Showing papers in "Journal of Animal Ecology in 2020"

Optimizing the use of biologgers for movement ecology research

Abstract: The paradigm-changing opportunities of biologging sensors for ecological research, especially movement ecology, are vast, but the crucial questions of how best to match the most appropriate sensors and sensor combinations to specific biological questions and how to analyse complex biologging data, are mostly ignored. Here, we fill this gap by reviewing how to optimize the use of biologging techniques to answer questions in movement ecology and synthesize this into an Integrated Biologging Framework (IBF). We highlight that multisensor approaches are a new frontier in biologging, while identifying current limitations and avenues for future development in sensor technology. We focus on the importance of efficient data exploration, and more advanced multidimensional visualization methods, combined with appropriate archiving and sharing approaches, to tackle the big data issues presented by biologging. We also discuss the challenges and opportunities in matching the peculiarities of specific sensor data to the statistical models used, highlighting at the same time the large advances which will be required in the latter to properly analyse biologging data. Taking advantage of the biologging revolution will require a large improvement in the theoretical and mathematical foundations of movement ecology, to include the rich set of high-frequency multivariate data, which greatly expand the fundamentally limited and coarse data that could be collected using location-only technology such as GPS. Equally important will be the establishment of multidisciplinary collaborations to catalyse the opportunities offered by current and future biologging technology. If this is achieved, clear potential exists for developing a vastly improved mechanistic understanding of animal movements and their roles in ecological processes and for building realistic predictive models.

Applying the core microbiome to understand host–microbe systems

Abstract: The host-associated core microbiome was originally coined to refer to common groups of microbes or genes that were likely to be particularly important for host biological function. However, the term has evolved to encompass variable definitions across studies, often identifying key microbes with respect to their spatial distribution, temporal stability or ecological influence, as well as their contribution to host function and fitness. A major barrier to reaching a consensus over how to define the core microbiome and its relevance to biological, ecological and evolutionary theory is a lack of precise terminology and associated definitions, as well the persistent association of the core microbiome with host function. Common, temporal and ecological core microbiomes can together generate insights into ecological processes that act independently of host function, while functional and host-adapted cores distinguish between facultative and near-obligate symbionts that differ in their effects on host fitness. This commentary summarizes five broad definitions of the core microbiome that have been applied across the literature, highlighting their strengths and limitations for advancing our understanding of host-microbe systems, noting where they are likely to overlap, and discussing their potential relevance to host function and fitness. No one definition of the core microbiome is likely to capture the range of key microbes across a host population. Applied together, they have the potential to reveal different layers of microbial organization from which we can begin to understand the ecological and evolutionary processes that govern host-microbe interactions.

Accounting for individual-specific variation in habitat-selection studies: Efficient estimation of mixed-effects models using Bayesian or frequentist computation

Abstract: Popular frameworks for studying habitat selection include resource-selection functions (RSFs) and step-selection functions (SSFs), estimated using logistic and conditional logistic regression, respectively. Both frameworks compare environmental covariates associated with locations animals visit with environmental covariates at a set of locations assumed available to the animals. Conceptually, slopes that vary by individual, that is, random coefficient models, could be used to accommodate inter-individual heterogeneity with either approach. While fitting such models for RSFs is possible with standard software for generalized linear mixed-effects models (GLMMs), straightforward and efficient one-step procedures for fitting SSFs with random coefficients are currently lacking. To close this gap, we take advantage of the fact that the conditional logistic regression model (i.e. the SSF) is likelihood-equivalent to a Poisson model with stratum-specific fixed intercepts. By interpreting the intercepts as a random effect with a large (fixed) variance, inference for random-slope models becomes feasible with standard Bayesian techniques, or with frequentist methods that allow one to fix the variance of a random effect. We compare this approach to other commonly applied alternatives, including models without random slopes and mixed conditional regression models fit using a two-step algorithm. Using data from mountain goats (Oreamnos americanus) and Eurasian otters (Lutra lutra), we illustrate that our models lead to valid and feasible inference. In addition, we conduct a simulation study to compare different estimation approaches for SSFs and to demonstrate the importance of including individual-specific slopes when estimating individual- and population-level habitat-selection parameters. By providing coded examples using integrated nested Laplace approximations (INLA) and Template Model Builder (TMB) for Bayesian and frequentist analysis via the R packages R-INLA and glmmTMB, we hope to make efficient estimation of RSFs and SSFs with random effects accessible to anyone in the field. SSFs with individual-specific coefficients are particularly attractive since they can provide insights into movement and habitat-selection processes at fine-spatial and temporal scales, but these models had previously been very challenging to fit.

Estimates for energy expenditure in free-living animals using acceleration proxies: A reappraisal

Abstract: It is fundamentally important for many animal ecologists to quantify the costs of animal activities, although it is not straightforward to do so. The recording of triaxial acceleration by animal-attached devices has been proposed as a way forward for this, with the specific suggestion that dynamic body acceleration (DBA) be used as a proxy for movement-based power. Dynamic body acceleration has now been validated frequently, both in the laboratory and in the field, although the literature still shows that some aspects of DBA theory and practice are misunderstood. Here, we examine the theory behind DBA and employ modelling approaches to assess factors that affect the link between DBA and energy expenditure, from the deployment of the tag, through to the calibration of DBA with energy use in laboratory and field settings. Using data from a range of species and movement modes, we illustrate that vectorial and additive DBA metrics are proportional to each other. Either can be used as a proxy for energy and summed to estimate total energy expended over a given period, or divided by time to give a proxy for movement-related metabolic power. Nonetheless, we highlight how the ability of DBA to predict metabolic rate declines as the contribution of non-movement-related factors, such as heat production, increases. Overall, DBA seems to be a substantive proxy for movement-based power but consideration of other movement-related metrics, such as the static body acceleration and the rate of change of body pitch and roll, may enable researchers to refine movement-based metabolic costs, particularly in animals where movement is not characterized by marked changes in body acceleration.

Navigating through the r packages for movement

Abstract: The advent of miniaturized biologging devices has provided ecologists with unprecedented opportunities to record animal movement across scales, and led to the collection of ever-increasing quantities of tracking data. In parallel, sophisticated tools have been developed to process, visualize and analyse tracking data; however, many of these tools have proliferated in isolation, making it challenging for users to select the most appropriate method for the question in hand. Indeed, within the r software alone, we listed 58 packages created to deal with tracking data or 'tracking packages'. Here, we reviewed and described each tracking package based on a workflow centred around tracking data (i.e. spatio-temporal locations (x, y, t)), broken down into three stages: pre-processing, post-processing and analysis, the latter consisting of data visualization, track description, path reconstruction, behavioural pattern identification, space use characterization, trajectory simulation and others. Supporting documentation is key to render a package accessible for users. Based on a user survey, we reviewed the quality of packages' documentation and identified 11 packages with good or excellent documentation. Links between packages were assessed through a network graph analysis. Although a large group of packages showed some degree of connectivity (either depending on functions or suggesting the use of another tracking package), one third of the packages worked in isolation, reflecting a fragmentation in the r movement-ecology programming community. Finally, we provide recommendations for users when choosing packages, and for developers to maximize the usefulness of their contribution and strengthen the links within the programming community.

Light-level geolocator analyses: A user's guide.

Abstract: Light‐level geolocator tags use ambient light recordings to estimate the whereabouts of an individual over the time it carried the device. Over the past decade, these tags have emerged as an important tool and have been used extensively for tracking animal migrations, most commonly small birds. Analysing geolocator data can be daunting to new and experienced scientists alike. Over the past decades, several methods with fundamental differences in the analytical approach have been developed to cope with the various caveats and the often complicated data. Here, we explain the concepts behind the analyses of geolocator data and provide a practical guide for the common steps encompassing most analyses – annotation of twilights, calibration, estimating and refining locations, and extraction of movement patterns – describing good practices and common pitfalls for each step. We discuss criteria for deciding whether or not geolocators can answer proposed research questions, provide guidance in choosing an appropriate analysis method and introduce key features of the newest open‐source analysis tools. We provide advice for how to interpret and report results, highlighting parameters that should be reported in publications and included in data archiving. Finally, we introduce a comprehensive supplementary online manual that applies the concepts to several datasets, demonstrates the use of open‐source analysis tools with step‐by‐step instructions and code and details our recommendations for interpreting, reporting and archiving.

Macroimmunology: The drivers and consequences of spatial patterns in wildlife immune defence.

Abstract: The prevalence and intensity of parasites in wild hosts varies across space and is a key determinant of infection risk in humans, domestic animals and threatened wildlife. Because the immune system serves as the primary barrier to infection, replication and transmission following exposure, we here consider the environmental drivers of immunity. Spatial variation in parasite pressure, abiotic and biotic conditions, and anthropogenic factors can all shape immunity across spatial scales. Identifying the most important spatial drivers of immunity could help pre-empt infectious disease risks, especially in the context of how large-scale factors such as urbanization affect defence by changing environmental conditions. We provide a synthesis of how to apply macroecological approaches to the study of ecoimmunology (i.e. macroimmunology). We first review spatial factors that could generate spatial variation in defence, highlighting the need for large-scale studies that can differentiate competing environmental predictors of immunity and detailing contexts where this approach might be favoured over small-scale experimental studies. We next conduct a systematic review of the literature to assess the frequency of spatial studies and to classify them according to taxa, immune measures, spatial replication and extent, and statistical methods. We review 210 ecoimmunology studies sampling multiple host populations. We show that whereas spatial approaches are relatively common, spatial replication is generally low and unlikely to provide sufficient environmental variation or power to differentiate competing spatial hypotheses. We also highlight statistical biases in macroimmunology, in that few studies characterize and account for spatial dependence statistically, potentially affecting inferences for the relationships between environmental conditions and immune defence. We use these findings to describe tools from geostatistics and spatial modelling that can improve inference about the associations between environmental and immunological variation. In particular, we emphasize exploratory tools that can guide spatial sampling and highlight the need for greater use of mixed-effects models that account for spatial variability while also allowing researchers to account for both individual- and habitat-level covariates. We finally discuss future research priorities for macroimmunology, including focusing on latitudinal gradients, range expansions and urbanization as being especially amenable to large-scale spatial approaches. Methodologically, we highlight critical opportunities posed by assessing spatial variation in host tolerance, using metagenomics to quantify spatial variation in parasite pressure, coupling large-scale field studies with small-scale field experiments and longitudinal approaches, and applying statistical tools from macroecology and meta-analysis to identify generalizable spatial patterns. Such work will facilitate scaling ecoimmunology from individual- to habitat-level insights about the drivers of immune defence and help predict where environmental change may most alter infectious disease risk.

Non-consumptive predator effects on prey population size: A dearth of evidence.

Abstract: There is a large and growing interest in non-consumptive effects (NCEs) of predators. Diverse and extensive evidence shows that predation risk directly influences prey traits, such as behaviour, morphology and physiology, which in turn, may cause a reduction in prey fitness components (i.e. growth rate, survival and reproduction). An intuitive expectation is that NCEs that reduce prey fitness will extend to alter population growth rate and therefore population size. However, our intensive literature search yielded only 10 studies that examined how predator-induced changes in prey traits translate to changes in prey population size. Further, the scant evidence for risk-induced changes on prey population size have been generated from studies that were performed in very controlled systems (mesocosm and laboratory), which do not have the complexity and feedbacks of natural settings. Thus, although likely that predation risk alone can alter prey population size, there is little direct empirical evidence that demonstrates that it does. There are also clear reasons that risk effects on population size may be much smaller than the responses on phenotype and fitness components that are typically measured, magnifying the need to show, rather than infer, effects on population size. Herein we break down the process of how predation risk influences prey population size into a chain of events (predation risk affects prey traits, which affect prey fitness components and population growth rate, which affect prey population size), and highlight the complexity of each transition. We illustrate how the outcomes of these transitions are not straightforward, and how environmental context strongly dictates the direction and magnitude of effects. Indeed, the high variance in prey responses is reflected in the variance of results reported in the few studies that have empirically quantified risk effects on population size. It is therefore a major challenge to predict population effects given the complexity of how environmental context interacts with predation risk and prey responses. We highlight the critical need to appreciate risk effects at each level in the chain of events, and that changes at one level cannot be assumed to translate into changes in the next because of the interplay between risk, prey responses, and the environment. The gaps in knowledge we illuminate underscore the need for more evidence to substantiate the claim that predation risk effects extend to prey population size. The lacunae we identify should inspire future studies on the impact of predation risk on population-level responses in free-living animals.

Corridors or risk? Movement along, and use of, linear features varies predictably among large mammal predator and prey species.

Abstract: Space-use behaviour reflects trade-offs in meeting ecological needs and can have consequences for individual survival and population demographics. The mechanisms underlying space use can be understood by simultaneously evaluating habitat selection and movement patterns, and fine-resolution locational data are increasing our ability to do so. We use high-resolution location data and an integrated step-selection analysis to evaluate caribou, moose, bear, and wolf habitat selection and movement behaviour in response to anthropogenic habitat modification, though caribou data were limited. Space-use response to anthropogenic linear features (LFs) by predators and prey is hypothesized to increase predator hunting efficiency and is thus believed to be a leading factor in woodland caribou declines in western Canada. We found that all species moved faster while on LFs. Wolves and bears were also attracted towards LFs, whereas prey species avoided them. Predators and prey responded less strongly and consistently to natural features such as streams, rivers and lakeshores. These findings are consistent with the hypothesis that LFs facilitate predator movement and increase hunting efficiency, while prey perceive such features as risky. Understanding the behavioural mechanisms underlying space-use patterns is important in understanding how future land-use may impact predator-prey interactions. Explicitly linking behaviour to fitness and demography will be important to fully understand the implications of management strategies.

Food availability limits avian reproduction in the city: An experimental study on great tits Parus major.

Abstract: 1. The altered ecological and environmental conditions in towns and cities strongly affect demographic traits of urban animal populations, for example avian reproductive success is often reduced. Previous work suggests that this is partly driven by low insect availability during the breeding season, but robust experimental evidence that supports this food limitation hypothesis is not yet available. 2. We tested core predictions of the food limitation hypothesis using a controlled experiment that provided supplementary insect food (nutritionally enhanced mealworms supplied daily to meet 40%–50% of each supplemented brood's food requirements) to great tit nestlings in urban and forest habitats. 3. We measured parental provisioning rates and estimated the amount of supplementary food consumed by control and experimental nestlings, and assessed their body size and survival rates. 4. Provisioning rates were similar across habitats and control and supplemented broods, but supplemented (and not control) broods consumed large quantities of supplementary food. As predicted by the food limitation hypothesis we found that nestlings in (a) urban control broods had smaller body size and nestling survival rates than those in forest control broods; (b) forest supplemented and control broods had similar body size and survival rates; (c) urban supplemented nestlings had larger body size and survival rates than those in urban control broods; and crucially (d) urban supplemented broods had similar body size and survival rates to nestlings in forest control broods. 5. Our results provide rare experimental support for the strong negative effects of food limitation during the nestling rearing period on urban birds' breeding success. Furthermore, the fact that supplementary food almost completely eliminated habitat differences in survival rate and nestling body size suggest that urban stressors other than food shortage contributed relatively little to the reduced avian breeding success. Finally, given the impacts of the amount of supplementary food that we provided and taking clutch size differences into account, our results suggest that urban insect populations in our study system would need to be increased by a factor of at least 2.5 for urban and forest great tits to have similar reproductive success.

Fidelity to foraging sites after long migrations.

Abstract: Patterns of animal movement associated with foraging lie at the heart of many ecological studies and often animals face decisions of staying in an environment they know versus relocating to new sites. The lack of knowledge of new foraging sites means there is risk associated with a decision to relocate (e.g. poor foraging) as well as a potential benefit (e.g. improved foraging). Using a unique long‐term satellite tracking dataset for several sea turtle species, combined with capture–mark–recapture data extending over 50 years, we show how, across species, individuals generally maintain tight fidelity to specific foraging sites after extended (up to almost 10,000 km) migration to and from distant breeding sites as well as across many decades. Migrating individuals often travelled through suitable foraging areas en route to their ‘home’ site and so extended their journeys to maintain foraging site fidelity. We explore the likely mechanistic underpinnings of this trait, which is also seen in some migrating birds, and suggest that individuals will forgo areas of suitable forage encountered en route during migration when they have poor knowledge of the long‐term suitability of those sites, making relocation to those sites risky.

Weak effects of geolocators on small birds: A meta-analysis controlled for phylogeny and publication bias.

Abstract: Currently, the deployment of tracking devices is one of the most frequently used approaches to study movement ecology of birds. Recent miniaturization of light-level geolocators enabled studying small bird species whose migratory patterns were widely unknown. However, geolocators may reduce vital rates in tagged birds and may bias obtained movement data. There is a need for a thorough assessment of the potential tag effects on small birds, as previous meta-analyses did not evaluate unpublished data and impact of multiple life-history traits, focused mainly on large species and the number of published studies tagging small birds has increased substantially. We quantitatively reviewed 549 records extracted from 74 published and 48 unpublished studies on over 7,800 tagged and 17,800 control individuals to examine the effects of geolocator tagging on small bird species (body mass <100 g). We calculated the effect of tagging on apparent survival, condition, phenology and breeding performance and identified the most important predictors of the magnitude of effect sizes. Even though the effects were not statistically significant in phylogenetically controlled models, we found a weak negative impact of geolocators on apparent survival. The negative effect on apparent survival was stronger with increasing relative load of the device and with geolocators attached using elastic harnesses. Moreover, tagging effects were stronger in smaller species. In conclusion, we found a weak effect on apparent survival of tagged birds and managed to pinpoint key aspects and drivers of tagging effects. We provide recommendations for establishing matched control group for proper effect size assessment in future studies and outline various aspects of tagging that need further investigation. Finally, our results encourage further use of geolocators on small bird species but the ethical aspects and scientific benefits should always be considered.

Wind turbines cause functional habitat loss for migratory soaring birds.

Abstract: Wind energy production has expanded to meet climate change mitigation goals, but negative impacts of wind turbines have been reported on wildlife. Soaring birds are among the most affected groups with alarming fatality rates by collision with wind turbines and an escalating occupation of their migratory corridors. These birds have been described as changing their flight trajectories to avoid wind turbines, but this behaviour may lead to functional habitat loss, as suitable soaring areas in the proximity of wind turbines will likely be underused. We modelled the displacement effect of wind turbines on black kites (Milvus migrans) tracked by GPS. We also evaluated the impact of this effect at the scale of the landscape by estimating how much suitable soaring area was lost to wind turbines. We used state-of-the-art tracking devices to monitor the movements of 130 black kites in an area populated by wind turbines, at the migratory bottleneck of the Strait of Gibraltar. Landscape use by birds was mapped from GPS data using dynamic Brownian bridge movement models, and generalized additive mixed modelling was used to estimate the effect of wind turbine proximity on bird use while accounting for orographic and thermal uplift availability. We found that areas up to approximately 674 m away from the turbines were less used than expected given their uplift potential. Within that distance threshold, bird use decreased with the proximity to wind turbines. We estimated that the footprint of wind turbines affected 3%-14% of the areas suitable for soaring in our study area. We present evidence that the impacts of wind energy industry on soaring birds are greater than previously acknowledged. In addition to the commonly reported fatalities, the avoidance of turbines by soaring birds causes habitat losses in their movement corridors. Authorities should recognize this further impact of wind energy production and establish new regulations that protect soaring habitat. We also showed that soaring habitat for birds can be modelled at a fine scale using publicly available data. Such an approach can be used to plan low-impact placement of turbines in new wind energy developments.

Predator responses to fire: A global systematic review and meta-analysis.

Abstract: Knowledge of how disturbances such as fire shape habitat structure and composition, and affect animal interactions, is fundamental to ecology and ecosystem management. Predators also exert strong effects on ecological communities, through top-down regulation of prey and competitors, which can result in trophic cascades. Despite their ubiquity, ecological importance and potential to interact with fire, our general understanding of how predators respond to fire remains poor, hampering ecosystem management. To address this important knowledge gap, we conducted a systematic review and meta-analysis of the effects of fire on terrestrial, vertebrate predators world-wide. We found 160 studies spanning 1978-2018. There were 36 studies with sufficient information for meta-analysis, from which we extracted 96 effect sizes (Hedges' g) for 67 predator species relating to changes in abundance indices, occupancy or resource selection in burned and unburned areas, or before and after fire. Studies spanned geographic locations, taxonomic families and study designs, but most were located in North America and Oceania (59% and 24%, respectively), and largely focussed on felids (24%) and canids (25%). Half (50%) of the studies reported responses to wildfire, and nearly one third concerned prescribed (management) fires. There were no clear, general responses of predators to fire, nor relationships with geographic area, biome or life-history traits (e.g. body mass, hunting strategy and diet). Responses varied considerably between species. Analysis of species for which at least three effect sizes had been reported in the literature revealed that red foxes Vulpes vulpes mostly responded positively to fire (e.g. higher abundance in burned compared to unburned areas) and eastern racers Coluber constrictor negatively, with variances overlapping zero only slightly for both species. Our systematic review and meta-analysis revealed strong variation in predator responses to fire, and major geographic and taxonomic knowledge gaps. Varied responses of predator species to fire likely depend on ecosystem context. Consistent reporting of ongoing monitoring and management experiments is required to improve understanding of the mechanisms driving predator responses to fire, and any broader effects (e.g. trophic interactions). The divergent responses of species in our study suggest that adaptive, context-specific management of predator-fire relationships is required.

An inverse latitudinal gradient in infection probability and phylogenetic diversity for Leucocytozoon blood parasites in New World birds.

Abstract: Geographic variation in environmental conditions as well as host traits that promote parasite transmission may impact infection rates and community assembly of vector-transmitted parasites. Identifying the ecological, environmental and historical determinants of parasite distributions and diversity is therefore necessary to understand disease outbreaks under changing environments. Here, we identified the predictors and contributions of infection probability and phylogenetic diversity of Leucocytozoon (an avian blood parasite) at site and species levels across the New World. To explore spatial patterns in infection probability and lineage diversity for Leucocytozoon parasites, we surveyed 69 bird communities from Alaska to Patagonia. Using phylogenetic Bayesian hierarchical models and high-resolution satellite remote-sensing data, we determined the relative influence of climate, landscape, geography and host phylogeny on regional parasite community assembly. Infection rates and parasite diversity exhibited considerable variation across regions in the Americas. In opposition to the latitudinal gradient hypothesis, both the diversity and prevalence of Leucocytozoon parasites decreased towards the equator. Host relatedness and traits known to promote vector exposure neither predicted infection probability nor parasite diversity. Instead, the probability of a bird being infected with Leucocytozoon increased with increasing vegetation cover (NDVI) and moisture levels (NDWI), whereas the diversity of parasite lineages decreased with increasing NDVI. Infection rates and parasite diversity also tended to be higher in cooler regions and higher latitudes. Whereas temperature partially constrains Leucocytozoon diversity and infection rates, landscape features, such as vegetation cover and water body availability, play a significant role in modulating the probability of a bird being infected. This suggests that, for Leucocytozoon, the barriers to host shifting and parasite host range expansion are jointly determined by environmental filtering and landscape, but not by host phylogeny. Our results show that integrating host traits, host ancestry, bioclimatic data and microhabitat characteristics that are important for vector reproduction are imperative to understand and predict infection prevalence and diversity of vector-transmitted parasites. Unlike other vector-transmitted diseases, our results show that Leucocytozoon diversity and prevalence will likely decrease with warming temperatures.

Personality predicts foraging site fidelity and trip repeatability in a marine predator.

Abstract: Animal populations are often comprised of both foraging specialists and generalists. For instance, some individuals show higher foraging site fidelity (spatial specialization) than others. Such individual differences in degree of specialization can persist over time-scales of months or even years in long-lived animals, but the mechanisms leading to these different individual strategies are not fully understood. There is accumulating evidence that individual variation in foraging behaviour is shaped by animal personality traits, such as boldness. Despite this, the potential for boldness to drive differences in the degree of specialization is unknown. In this study, we used novel object tests to measure boldness in black-legged kittiwakes (Rissa tridactyla) breeding at four colonies in Svalbard and deployed GPS loggers to examine their at-sea foraging behaviour. We estimated the repeatability of foraging trips and used a hidden Markov model to identify locations of foraging sites in order to quantify individual foraging site fidelity. Across the breeding season, bolder birds were more repeatable than shy individuals in the distance and range of their foraging trips, and during the incubation period (but not chick rearing), bolder individuals were more site-faithful. Birds exhibited these differences while showing high spatial similarity in foraging areas, indicating that site selection was not driven by personality-dependent spatial partitioning. We instead suggest that a relationship between boldness and site fidelity may be driven by differences in behavioural flexibility between bold and shy individuals. Together, these results provide a potential mechanism by which widely reported individual differences in foraging specialization may emerge.

rKIN: Kernel-based method for estimating isotopic niche size and overlap

Abstract: The isotopic niche of consumers represents biologically relevant information on resource and habitat use. Several tools have been developed to quantify niche size and overlap. Nonetheless, methods adapted by spatial ecologists to quantify animal home ranges can be modified for use in stable isotope ecology when data are not normally distributed in bivariate space. We offer a tool that draws on existing spatial metrics, such as minimum convex polygon (MCP) and standard ellipse area (SEA), and add novel metrics using kernel utilization density (KUD) estimators to measure isotopic niche size and overlap. We present examples using empirical and simulated data to demonstrate the performance of the package kernel isotopic niches in r (rKIN) under various scenarios. Results of niche size from MCP, SEA and KUD were highly correlated but divergent among datasets. Overall, the KUD method produced the largest niche sizes and was more sensitive to the distribution of the isotopic data. Pairwise estimates of overlap were highly variable, likely because MCP and SEA inherently include or exclude unused areas in the resulting niche estimate. Four bandwidth methods (reference, normal scale, plug-in and biased cross-validation) produced comparable estimates of niche size and overlap at various sample sizes (10-40). Niche size and overlap were consistent across sample sizes >15. Use of rKIN will allow isotope ecologists to quantify niche shifts, expansions or contractions, as well as assess the performance of several estimation methods. The package also can be applied to other data types (e.g. principal component analysis, multi-dimensional scaling) so long as axes and measurement units are identical and can be converted to Cartesian coordinates.

Metabolic costs of altered growth trajectories across life transitions in amphibians

Abstract: Climate change is causing increases in temperature and in the frequency of extreme weather events. Under this scenario, organisms should maintain or develop strategies to cope with environmental fluctuations, such as the capacity to modify growth trajectories. However, altering growth can have negative consequences for organisms' fitness. Here, we investigated the metabolic alterations induced by compensatory growth during the larval development of the common frog (Rana temporaria), quantifying changes in oxidative stress, corticosterone levels and telomere length. We induced compensatory growth responses by exposing frog embryos to cold conditions (i.e. a 'false spring' scenario), which cause a delay in hatching. Once hatched, we reared larvae at two different photoperiods (24:0, representing the natural photoperiod of larvae, and 18:6) to test also for the interactive effects of light on growth responses. Larvae experiencing delayed hatching showed fast compensatory responses and reached larger size at metamorphosis. Larvae shortened their developmental period in response to delayed hatching. Non-permanent light conditions resulted in relaxed growth compared with larvae reared under permanent light conditions, which grew at their natural photoperiod and closer to their maximal rates. Growth responses altered the redox status and corticosterone levels of larvae. These physiological changes were developmental stage-dependent and mainly affected by photoperiod conditions. At catch-up, larvae reared at 18:6 light:dark cycles showed higher antioxidant activities and glucocorticoid secretion. On the contrary, larvae reared at 24:0 developed at higher rates without altering their oxidative status, likely an adaptation to grow under very restricting seasonal conditions at early life. At metamorphosis, compensatory responses induced higher cellular antioxidant activities probably caused by enhanced metabolism. Telomere length remained unaltered by experimental treatments but apparently tended to elongate across larval ontogeny, which would be a first evidence of telomere lengthening across metamorphosis. Under the forecasted increase in extreme climatic events, adjusting growth and developmental rates to the dynamics of environmental fluctuations may be essential for survival, but it can carry metabolic costs and affect later performance. Understanding the implications of such costs will be essential to properly estimate the impact of climate change on wild animals.

High inter- and intraspecific niche overlap among three sympatrically breeding, closely related seabird species: Generalist foraging as an adaptation to a highly variable environment?

Abstract: Ecological niche theory predicts sympatric species to show segregation in their spatio-temporal habitat utilization or diet as a strategy to avoid competition. Similarly, within species individuals may specialize on specific dietary resources or foraging habitats. Such individual specialization seems to occur particularly in environments with predictable resource distribution and limited environmental variability. Still, little is known about how seasonal environmental variability affects segregation of resources within species and between closely related sympatric species. The aim of the study was to investigate the foraging behaviour of three closely related and sympatrically breeding fulmarine petrels (Antarctic petrels Thalassoica antarctica, cape petrels Daption capense and southern fulmars Fulmarus glacialoides) in a seasonally highly variable environment (Prydz Bay, Antarctica) with the aim of assessing inter- and intraspecific overlap in utilized habitat, timing of foraging and diet and to identify foraging habitat preferences. We used GPS loggers with wet/dry sensors to assess spatial habitat utilization over the entire breeding season. Trophic overlap was investigated using stable isotope analysis based on blood, feathers and egg membranes. Foraging locations were identified using wet/dry data recorded by the GPS loggers and expectation-maximization binary clustering. Foraging habitat preferences were modelled using generalized additive models and model cross-validation. During incubation and chick-rearing, the utilization distribution of all three species overlapped significantly and species also overlapped in the timing of foraging during the day-partly during incubation and completely during chick-rearing. Isotopic centroids showed no significant segregation between at least two species for feathers and egg membranes, and among all species during incubation (reflected by blood). Within species, there was no individual specialization in foraging sites or environmental space. Furthermore, no single environmental covariate predicted foraging activity along trip trajectories. Instead, best-explanatory environmental covariates varied within and between individuals even across short temporal scales, reflecting a highly generalist behaviour of birds. Our results may be explained by optimal foraging theory. In the highly productive but spatio-temporally variable Antarctic environment, being a generalist may be key to finding mobile prey-even though this increases the potential for competition within and among sympatric species.

Fear of the dark? Contrasting impacts of humans versus lynx on diel activity of roe deer across Europe.

Abstract: Humans, as super predators, can have strong effects on wildlife behaviour, including profound modifications of diel activity patterns. Subsequent to the return of large carnivores to human‐modified ecosystems, many prey species have adjusted their spatial behaviour to the contrasting landscapes of fear generated by both their natural predators and anthropogenic pressures. The effects of predation risk on temporal shifts in diel activity of prey, however, remain largely unexplored in human‐dominated landscapes. We investigated the influence of the density of lynx Lynx lynx, a nocturnal predator, on the diel activity patterns of their main prey, the roe deer Capreolus capreolus, across a gradient of human disturbance and hunting at the European scale. Based on 11 million activity records from 431 individually GPS‐monitored roe deer in 12 populations within the EURODEER network (http://eurodeer.org), we investigated how lynx predation risk in combination with both lethal and non‐lethal human activities affected the diurnality of deer. We demonstrated marked plasticity in roe deer diel activity patterns in response to spatio‐temporal variations in risk, mostly due to human activities. In particular, roe deer decreased their level of diurnality by a factor of 1.37 when the background level of general human disturbance was high. Hunting exacerbated this effect, as during the hunting season deer switched most of their activity to night‐time and, to a lesser extent, to dawn, although this pattern varied noticeably in relation to lynx density. Indeed, in the presence of lynx, their main natural predator, roe deer were relatively more diurnal. Overall, our results revealed a strong influence of human activities and the presence of lynx on diel shifts in roe deer activity. In the context of the recovery of large carnivores across Europe, we provide important insights about the effects of predators on the behavioural responses of their prey in human‐dominated ecosystems. Modifications in the temporal partitioning of ungulate activity as a response to human activities may facilitate human–wildlife coexistence, but likely also have knock‐on effects for predator–prey interactions, with cascading effects on ecosystem functioning.

Sickness effects on social interactions depend on the type of behaviour and relationship.

Abstract: Infections can change social behaviour in multiple ways, with profound impacts on pathogen transmission. However, these impacts might depend on the type of behaviour, how sociality as a biological trait is defined (e.g. network degree vs. mean edge strength) and the type of social relationship between the interacting individuals. We used the highly social common vampire bat Desmodus rotundus to test how an immune challenge by lipopolysaccharide (LPS) injections affects two different social behaviours and three alternate measures of sociality, and whether the LPS effect differs by kinship relationship. Effects of sickness should be lower for social behaviours that bestow greater benefits to inclusive fitness, such as food sharing. As predicted, immune-challenged bats experienced a greater reduction in allogrooming received than food sharing received. Sickness effects might also depend on how a social interaction is defined (e.g. the number of grooming partners vs. the duration of grooming events). We predicted that sickness would impact both the number and duration of social encounters, but we only detected a decrease in the number of grooming partners. Finally, sickness effects might vary with social relationship type. We predicted that sickness effects should be smaller for interactions among close kin. As expected, the immune challenge had smaller effects on mother-offspring interactions. In conclusion, our results highlight the need to explicitly consider how the effects of sickness on social network structure can differ depending on the 'who, what, and how' of social interactions, because these factors are likely to influence how sickness behaviour alters pathogen transmission.

An ontogenetic perspective on migratory strategy of a long-lived pelagic seabird: Timings and destinations change progressively during maturation.

Abstract: The processes that drive the ontogeny of migratory strategies in long-lived animals with slow maturation remain enigmatic. While some short-lived migrants are known or believed to repeat the same migratory patterns throughout their lives, little is known on the time required for immature long-lived migrants to progressively acquire adult-like migratory behaviours, or which aspects take longer to refine during the maturation process. Here, we studied the ontogeny of long-distance migratory strategies and related patterns of spatial distribution in a long-lived seabird species during the annual cycle. To do so, we deployed light-level geolocators on 4- to 9-year-old immature Cory's shearwaters (Calonectris borealis) and on breeding adults. We revealed that migratory timings and destinations of young shearwaters progressively changed with age. The effect of ageing was remarkably evident on spring migratory performance and phenology. Birds gradually shortened the duration of the non-breeding period by advancing departure date and reducing travelling time, which resulted in a sequential arrival at the colony of the various age contingents. Ageing immatures gradually changed from a more exploratory strategy to a more conservative way of exploiting resources, reducing both their year-round spatial spread across oceanic domains and the total distance travelled. Immatures always performed a trans-equatorial migration to the Southern Hemisphere, contrasting with 17% of the adults which remained in the North Atlantic year-round. Finally, during the breeding season immatures were widely dispersed through the North Atlantic reducing their overlap with breeding adults. Our long-term study provides empirical support to the hypothesis that in long-lived species, the refinement of migratory behaviour and year-round spatial distribution is a progressive process mediated by age and experience, where life stage constraints and competition for resources may also play a role. The emerging pattern suggests that for some avian taxa, the ontogeny of migratory strategy is a prolonged, complex and dynamic process.

Macronutrients modulate survival to infection and immunity in Drosophila.

Abstract: 1. Immunity and nutrition are two essential modulators of individual fitness. However, while the implications of immune function and nutrition on an individual’s lifespan and reproduction are well established, the interplay between feeding behaviour, infection, and immune function, remains poorly understood. Asking how ecological and physiological factors affect immune responses and resistance to infections is a central theme of eco-immunology. 2. In this study, we used the fruit fly, Drosophila melanogaster, to investigate how infection through septic injury modulates nutritional intake, and how macronutrient balance affects survival to infection by the pathogenic Grampositive bacterium Micrococcus luteus. 3. Our results show that infected flies maintain carbohydrate intake, but reduce protein intake, thereby shifting from a protein-to-carbohydrate (P:C) ratio of ~1:4 to ~1:10 relative to non-infected and sham-infected flies. Strikingly, the proportion of flies dying after M. luteus infection was significantly lower when flies were fed a low-P high-C diet, revealing that flies shift their macronutrient intake as means of nutritional self-medication against bacterial infection. 4. These results are likely due to the effects of the macronutrient balance on the regulation of the constitutive expression of innate immune genes, as a low-P high-C diet was linked to an up-regulation in the expression of key antimicrobial peptides. 5. Together, our results reveal the intricate relationship between macronutrient intake and resistance to infection, and integrate the molecular cross-talk between metabolic and immune pathways into the framework of nutritional immunology.

The potential role of the gut microbiota in shaping host energetics and metabolic rate.

Abstract: It is increasingly recognized that symbiotic microbiota (especially those present in the gut) have important influences on the functioning of their host. Here, we review the interplay between this microbial community and the growth, metabolic rate and nutritional energy harvest of the host. We show how recent developments in experimental and analytical methods have allowed much easier characterization of the nature, and increasingly the functioning, of the gut microbiota. Manipulation studies that remove or augment gut microorganisms or transfer them between hosts have allowed unprecedented insights into their impact. Whilst much of the information to date has come from studies of laboratory model organisms, recent studies have used a more diverse range of host species, including those living in natural conditions, revealing their ecological relevance. The gut microbiota can provide the host with dietary nutrients that would be otherwise unobtainable, as well as allow the host flexibility in its capacity to cope with changing environments. The composition of the gut microbial community of a species can vary seasonally or when the host moves between environments (e.g. fresh and sea water in the case of migratory fish). It can also change with host diet choice, metabolic rate (or demands) and life stage. These changes in gut microbial community composition enable the host to live within different environments, adapt to seasonal changes in diet and maintain performance throughout its entire life history, highlighting the ecological relevance of the gut microbiota. Whilst it is evident that gut microbes can underpin host metabolic plasticity, the causal nature of associations between particular microorganisms and host performance is not always clear unless a manipulative approach has been used. Many studies have focussed on a correlative approach by characterizing microbial community composition, but there is now a need for more experimental studies in both wild and laboratory-based environments, to reveal the true role of gut microbiota in influencing the functioning of their hosts, including its capacity to tolerate environmental change. We highlight areas where these would be particularly fruitful in the context of ecological energetics.

Individual variation in age-dependent reproduction: Fast explorers live fast but senesce young?

Abstract: Adaptive integration of life history and behaviour is expected to result in variation in the pace-of-life. Previous work focused on whether 'risky' phenotypes live fast but die young, but reported conflicting support. We posit that individuals exhibiting risky phenotypes may alternatively invest heavily in early-life reproduction but consequently suffer greater reproductive senescence. We used a 7-year longitudinal dataset with >1,200 breeding records of >800 female great tits assayed annually for exploratory behaviour to test whether within-individual age dependency of reproduction varied with exploratory behaviour. We controlled for biasing effects of selective (dis)appearance and within-individual behavioural plasticity. Slower and faster explorers produced moderate-sized clutches when young; faster explorers subsequently showed an increase in clutch size that diminished with age (with moderate support for declines when old), whereas slower explorers produced moderate-sized clutches throughout their lives. There was some evidence that the same pattern characterized annual fledgling success, if so, unpredictable environmental effects diluted personality-related differences in this downstream reproductive trait. Support for age-related selective appearance was apparent, but only when failing to appreciate within-individual plasticity in reproduction and behaviour. Our study identifies within-individual age-dependent reproduction, and reproductive senescence, as key components of life-history strategies that vary between individuals differing in risky behaviour. Future research should thus incorporate age-dependent reproduction in pace-of-life studies.

Habitat selection patterns are density-dependent under the Ideal Free Distribution.

Abstract: 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.

Identifying stationary phases in multivariate time series for highlighting behavioural modes and home range settlements

Abstract: Recent advances in biologging open promising perspectives in the study of animal movements at numerous scales. It is now possible to record time series of animal locations and ancillary data (e.g. activity level derived from on‐board accelerometers) over extended areas and long durations with a high spatial and temporal resolution. Such time series are often piecewise stationary, as the animal may alternate between different stationary phases (i.e. characterized by a specific mean and variance of some key parameter for limited periods). Identifying when these phases start and end is a critical first step to understand the dynamics of the underlying movement processes. We introduce a new segmentation‐clustering method we called segclust2d (available as a r package at cran.r-project.org/package=segclust2d). It can segment bivariate (or more generally multivariate) time series and possibly cluster the various segments obtained, corresponding to different phases assumed to be stationary. This method is easy to use, as it only requires specifying a minimum segment length (to prevent over‐segmentation), based on biological rather than statistical considerations. This method can be applied to bivariate piecewise time series of any nature. We focus here on two types of time series related to animal movement, corresponding to (a) at large scale, series of bivariate coordinates of relocations, to highlight temporary home ranges, and (b) at smaller scale, bivariate series derived from relocations data, such as speed and turning angle, to highlight different behavioural modes such as transit, feeding and resting. Using computer simulations, we show that segclust2d can rival and even outperform previous, more complex methods, which were specifically developed to highlight changes of movement modes or home range shifts (based on hidden Markov and Ornstein–Uhlenbeck modelling), which, contrary to our method, usually require the user to provide relevant initial guesses to be efficient. Furthermore, we demonstrate it on actual examples involving a zebra's small‐scale movements and an elephant's large‐scale movements, to illustrate how various movement modes and home range shifts, respectively, can be identified.

Darker ants dominate the canopy: Testing macroecological hypotheses for patterns in colour along a microclimatic gradient

Abstract: 1. Gradients in cuticle lightness of ectotherms have been demonstrated across latitudes and elevations. Three key hypotheses have been used to explain these macroecological patterns: the thermal melanism hypothesis (TMH), the melanism-desiccation hypothesis (MDH) and the photo-protection hypothesis (PPH). Yet the broad abiotic measures, such as temperature, humidity and UV-B radiation, typically used to detect these ecogeographical patterns, are a poor indication of the microenvironment experienced by small, cursorial ectotherms like ants. 2. We tested whether these macroecological hypotheses explaining cuticle lightness held at habitat and microclimatic level by using a vertical gradient within a tropical rainforest. 3. We sampled 222 ant species in lowland, tropical rainforest across four vertical strata: subterranean, ground, understory and canopy. We recorded cuticle lightness, abundance and estimated body size for each species and calculated an assemblage-weighted mean for cuticle lightness and body size for each vertical stratum. Abiotic variables (air temperature, vapour pressure deficit and UV-B radiation) were recorded for each vertical stratum. 4. We found that cuticle lightness of ant assemblages was vertically stratified: ant assemblages in the canopy and understory were twice as dark as assemblages in ground and subterranean strata. Cuticle lightness was not correlated with body size, and there was no support for the TMH. Rather, we attribute this cline in cuticle lightness to a combination of the MDH and the PPH. 5. Our findings indicate that broad macroecological patterns can be detected at much smaller spatial scales and that microclimatic gradients can shape trait variation, specifically the cuticle lightness of ants. These results suggest that any changes to microclimate that occur due to land-use change or climate warming could drive selection of ants based on cuticle colour, altering assemblage structure and potentially ecosystem functioning.

Urbanization can increase the invasive potential of alien species

Abstract: Alien species often flourish and become invasive in urban ecosystems. How and why invaders succeed in urban systems is an important, yet poorly understood, question. We investigate whether the success of urban invaders is related to changes in species traits that enhance invasive potential. We also explore whether a trophic mechanism helps explain the success of invaders in urban systems. We use the guppy Poecilia reticulata, a globally distributed alien species that has invaded both urban and non-urban systems, as our model. We first characterize the effect of urbanization on streams where guppies are present. We measure guppy invasion success using their population density and size-frequency. Then we assess how traits that are related to the potential of guppies to invade (life history and condition) respond to urbanization. Next, we explore how urbanization affects the availability of food for guppies and their diets. We also test if the presence of other fish species grants biological resistance to invasion by dampening guppy invasive potential. We find that urban streams have high concentrations of ammonium and faecal coliforms, indicating contamination from sewage. On average, guppy populations from urban streams have 26× higher density and larger body sizes than non-urban populations. Urban guppies are in better condition and have on average five more offspring than non-urban guppies. Urbanization increases the availability and consumption of highly nutritious food (chironomid larvae) by guppies. We find a positive relationship between the consumption of chironomids and both fecundity and condition. The presence of other fish species in urban streams often has a negative but small effect on guppy traits and density. Our data suggest a relaxation of trade-offs that shape life-history traits which is related to increased food resources in urban streams. These indicate that urbanization enhances the invasive potential of guppies through a trophic mechanism that simultaneously increases reproduction and somatic investment. Such mechanism is likely widespread because chironomids are often highly abundant in urban systems. Thus, not only guppies but also other invasive species can take advantage of such a resource to invest in traits that enhance invasion success.

Multiple dimensions of dietary diversity in large mammalian herbivores.

Abstract: Theory predicts that trophic specialization (i.e. low dietary diversity) should make consumer populations sensitive to environmental disturbances. Yet diagnosing specialization is complicated both by the difficulty of precisely quantifying diet composition and by definitional ambiguity: what makes a diet 'diverse'? We sought to characterize the relationship between taxonomic dietary diversity (TDD) and phylogenetic dietary diversity (PDD) in a species-rich community of large mammalian herbivores in a semi-arid East African savanna. We hypothesized that TDD and PDD would be positively correlated within and among species, because taxonomically diverse diets are likely to include plants from many lineages. By using DNA metabarcoding to analyse 1,281 faecal samples collected across multiple seasons, we compiled high-resolution diet profiles for 25 sympatric large-herbivore species. For each of these populations, we calculated TDD and PDD with reference to a DNA reference library for local plants. Contrary to our hypothesis, measures of TDD and PDD were either uncorrelated or negatively correlated with each other. Thus, these metrics reflect distinct dimensions of dietary specialization both within and among species. In general, grazers and ruminants exhibited greater TDD, but lower PDD, than did browsers and non-ruminants. We found significant seasonal variation in TDD and/or PDD for all but four species (Grevy's zebra, buffalo, elephant, Grant's gazelle); however, the relationship between TDD and PDD was consistent across seasons for all but one of the 12 best-sampled species (plains zebra). Our results show that taxonomic generalists can be phylogenetic specialists, and vice versa. These two dimensions of dietary diversity suggest contrasting implications for efforts to predict how consumers will respond to climate change and other environmental perturbations. For example, populations with low TDD may be sensitive to phylogenetically 'random' losses of food species, whereas populations with low PDD may be comparatively more sensitive to environmental changes that disadvantage entire plant lineages-and populations with low dietary diversity in both taxonomic and phylogenetic dimensions may be most vulnerable of all.