June), when bears inhabit the sea ice. We developed an error-tolerant method to correct for sea ice drift in tracking data. Next, we used hidden Markov models with movement and orientation relative to wind to study three behaviors (stationary, area-restricted search, and olfactory search) and examine effects of 11 covariates on behavior.

RESULTS

Polar bears spent approximately 47% of their time in the stationary drift state, 29% in olfactory search, and 24% in area-restricted search. High energy behaviors occurred later in the day (around 20:00) compared to other populations. Second, olfactory search increased as the season progressed, which may reflect a shift in foraging strategy from still-hunting to active search linked to a shift in seal availability (i.e., increase in haul-outs from winter to the spring pupping and molting seasons). Last, we found spatial patterns of distribution linked to season, ice concentration, and bear age that may be tied to habitat quality and competitive exclusion.

CONCLUSIONS

Our observations were generally consistent with predictions of the marginal value theorem, and differences between our findings and other populations could be explained by regional or temporal variation in resource availability. Our novel movement analyses and finding can help identify periods, regions, and conditions of critical habitat.

An integrated path for spatial capture-recapture and animal movement modeling

Ecologists and conservation biologists increasingly rely on spatial capture-recapture (SCR) and movement modeling to study animal populations. Historically, SCR has focused on population-level processes (e.g., vital rates, abundance, density, and distribution), whereas animal movement modeling has focused on the behavior of individuals (e.g., activity budgets, resource selection, migration). Even though animal movement is clearly a driver of population-level patterns and dynamics, technical and conceptual developments to date have not forged a firm link between the two fields. Instead, movement modeling has typically focused on the individual level without providing a coherent scaling from individual- to population-level processes, whereas SCR has typically focused on the population level while greatly simplifying the movement processes that give rise to the observations underlying these models. In our view, the integration of SCR and animal movement modeling has tremendous potential for allowing ecologists to scale up from individuals to populations and advancing the types of inferences that can be made at the intersection of population, movement, and landscape ecology. Properly accounting for complex animal movement processes can also potentially reduce bias in estimators of population-level parameters, thereby improving inferences that are critical for species conservation and management. This introductory article to the Special Feature reviews recent advances in SCR and animal movement modeling, establishes a common notation, highlights potential advantages of linking individual-level (Lagrangian) movements to population-level (Eulerian) processes, and outlines a general conceptual framework for the integration of movement and SCR models. We then identify important avenues for future research, including key challenges and potential pitfalls in the developments and applications that lie ahead.

Multi-mode movement decisions across widely ranging behavioral processes

Movement of organisms plays a fundamental role in the evolution and diversity of life. Animals typically move at an irregular pace over time and space, alternating among movement states. Understanding movement decisions and developing mechanistic models of animal distribution dynamics can thus be contingent to adequate discrimination of behavioral phases. Existing methods to disentangle movement states typically require a follow-up analysis to identify state-dependent drivers of animal movement, which overlooks statistical uncertainty that comes with the state delineation process. Here, we developed population-level, multi-state step selection functions (HMM-SSF) that can identify simultaneously the different behavioral bouts and the specific underlying behavior-habitat relationship. Using simulated data and relocation data from mule deer (Odocoileus hemionus), plains bison (Bison bison bison) and plains zebra (Equus quagga), we illustrated the HMM-SSF robustness, versatility, and predictive ability for animals involved in distinct behavioral processes: foraging, migrating and avoiding a nearby predator. Individuals displayed different habitat selection pattern during the encamped and the travelling phase. Some landscape attributes switched from being selected to avoided, depending on the movement phase. We further showed that HMM-SSF can detect multi-modes of movement triggered by predators, with prey switching to the travelling phase when predators are in close vicinity. HMM-SSFs thus can be used to gain a mechanistic understanding of how animals use their environment in relation to the complex interplay between their needs to move, their knowledge of the environment and navigation capacity, their motion capacity and the external factors related to landscape heterogeneity.

Braitenberg Vehicles as Developmental Neurosimulation

Connecting brain and behavior is a longstanding issue in the areas of behavioral science, artificial intelligence, and neurobiology. As is standard among models of artificial and biological neural networks, an analogue of the fully mature brain is presented as a blank slate. However, this does not consider the realities of biological development and developmental learning. Our purpose is to model the development of an artificial organism that exhibits complex behaviors. We introduce three alternate approaches to demonstrate how developmental embodied agents can be implemented. The resulting developmental Braitenberg vehicles (dBVs) will generate behaviors ranging from stimulus responses to group behavior that resembles collective motion. We will situate this work in the domain of artificial brain networks along with broader themes such as embodied cognition, feedback, and emergence. Our perspective is exemplified by three software instantiations that demonstrate how a BV-genetic algorithm hybrid model, a multisensory Hebbian learning model, and multi-agent approaches can be used to approach BV development. We introduce use cases such as optimized spatial cognition (vehicle-genetic algorithm hybrid model), hinges connecting behavioral and neural models (multisensory Hebbian learning model), and cumulative classification (multi-agent approaches). In conclusion, we consider future applications of the developmental neurosimulation approach.

Telomere length correlates with physiological and behavioural responses of a long-lived seabird to an ecologically relevant challenge

Determinants of individual variation in reallocation of limited resources towards self-maintenance versus reproduction are not well known. We tested the hypothesis that individual heterogeneity in long-term 'somatic state' (i) explains variation in endocrine and behavioural responses to environmental challenges, and (ii) is associated with variation in strategies for allocating to self-maintenance versus reproduction. We used relative telomere length as an indicator of somatic state and experimentally generated an abrupt short-term reduction of food availability (withdrawal of food supplementation) for free-living seabirds (black-legged kittiwakes, Rissa tridactyla). Incubating male kittiwakes responded to withdrawal by increasing circulating corticosterone and losing more weight compared to continuously supplemented controls. Males with longer telomeres increased time in directed travel regardless of treatment, while experiencing smaller increases in corticosterone. Males with longer telomeres fledged more chicks in the control group and tended to be more likely to return regardless of treatment. This study supports the hypothesis that somatic state can explain variation in short-term physiological and behavioural responses to challenges, and longer-term consequences for fitness. Male kittiwakes with longer telomeres appear to have prioritized investment in self over investment in offspring under challenging conditions.

Recent trends in movement ecology of animals and human mobility

Movement is fundamental to life, shaping population dynamics, biodiversity patterns, and ecosystem structure. In 2008, the movement ecology framework (MEF Nathan et al. in PNAS 105(49):19052-19059, 2008) introduced an integrative theory of organismal movement-linking internal state, motion capacity, and navigation capacity to external factors-which has been recognized as a milestone in the field. Since then, the study of movement experienced a technological boom, which provided massive quantities of tracking data of both animal and human movement globally and at ever finer spatio-temporal resolutions. In this work, we provide a quantitative assessment of the state of research within the MEF, focusing on animal movement, including humans and invertebrates, and excluding movement of plants and microorganisms. Using a text mining approach, we digitally scanned the contents of [Formula: see text] papers from 2009 to 2018 available online, identified tools and methods used, and assessed linkages between all components of the MEF. Over the past decade, the publication rate has increased considerably, along with major technological changes, such as an increased use of GPS devices and accelerometers and a majority of studies now using the R software environment for statistical computing. However, animal movement research still largely focuses on the effect of environmental factors on movement, with motion and navigation continuing to receive little attention. A search of topics based on words featured in abstracts revealed a clustering of papers among marine and terrestrial realms, as well as applications and methods across taxa. We discuss the potential for technological and methodological advances in the field to lead to more integrated and interdisciplinary research and an increased exploration of key movement processes such as navigation, as well as the evolutionary, physiological, and life-history consequences of movement.

A real-time data assimilative forecasting system for animal tracking

Monitoring technologies now provide real‐time animal location information, which opens up the possibility of developing forecasting systems to fuse these data with movement models to predict future trajectories. State‐space modeling approaches are well established for retrospective location estimation and behavioral inference through state and parameter estimation. Here we use a state‐space model within a comprehensive data assimilative framework for probabilistic animal movement forecasting. Real‐time location information is combined with stochastic movement model predictions to provide forecasts of future animal locations and trajectories, as well as estimates of key behavioral parameters. Implementation uses ensemble‐based sequential Monte Carlo methods (a particle filter). We first apply the framework to an idealized case using a nondimensional animal movement model based on a continuous‐time random walk process. A set of numerical forecasting experiments demonstrates the workflow and key features, such as the online estimation of behavioral parameters using state augmentation, the use of potential functions for habitat preference, and the role of observation error and sampling frequency on forecast skill. For a realistic demonstration, we adapt the framework to short‐term forecasting of the endangered southern resident killer whale (SRKW) in the Salish Sea using visual sighting information wherein the potential function reflects historical habitat utilization of SRKW. We successfully estimate whale locations up to 2.5 h in advance with a moderate prediction error (<5 km), providing reasonable lead‐in time to mitigate vessel–whale interactions. It is argued that this forecasting framework can be used to synthesize diverse data types and improve animal movement models and behavioral understanding and has the potential to lead to important advances in movement ecology.

Automatic selection of the number of clusters using Bayesian clustering and sparsity-inducing priors

Clustering is a ubiquitous task in ecological and environmental sciences and multiple methods have been developed for this purpose. Because these clustering methods typically require users to a priori specify the number of groups, the standard approach is to run the algorithm for different numbers of groups and then choose the optimal number using a criterion (e.g., AIC or BIC). The problem with this approach is that it can be computationally expensive to run these clustering algorithms multiple times (i.e., for different numbers of groups) and some of these information criteria can lead to an overestimation of the number of groups. To address these concerns, we advocate for the use of sparsity-inducing priors within a Bayesian clustering framework. In particular, we highlight how the truncated stick-breaking (TSB) prior, a prior commonly adopted in Bayesian nonparametrics, can be used to simultaneously determine the number of groups and estimate model parameters for a wide range of Bayesian clustering models without requiring the fitting of multiple models. We illustrate the ability of this prior to successfully recover the true number of groups for three clustering models (two types of mixture models, applied to GPS movement data and species occurrence data, as well as the species archetype model) using simulated data in the context of movement ecology and community ecology. We then apply these models to armadillo movement data in Brazil, plant occurrence data from Alberta (Canada), and bird occurrence data from North America. We believe that many ecological and environmental sciences applications will benefit from Bayesian clustering methods with sparsity-inducing priors given the ubiquity of clustering and the associated challenge of determining the number of groups. Two R packages, EcoCluster and bayesmove, are provided that enable the straightforward fitting of these models with the TSB prior.

Assessing behaviour states of a forest carnivore in a road-dominated landscape using Hidden Markov Models

Anthropogenic infrastructures and land-use changes are major threats to animal movements across heterogeneous landscapes. Yet, the behavioural consequences of such constraints remain poorly understood. We investigated the relationship between the behaviour of the Common genet (Genetta genetta) and road proximity, within a dominant mixed forest-agricultural landscape in southern Portugal, fragmented by roads. Specifically, we aimed to: (i) identify and characterise the behavioural states displayed by genets and related movement patterns; and (ii) understand how behavioural states are influenced by proximity to main paved roads and landscape features. We used a multivariate Hidden Markov Model (HMM) to characterise the fine-scale movements (10-min fixes GPS) of seven genets tracked during 187 nights (mean 27 days per individual) during the period 2016–2019, using distance to major paved roads and landscape features as predictors. Our findings indicated that genet’s movement patterns were composed of three basic behavioural states, classified as “resting” (short step-lengths [mean = 10.6 m] and highly tortuous), “foraging” (intermediate step-lengths [mean = 46.1 m] and with a wide range in turning angle) and “travelling” (longer step-lengths [mean = 113.7 m] and mainly linear movements). Within the genet’s main activity-period (17.00 h-08.00 h), the movement model predicts that genets spend 36.7% of their time travelling, 35.4% foraging and 28.0% resting. The probability of genets displaying the travelling state was highest in areas far away from roads (&gt; 500 m), whereas foraging and resting states were more likely in areas relatively close to roads (up to 500 m). Landscape features also had a pronounced effect on behaviour state occurrence. More specifically, travelling was most likely to occur in areas with lower forest edge density and close to riparian habitats, while foraging was more likely to occur in areas with higher forest edge density and far away from riparian habitats. The results suggest that, although roads represent a behavioural barrier to the movement of genets, they also take advantage of road proximity as foraging areas. Our study demonstrates that the HMM approach is useful for disentangling movement behaviour and understanding how animals respond to roadsides and fragmented habitats. We emphasise that road-engaged stakeholders need to consider movement behaviour of genets when targeting management practices to maximise road permeability for wildlife.

Big-data approaches lead to an increased understanding of the ecology of animal movement

Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences.

Automatic mapping of multiplexed social receptive fields by deep learning and GPU-accelerated 3D videography

Social interactions powerfully impact the brain and the body, but high-resolution descriptions of these important physical interactions and their neural correlates are lacking. Currently, most studies rely on labor-intensive methods such as manual annotation. Scalable and objective tracking methods are required to understand the neural circuits underlying social behavior. Here we describe a hardware/software system and analysis pipeline that combines 3D videography, deep learning, physical modeling, and GPU-accelerated robust optimization, with automatic analysis of neuronal receptive fields recorded in interacting mice. Our system ("3DDD Social Mouse Tracker") is capable of fully automatic multi-animal tracking with minimal errors (including in complete darkness) during complex, spontaneous social encounters, together with simultaneous electrophysiological recordings. We capture posture dynamics of multiple unmarked mice with high spatiotemporal precision (~2 mm, 60 frames/s). A statistical model that relates 3D behavior and neural activity reveals multiplexed 'social receptive fields' of neurons in barrel cortex. Our approach could be broadly useful for neurobehavioral studies of multiple animals interacting in complex low-light environments.

Classifying behavior from short-interval biologging data: An example with GPS tracking of birds

Recent advances in digital data collection have spurred accumulation of immense quantities of data that have potential to lead to remarkable ecological insight, but that also present analytic challenges. In the case of biologging data from birds, common analytical approaches to classifying movement behaviors are largely inappropriate for these massive data sets.We apply a framework for using K-means clustering to classify bird behavior using points from short time interval GPS tracks. K-means clustering is a well-known and computationally efficient statistical tool that has been used in animal movement studies primarily for clustering segments of consecutive points. To illustrate the utility of our approach, we apply K-means clustering to six focal variables derived from GPS data collected at 1-11 s intervals from free-flying bald eagles (Haliaeetus leucocephalus) throughout the state of Iowa, USA. We illustrate how these data can be used to identify behaviors and life-stage- and age-related variation in behavior.After filtering for data quality, the K-means algorithm identified four clusters in >2 million GPS telemetry data points. These four clusters corresponded to three movement states: ascending, flapping, and gliding flight; and one non-moving state: perching. Mapping these states illustrated how they corresponded tightly to expectations derived from natural history observations; for example, long periods of ascending flight were often followed by long gliding descents, birds alternated between flapping and gliding flight.The K-means clustering approach we applied is both an efficient and effective mechanism to classify and interpret short-interval biologging data to understand movement behaviors. Furthermore, because it can apply to an abundance of very short, irregular, and high-dimensional movement data, it provides insight into small-scale variation in behavior that would not be possible with many other analytical approaches.

Discrete-space continuous-time models of marine mammal exposure to Navy sonar

Assessing the patterns of wildlife attendance to specific areas is relevant across many fundamental and applied ecological studies, particularly when animals are at risk of being exposed to stressors within or outside the boundaries of those areas. Marine mammals are increasingly being exposed to human activities that may cause behavioral and physiological changes, including military exercises using active sonars. Assessment of the population-level consequences of anthropogenic disturbance requires robust and efficient tools to quantify the levels of aggregate exposure for individuals in a population over biologically relevant time frames. We propose a discrete-space, continuous-time approach to estimate individual transition rates across the boundaries of an area of interest, informed by telemetry data collected with uncertainty. The approach allows inferring the effect of stressors on transition rates, the progressive return to baseline movement patterns, and any difference among individuals. We apply the modeling framework to telemetry data from Blainville's beaked whale (Mesoplodon densirostris) tagged in the Bahamas at the Atlantic Undersea Test and Evaluation Center (AUTEC), an area used by the U.S. Navy for fleet readiness training. We show that transition rates changed as a result of exposure to sonar exercises in the area, reflecting an avoidance response. Our approach supports the assessment of the aggregate exposure of individuals to sonar and the resulting population-level consequences. The approach has potential applications across many applied and fundamental problems where telemetry data are used to characterize animal occurrence within specific areas.

Estimating the movements of terrestrial animal populations using broad-scale occurrence data

As human and automated sensor networks collect increasingly massive volumes of animal observations, new opportunities have arisen to use these data to infer or track species movements. Sources of broad scale occurrence datasets include crowdsourced databases, such as eBird and iNaturalist, weather surveillance radars, and passive automated sensors including acoustic monitoring units and camera trap networks. Such data resources represent static observations, typically at the species level, at a given location. Nonetheless, by combining multiple observations across many locations and times it is possible to infer spatially continuous population-level movements. Population-level movement characterizes the aggregated movement of individuals comprising a population, such as range contractions, expansions, climate tracking, or migration, that can result from physical, behavioral, or demographic processes. A desire to model population movements from such forms of occurrence data has led to an evolving field that has created new analytical and statistical approaches that can account for spatial and temporal sampling bias in the observations. The insights generated from the growth of population-level movement research can complement the insights from focal tracking studies, and elucidate mechanisms driving changes in population distributions at potentially larger spatial and temporal scales. This review will summarize current broad-scale occurrence datasets, discuss the latest approaches for utilizing them in population-level movement analyses, and highlight studies where such analyses have provided ecological insights. We outline the conceptual approaches and common methodological steps to infer movements from spatially distributed occurrence data that currently exist for terrestrial animals, though similar approaches may be applicable to plants, freshwater, or marine organisms.

Energy-mediated responses to changing prey size and distribution in marine top predator movements and population dynamics

Climate change is modifying the structure of marine ecosystems, including that of fish communities. Alterations in abiotic and biotic conditions can decrease fish size and change community spatial arrangement, ultimately impacting predator species which rely on these communities. To conserve predators and understand the drivers of observed changes in their population dynamics, we must advance our understanding of how shifting environmental conditions can impact populations by limiting food available to individuals. To investigate the impacts of changing fish size and spatial aggregation on a top predator population, we applied an existing agent-based model parameterized for harbour porpoises Phocoena phocoena which represents animal energetics and movements in high detail. We used this framework to quantify the impacts of shifting prey size and spatial aggregation on porpoise movement, space use, energetics and population dynamics. Simulated individuals were more likely to switch from area-restricted search to transit behaviour with increasing prey size, particularly when starving, due to elevated resource competition. In simulations with highly aggregated prey, higher prey encounter rates counteracted resource competition, resulting in no impacts of prey spatial aggregation on movement behaviour. Reduced energy intake with decreasing prey size and aggregation level caused population decline, with a 15% decrease in fish length resulting in total population collapse Increasing prey consumption rates by 42.8 ± 4.5% could offset population declines; however, this increase was 21.3 ± 12.7% higher than needed to account for changes in total energy availability alone. This suggests that animals in realistic seascapes require additional energy to locate smaller prey which should be considered when assessing the impacts of decreased energy availability. Changes in prey size and aggregation influenced movements and population dynamics of simulated harbour porpoises, revealing that climate-induced changes in prey structure, not only prey abundance, may threaten predator populations. We demonstrate how a population model with realistic animal movements and process-based energetics can be used to investigate population consequences of shifting food availability, such as those mediated by climate change, and provide a mechanistic explanation for how changes in prey structure can impact energetics, behaviour and ultimately viability of predator populations.

Individual decisions drive the changes in movement patterns of ground beetles between forestry management types

Moving from one habitat to another, the dispersal of individuals has consequences for their conditions, population dynamics and gene flow. Our major motivation was to explore the effects of different forestry treatments, such as preparation (partial) cuts and clear cuts, on the selected population of the forest ground beetle, Carabus coriaceus (Coleoptera: Carabidae). We tagged six individuals (three males and three females) with small radio-transmitters and each was released in the treatment habitat core, at the edges and in the core of control forests respectively. The recorded trajectories were divided into two major movement phases: a random walk and a directional movement using hidden Markov models. Our results revealed that in the core zone of preparation cuts, the random walk and the directional movement were equally distributed in the trajectory. A clear directional movement was observed in the clear cuts suggesting the beetles moved directly toward the adjacent (control) forest interior. The trajectories at the edges of both treatments were dominated by the random walk and so for the controls. These results suggest that forest ground beetles can avoid the forestry treatments especially clear cuts, however edge habitats and (the studied) preparation cuts can mitigate the migration constraints due to their more favorable environmental conditions compared to clear cuts.

Diving deeper into the underlying white shark behaviors at Guadalupe Island, Mexico

Fine-scale movement patterns are driven by both biotic (hunting, physiological needs) and abiotic (environmental conditions) factors. The energy balance governs all movement-related strategic decisions.Marine environments can be better understood by considering the vertical component. From 24 acoustic trackings of 10 white sharks in Guadalupe Island, this study linked, for the first time, horizontal and vertical movement data and inferred six different behavioral states along with movement states, through the use of hidden Markov models, which allowed to draw a comprehensive picture of white shark behavior.Traveling was the most frequent state of behavior for white sharks, carried out mainly at night and twilight. In contrast, area-restricted searching was the least used, occurring primarily in daylight hours.Time of day, distance to shore, total shark length, and, to a lesser extent, tide phase affected behavioral states. Chumming activity reversed, in the short term and in a nonpermanent way, the behavioral pattern to a general diel vertical pattern.

A role for lakes in revealing the nature of animal movement using high dimensional telemetry systems

Movement ecology is increasingly relying on experimental approaches and hypothesis testing to reveal how, when, where, why, and which animals move. Movement of megafauna is inherently interesting but many of the fundamental questions of movement ecology can be efficiently tested in study systems with high degrees of control. Lakes can be seen as microcosms for studying ecological processes and the use of high-resolution positioning systems to triangulate exact coordinates of fish, along with sensors that relay information about depth, temperature, acceleration, predation, and more, can be used to answer some of movement ecology's most pressing questions. We describe how key questions in animal movement have been approached and how experiments can be designed to gather information about movement processes to answer questions about the physiological, genetic, and environmental drivers of movement using lakes. We submit that whole lake telemetry studies have a key role to play not only in movement ecology but more broadly in biology as key scientific arenas for knowledge advancement. New hardware for tracking aquatic animals and statistical tools for understanding the processes underlying detection data will continue to advance the potential for revealing the paradigms that govern movement and biological phenomena not just within lakes but in other realms spanning lands and oceans.

A random walk model that accounts for space occupation and movements of a large herbivore

Animal movement has been identified as a key feature in understanding animal behavior, distribution and habitat use and foraging strategies among others. Large datasets of invididual locations often remain unused or used only in part due to the lack of practical models that can directly infer the desired features from raw GPS locations and the complexity of existing approaches. Some of them being disputed for their lack of biological justifications in their design. We propose a simple model of individual movement with explicit parameters, based on a two-dimensional biased and correlated random walk with three forces related to advection (correlation), attraction (bias) and immobility of the animal. These forces can be directly estimated using individual data. We demonstrate the approach by using GPS data of 5 red deer with a high frequency sampling. The results show that a simple random walk template can account for the spatial complexity of wild animals. The practical design of the model is also verified for detecting spatial feature abnormalities and for providing estimates of density and abundance of wild animals. Integrating even more additional features of animal movement, such as individuals’ interactions or environmental repellents, could help to better understand the spatial behavior of wild animals.

Temporal Non-stationarity of Path-Selection Movement Models and Connectivity: An Example of African Elephants in Kruger National Park

Effective conservation and land management require robust understanding of how landscape features spatially and temporally affect population distribution, abundance and connectivity. This is especially important for keystone species known to shape ecosystems, such as the African elephant (Loxodonta africana). This work investigates monthly patterns of elephant movement and connectivity in Kruger National Park (KNP; South Africa), and their temporal relationship with landscape features over a 12-month period associated with the occurrence of a severe drought. Based on elephant locations from GPS collars with a short acquisition interval, we explored the monthly patterns of spatial-autocorrelation of elephant movement using Mantel correlograms, and we developed scale-optimized monthly path-selection movement and resistant kernel connectivity models. Our results showed high variability in patterns of autocorrelation in elephant movements across individuals and months, with a preponderance of directional movement, which we believe is related to drought induced range shifts. We also found high non-stationarity of monthly movement and connectivity models; most models exhibited qualitative similarity in the general nature of the predicted ecological relationships, but large quantitative differences in predicted landscape resistance and connectivity across the year. This suggests high variation in space-utilization and temporal shifts of core habitat areas for elephants in KNP. Even during extreme drought, rainfall itself was not a strong driver of elephant movement; elephant movements, instead, were strongly driven by selection for green vegetation and areas near waterholes and small rivers. Our findings highlight a potentially serious problem in using movement models from a particular temporal snapshot to infer general landscape effects on movement. Conservation and management strategies focusing only on certain areas identified by temporarily idiosyncratic models might not be appropriate or efficient as a guide for allocating scarce resources for management or for understanding general ecological relationships.

Individuality counts: A new comprehensive approach to foraging strategies of a tropical marine predator

Foraging strategies are of great ecological interest, as they have a strong impact on the fitness of an individual and can affect its ability to cope with a changing environment. Recent studies on foraging strategies show a higher complexity than previously thought due to intraspecific variability. To reliably identify foraging strategies and describe the different foraging niches they allow individual animals to realize, high-resolution multivariate approaches which consider individual variation are required. Here we dive into the foraging strategies of Galápagos sea lions (Zalophus wollebaeki), a tropical predator confronted with substantial annual variation in sea surface temperature. This affects prey abundance, and El Niño events, expected to become more frequent and severe with climate change, are known to have dramatic effects on sea lions. This study used high-resolution measures of depth, GPS position and acceleration collected from 39 lactating sea lion females to analyze their foraging strategies at an unprecedented level of detail using a novel combination of automated broken stick algorithm, hierarchical cluster analysis and individually fitted multivariate hidden Markov models. We found three distinct foraging strategies (pelagic, benthic, and night divers), which differed in their horizontal, vertical and temporal distribution, most likely corresponding to different prey species, and allowed us to formulate hypotheses with regard to adaptive values under different environmental scenarios. We demonstrate the advantages of our multivariate approach and inclusion of individual variation to reliably gain a deeper understanding of the adaptive value and ecological relevance of foraging strategies of marine predators in dynamic environments.

Uncovering ecological state dynamics with hidden Markov models

Ecological systems can often be characterised by changes among a finite set of underlying states pertaining to individuals, populations, communities or entire ecosystems through time. Owing to the inherent difficulty of empirical field studies, ecological state dynamics operating at any level of this hierarchy can often be unobservable or 'hidden'. Ecologists must therefore often contend with incomplete or indirect observations that are somehow related to these underlying processes. By formally disentangling state and observation processes based on simple yet powerful mathematical properties that can be used to describe many ecological phenomena, hidden Markov models (HMMs) can facilitate inferences about complex system state dynamics that might otherwise be intractable. However, HMMs have only recently begun to gain traction within the broader ecological community. We provide a gentle introduction to HMMs, establish some common terminology, review the immense scope of HMMs for applied ecological research and provide a tutorial on implementation and interpretation. By illustrating how practitioners can use a simple conceptual template to customise HMMs for their specific systems of interest, revealing methodological links between existing applications, and highlighting some practical considerations and limitations of these approaches, our goal is to help establish HMMs as a fundamental inferential tool for ecologists.

Habitat selection patterns are density dependent under the ideal free distribution

Despite being widely used, habitat selection models are rarely reliable and informative when applied across different ecosystems or over time. One possible explanation is that habitat selection is context-dependent due to variation in consumer density and/or resource availability. The goal of this paper is to provide a general theoretical perspective on the contributory mechanisms of consumer and resource density-dependent habitat selection, as well as on our capacity to account for their effects. Towards this goal we revisit the ideal free distribution (IFD), where consumers are assumed to be omniscient, equally competitive and freely moving, and are hence expected to instantaneously distribute themselves across a heterogeneous landscape such that fitness is equalised across the population. Although these assumptions are clearly unrealistic to some degree, the simplicity of the structure in IFD provides a useful theoretical vantage point to help clarify our understanding of more complex spatial processes. Of equal importance, IFD assumptions are compatible with the assumptions underlying common habitat selection models. Here we show how a fitness-maximising space use model, based on IFD, gives rise to resource and consumer density-dependent shifts in consumer distribution, providing a mechanistic explanation for the context-dependent outcomes often reported in habitat selection analysis. Our model suggests that adaptive shifts in consumer distribution patterns would be expected to lead to nonlinear and often non-monotonic patterns of habitat selection. These results indicate that even under the simplest of assumptions about adaptive organismal behaviour, habitat selection strength should critically depend on system-wide characteristics. Clarifying the impact of adaptive behavioural responses may be pivotal in making meaningful ecological inferences about observed patterns of habitat selection and allow reliable transferability of habitat selection predictions across time and space.