The effect of the demographic history on the evolution of senescence: A potential new test of the mutation accumulation theory.

The different evolutionary theories of senescence predict different directions for the correlation between the population size and the intensity of senescence. Using simulations, I highlighted how the effect of the population size on the intensity of senescence could be reinforced by the time since populations have been large or small. I devised a mutation-selection model in which the effect of the mutations was age-specific. Several small populations diverged from a same large population at different points in time. At the end of the simulation, the correlation between the time since the populations had been small and the rate of senescence was positive under the mutation accumulation theory and negative under the antagonistic pleiotropy theory. The phenomenon was strong enough to reverse the usually negative relationship between the intensity of senescence and the generation time. These mutually-exclusive predictions could help broaden the taxonomic support for the mutation accumulation theory of senescence, currently mostly supported in humans and lab invertebrates. I briefly mention a few potential applications in real-life systems.

Positive early-late life-history trait correlations in elephant seals.

Correlations between early- and late-life performance are a major prediction of life-history theory. Negative early-late correlations can emerge because biological processes are optimized for early but not late life (e.g., rapid development may accelerate the onset of senescence; "developmental theory of aging") or because allocation to early-life performance comes at a cost in terms of late-life performance (as in the disposable soma theory). But variation in genetic and environmental challenges that each individual has to cope with during early life may also lead to positive early-late life-history trait correlations (the "fixed heterogeneity" or "individual quality" hypothesis). We analyzed individual life-history trajectories of 7,420 known-age female southern elephant seals (Mirounga leonina) monitored over 36 yr to determine how actuarial senescence (a proxy for late-life performance) correlate with age at first reproduction (a proxy for early-life performance). As some breeding events may not be detected in this field study, we used a custom "multievent" hierarchical model to estimate the age at first reproduction and correlate it to other life-history traits. The probability of first reproduction was 0.34 at age 3, with most females breeding for the first time at age 4, and comparatively few at older ages. Females with an early age of first reproduction outperformed delayed breeders in all aspects we considered (survival, rate of senescence, net reproductive output) but one: early breeders appeared to have an onset of actuarial senescence 1 yr earlier compared to late breeders. Genetics and environmental conditions during early life likely explain the positive correlation between early- and late-life performance. Our results provide the first evidence of actuarial senescence in female southern elephant seals.

Distance sampling of duikers in the rainforest: Dealing with transect avoidance.

Bushmeat is a major source of protein and income in tropical regions but is often over-harvested. A better monitoring of bushmeat stocks could help achieve sustainability. We used a combination of simulations and transect survey data collected from blue duikers (Philantomba monticola) in the Lomako wildlife reserve, Democratic Republic of the Congo, to investigate the use of transect-based distance sampling to monitor bushmeat stocks. The comparison of dung piles and direct observations of duikers evidenced that animals avoided both the transects in the absence of observers, and the observers themselves. This type of behavioural response appeared common in a literature survey. It causes a negative bias in the estimates of population densities from the standard distance sampling methodology. This negative bias would lead to over-pessimistic predictions of population viability, especially if the behavioural response is more intense in the locations where the animals are hunted. In turn, this would lead to excessively conservative management recommendations. To correct for the effect of the behavioural response of the animals to either the transects or the observers, we recommend recording both the forward and perpendicular distances to the observers (2D distance sampling), not just the perpendicular distance. We also recommend multiple-observer protocols. As a cautionary note, we also demonstrate a scenario where the intensity of the behavioural response is too high to reliably estimate the abundance of the population. As a perspective, we outline the general principles of a local stakeholder-based program combining distance sampling with less intensive types of ecological indicators to monitor wildlife populations.

The two oxpecker species reveal the role of movement rates and foraging intensity in species coexistence.

The two Buphagus oxpecker species are specialized passerines that forage for ticks and other food particles on the body of ungulates in the African savannahs. One of their intriguing features is their ability to coexist despite sharing the same, specialized diet. Using co-occurrence data (photographs of giraffes with oxpeckers on them) and approximate Bayesian computing, we demonstrate that yellow-billed oxpeckers changed host faster than red-billed oxpeckers and appeared to displace red-billed oxpeckers from preferred giraffe body parts. Conversely, red-billed oxpeckers exhibited a fuller use of each host and displaced yellow-billed oxpeckers from distal giraffe body parts. These findings highlight that the partition of giraffe hosts in two separate niches was only part of the coexistence story in this species pair. More precisely, the oxpeckers shared the resource by exploiting it at different rates. They engaged in different trade-offs between giving-up density, patch discovery rate and competitor displacement ability. They illustrate the importance of the time frame of interactions.

Variation in actuarial senescence does not reflect life span variation across mammals.

The concept of actuarial senescence (defined here as the increase in mortality hazards with age) is often confounded with life span duration, which obscures the relative role of age-dependent and age-independent processes in shaping the variation in life span. We use the opportunity afforded by the Species360 database, a collection of individual life span records in captivity, to analyze age-specific mortality patterns in relation to variation in life span. We report evidence of actuarial senescence across 96 mammal species. We identify the life stage (juvenile, prime-age, or senescent) that contributes the most to the observed variation in life span across species. Actuarial senescence only accounted for 35%-50% of the variance in life span across species, depending on the body mass category. We computed the sensitivity and elasticity of life span to five parameters that represent the three stages of the age-specific mortality curve-namely, the duration of the juvenile stage, the mean juvenile mortality, the prime-age (i.e., minimum) adult mortality, the age at the onset of actuarial senescence, and the rate of actuarial senescence. Next, we computed the between-species variance in these five parameters. Combining the two steps, we computed the relative contribution of each of the five parameters to the variance in life span across species. Variation in life span was increasingly driven by the intensity of actuarial senescence and decreasingly driven by prime-age adult mortality from small to large species because of changes in the elasticity of life span to these parameters, even if all the adult survival parameters consistently exhibited a canalization pattern of weaker variability among long-lived species than among short-lived ones. Our work unambiguously demonstrates that life span cannot be used to measure the strength of actuarial senescence, because a substantial and variable proportion of life span variation across mammals is not related to actuarial senescence metrics.

The time frame of home-range studies: from function to utilization.

As technological and statistical innovations open new avenues in movement ecology, I review the fundamental implications of the time frame of home-range studies, with the aim of associating terminologies consistently with research objectives and methodologies. There is a fundamental distinction between (a) extrapolations of stationary distributions, associated with long time scales and aiming at asymptotic consistency, and (b) period-specific techniques, aiming at specificity but typically sensitive to the sampling design. I then review the difference between function and utilization in home-range studies. Most home-range studies are based on phenomenological descriptions of the time budgets of the study animals, not the function of the visited areas. I highlight emerging trends in automated pattern-recognition techniques for inference about function rather than utilization.

Modified home range kernel density estimators that take environmental interactions into account.

BACKGROUND: Kernel density estimation (KDE) is a major tool in the movement ecologist toolbox that is used to delineate where geo-tracked animals spend their time. Because KDE bandwidth optimizers are sensitive to temporal autocorrelation, statistically-robust alternatives have been advocated, first, data-thinning procedures, and more recently, autocorrelated kernel density estimation (AKDE). These yield asymptotically consistent, but very smoothed distributions, which may feature biologically unrealistic aspects such as spilling beyond impassable borders. METHOD: I introduce a semi-parametric variant of AKDE designed to extrapolate more realistic home range shapes by incorporating movement mechanisms into the bandwidth optimizer and into the base kernels. I implement a first approximative version based on the step selection framework. This method allows accommodating land cover selection, permeability of linear features, and attraction for select landscape features when delineating home ranges. RESULTS: In a plains zebra (Equus quagga), the reluctance to cross a railway, the avoidance of dense woodland, and the preference for grassland when foraging created significant differences between the estimated home range contours by the new and by previous methods. CONCLUSION: There is a tradeoff to find between fully parametric density estimators, which can be very realistic but need to be provided with a good model and adequate environmental data, and non-parametric density estimators, which are more widely applicable and asymptotically consistent, but whose details are bandwidth-limited. The proposed semi-parametric approach attempts to strike this balance, but I outline a few areas of future improvement. I expect the approach to find its use in studies that compare extrapolated resource availability and interpolated resource use, in order to discover the movement mechanisms that we need to improve the extrapolations.

Coping with change in predation risk across space and time through complementary behavioral responses.

BACKGROUND: Our picture of behavioral management of risk by prey remains fragmentary. This partly stems from a lack of studies jointly analyzing different behavioral responses developed by prey, such as habitat use and fine-scale behavior, although they are expected to complement each other. We took advantage of a simple system on the Kerguelen archipelago, made of a prey species, European rabbit Oryctolagus cuniculus, a predator, feral cat Felis catus, and a mosaic of closed and open foraging patches, allowing reliable assessment of spatio-temporal change in predation risk. We investigated the way such a change triggered individual prey decisions on where, when and how to perform routine activities. RESULTS: Rabbit presence and behavior were recorded both day and night in patches with similar foraging characteristics, but contrasted in terms of openness. Cats, individually recognizable, were more active at night and in closed patches, in line with their expected higher hunting success in those conditions. Accordingly, rabbits avoided using closed patches at night and increased their vigilance if they did. Both day and night, rabbits increased their use of closed patches as compared to open patches in windy conditions, thereby probably reducing the thermoregulatory costs expected under such harsh environmental conditions. CONCLUSIONS: Overall, our data map the landscape of fear in this study system and indicate that prey habitat use and vigilance complement each other. Solely focusing on one or the other tactic may lead to erroneous conclusions regarding the way predation risk triggers prey decisions. Finally, future studies should investigate inter-individual variability in the relative use of these different types of complementary behavioral responses to perceived risk, along with the determinants and outcomes of such tactics.

Circadian periodicity in space use by ungulates of temperate regions: How much, when and why?

When they visit and revisit specific areas, animals may reveal what they need from their home range and how they acquire information. The temporal dimension of such movement recursions, that is, periodicity, is however rarely studied, yet potentially bears a species, population or individual-specific signature. A recent method allows estimating the contribution of periodic patterns to the variance in a movement path. We applied it to 709 individuals from five ungulate species, looking for species signatures in the form of seasonal variation in the intensity of circadian patterns. Circadian patterns were commonplace in the movement tracks, but the amount of variance they explained was highly variable among individuals. It increased in intensity during spring and summer, when key resources were spatially segregated, and decreased during winter, when food availability was more uniformly low. Other periodicity-inducing mechanisms supported by our comparison of species- and sex-specific patterns involve young antipredator behaviour, territoriality and behavioural thermoregulation. Model-based continuous-time movement metrics represent a new avenue for researchers interested in finding individual-, population- or species-specific signatures in heterogeneous movement databases featuring various study designs and sampling resolutions. However, we observed large amounts of individual variation, so comparative analyses should ideally use both GPS and animal-borne loggers to augment the discriminatory power and be based on large samples. We briefly outline potential uses of the intensity of circadian patterns as a metric for the study of animal personality and community ecology.

Migrating ospreys use thermal uplift over the open sea.

Most large raptors on migration avoid crossing the sea because of the lack of atmospheric convection over temperate seas. The osprey Pandion haliaetus is an exception among raptors, since it can fly over several hundred kilometres of open water. We equipped five juvenile ospreys with GPS-Accelerometer-Magnetometer loggers. All birds were able to find and use thermal uplift while crossing the Mediterranean Sea, on average 7.5 times per 100 km, and could reach altitudes of 900 m above the sea surface. Their climb rate was 1.6 times slower than over land, and birds kept flapping most of the time while circling in the thermals, indicating that convections cells were weaker than over land. The frequency of thermal soaring was correlated with the difference between the sea surface and air temperature, indicating that atmospheric convection occurred when surface waters were warmer than the overlaying air. These observations help explain the transoceanic cosmopolitan distribution of osprey, and question the widely held assumption that water bodies represent strict barriers for large raptors.

Partitioning prediction uncertainty in climate-dependent population models.

The science of complex systems is increasingly asked to forecast the consequences of climate change. As a result, scientists are now engaged in making predictions about an uncertain future, which entails the efficient communication of this uncertainty. Here we show the benefits of hierarchically decomposing the uncertainty in predicted changes in animal population size into its components due to structural uncertainty in climate scenarios (greenhouse gas emissions and global circulation models), structural uncertainty in the demographic model, climatic stochasticity, environmental stochasticity unexplained by climate-demographic trait relationships, and sampling variance in demographic parameter estimates. We quantify components of uncertainty surrounding the future abundance of a migratory bird, the greater snow goose (Chen caeruslescens atlantica), using a process-based demographic model covering their full annual cycle. Our model predicts a slow population increase but with a large prediction uncertainty. As expected from theoretical variance decomposition rules, the contribution of sampling variance to prediction uncertainty rapidly overcomes that of process variance and dominates. Among the sources of process variance, uncertainty in the climate scenarios contributed less than 3% of the total prediction variance over a 40-year period, much less than environmental stochasticity. Our study exemplifies opportunities to improve the forecasting of complex systems using long-term studies and the challenges inherent to predicting the future of stochastic systems.

Evidence of reduced individual heterogeneity in adult survival of long-lived species.

The canalization hypothesis postulates that the rate at which trait variation generates variation in the average individual fitness in a population determines how buffered traits are against environmental and genetic factors. The ranking of a species on the slow-fast continuum - the covariation among life-history traits describing species-specific life cycles along a gradient going from a long life, slow maturity, and low annual reproductive output, to a short life, fast maturity, and high annual reproductive output - strongly correlates with the relative fitness impact of a given amount of variation in adult survival. Under the canalization hypothesis, long-lived species are thus expected to display less individual heterogeneity in survival at the onset of adulthood, when reproductive values peak, than short-lived species. We tested this life-history prediction by analysing long-term time series of individual-based data in nine species of birds and mammals using capture-recapture models. We found that individual heterogeneity in survival was higher in species with short-generation time (< 3 years) than in species with long generation time (> 4 years). Our findings provide the first piece of empirical evidence for the canalization hypothesis at the individual level from the wild.

Uncovering periodic patterns of space use in animal tracking data with periodograms, including a new algorithm for the Lomb-Scargle periodogram and improved randomization tests.

BACKGROUND: Periodicity in activity level (rest/activity cycles) is ubiquitous in nature, but whether and how these periodicities translate into periodic patterns of space use by animals is much less documented. Here we introduce an analytical protocol based on the Lomb-Scargle periodogram (LSP) to facilitate exploration of animal tracking datasets for periodic patterns. The LSP accommodates missing observations and variation in the sampling intervals of the location time series. RESULTS: We describe a new, fast algorithm to compute the LSP. The gain in speed compared to other R implementations of the LSP makes it tractable to analyze long datasets (>10(6) records). We also give a detailed primer on periodicity analysis, focusing on the specificities of movement data. In particular, we warn against the risk of flawed inference when the sampling schedule creates artefactual periodicities and we introduce a new statistical test of periodicity that accommodates temporally autocorrelated background noise. Applying our LSP-based analytical protocol to tracking data from three species revealed that an ungulate exhibited periodicity in its movement speed but not in its locations, that a central place-foraging seabird tracked moon phase, and that the movements of a range-resident canid included a daily patrolling component that was initially masked by the stochasticity of the movements. CONCLUSION: The new, fast algorithm tailored for movement data analysis and now available in the R-package ctmm makes the LSP a convenient exploratory tool to detect periodic patterns in animal movement data.

Coupled range dynamics of brood parasites and their hosts responding to climate and vegetation changes.

As populations shift their ranges in response to global change, local species assemblages can change, setting the stage for new ecological interactions, community equilibria and evolutionary responses. Here, we focus on the range dynamics of four avian brood parasite species and their hosts in southern Africa, in a context of bush encroachment (increase in woody vegetation density in places previously occupied by savanna-grassland mosaics) favouring some species at the expense of others. We first tested whether hosts and parasites constrained each other's ability to expand or maintain their ranges. Secondly, we investigated whether range shifts represented an opportunity for new host-parasite and parasite-parasite interactions. We used multispecies dynamic occupancy models with interactions, fitted to citizen science data, to estimate the contribution of interspecific interactions to range shifts and to quantify the change in species co-occurrence probability over a 25-year period. Parasites were able to track their hosts' range shifts. We detected no deleterious effect of the parasites' presence on either the local population viability of host species or the hosts' ability to colonize newly suitable areas. In the recently diversified indigobird radiation (Vidua spp.), following bush encroachment, the new assemblages presented more potential opportunities for speciation via host switch, but also more potential for hybridization between extant lineages, also via host switch. Multispecies dynamic occupancy models with interactions brought new insights into the feedbacks between range shifts, biotic interactions and local demography: brood parasitism had little detected impact on extinction or colonization processes, but inversely the latter processes affected biotic interactions via the modification of co-occurrence patterns.

Departures from the Energy-Biodiversity Relationship in South African Passerines: Are the Legacies of Past Climates Mediated by Behavioral Constraints on Dispersal?

Legacies of paleoclimates in contemporary biodiversity patterns have mostly been investigated with global datasets, or with weakly dispersive organisms, and as a consequence been interpreted in terms of geographical or physical constraints. If paleoclimatic legacies also occurred at the regional scale in the distributions of vagile organisms within biomes, they would rather suggest behavioral constraints on dispersal, i.e., philopatric syndromes. We examined 1) the residuals of the regression between contemporary energy and passerine species richness in South African biomes and 2) phylogenetic dispersion of passerine assemblages, using occupancy models and quarter-degree resolution citizen science data. We found a northeast to southwest gradient within mesic biomes congruent with the location of Quaternary mesic refugia, overall suggesting that as distance from refugia increased, more clades were lacking from local assemblages. A similar but weaker pattern was detected in the arid Karoo Biomes. In mobile organisms such as birds, behavioral constraints on dispersal appear strong enough to influence species distributions thousands of years after historical range contractions.

Twenty-five years of change in southern African passerine diversity: nonclimatic factors of change.

We analysed more than 25 years of change in passerine bird distribution in South Africa, Swaziland and Lesotho, to show that species distributions can be influenced by processes that are at least in part independent of the local strength and direction of climate change: land use and ecological succession. We used occupancy models that separate species' detection from species' occupancy probability, fitted to citizen science data from both phases of the Southern African Bird Atlas Project (1987-1996 and 2007-2013). Temporal trends in species' occupancy probability were interpreted in terms of local extinction/colonization, and temporal trends in detection probability were interpreted in terms of change in abundance. We found for the first time at this scale that, as predicted in the context of bush encroachment, closed-savannah specialists increased where open-savannah specialists decreased. In addition, the trend in the abundance of species a priori thought to be favoured by agricultural conversion was negatively correlated with human population density, which is in line with hypotheses explaining the decline in farmland birds in the Northern Hemisphere. In addition to climate, vegetation cover and the intensity and time since agricultural conversion constitute important predictors of biodiversity changes in the region. Their inclusion will improve the reliability of predictive models of species distribution.

Satellite tagging and biopsy sampling of killer whales at subantarctic Marion Island: effectiveness, immediate reactions and long-term responses.

Remote tissue biopsy sampling and satellite tagging are becoming widely used in large marine vertebrate studies because they allow the collection of a diverse suite of otherwise difficult-to-obtain data which are critical in understanding the ecology of these species and to their conservation and management. Researchers must carefully consider their methods not only from an animal welfare perspective, but also to ensure the scientific rigour and validity of their results. We report methods for shore-based, remote biopsy sampling and satellite tagging of killer whales Orcinus orca at Subantarctic Marion Island. The performance of these methods is critically assessed using 1) the attachment duration of low-impact minimally percutaneous satellite tags; 2) the immediate behavioural reactions of animals to biopsy sampling and satellite tagging; 3) the effect of researcher experience on biopsy sampling and satellite tagging; and 4) the mid- (1 month) and long- (24 month) term behavioural consequences. To study mid- and long-term behavioural changes we used multievent capture-recapture models that accommodate imperfect detection and individual heterogeneity. We made 72 biopsy sampling attempts (resulting in 32 tissue samples) and 37 satellite tagging attempts (deploying 19 tags). Biopsy sampling success rates were low (43%), but tagging rates were high with improved tag designs (86%). The improved tags remained attached for 26±14 days (mean ± SD). Individuals most often showed no reaction when attempts missed (66%) and a slight reaction-defined as a slight flinch, slight shake, short acceleration, or immediate dive-when hit (54%). Severe immediate reactions were never observed. Hit or miss and age-sex class were important predictors of the reaction, but the method (tag or biopsy) was unimportant. Multievent trap-dependence modelling revealed considerable variation in individual sighting patterns; however, there were no significant mid- or long-term changes following biopsy sampling or tagging.

Intra-guild interactions and projected impact of climate and land use changes on North American pochard ducks.

The co-occurrence of functionally similar species is very common in nature, and is often put forward as a basis for ecosystem resilience to disturbance. At the same time, competition between similar species is also considered a strong driver of community composition. However, environmental stochasticity can alter this prediction, either because competitive abilities depend on time-varying factors or because covariance in species' responses to environmental conditions masks the effect of competition. Interactions other than competition can also influence community dynamics but have received less attention. We used a simplified community of two sympatric duck species (redhead Aythya americana and canvasback A. valisineria) and a previously published analysis of 50 years of demographic data to parameterize a stochastic, density-dependent, stage-structured model. These ducks interact via nest parasitism (mostly of canvasback by redhead) in addition to competition for food resources, with consequences at the demographic level; these interactions are modulated by habitat availability (number of ponds in the study landscape). We found that if habitat availability decreased there was a high risk of quasi-extinction, and redheads, although initially able to maintain their numerical dominance, quickly became the least abundant species because they perform worse during droughts. If habitat availability increased, we found that the initially more rare canvasback would increase in relative abundance, albeit slowly. We interpret this as a shift from a community influenced by nest parasitism (which is detrimental to canvasback) to a community mostly driven by species-specific dynamics due to relaxation of resource limitation.

Compensation and additivity of anthropogenic mortality: life-history effects and review of methods.

Demographic compensation, the increase in average individual performance following a perturbation that reduces population size, and, its opposite, demographic overadditivity (or superadditivity) are central processes in both population ecology and wildlife management. A continuum of population responses to changes in cause-specific mortality exists, of which additivity and complete compensation constitute particular points. The position of a population on that continuum influences its ability to sustain exploitation and predation. Here I describe a method for quantifying where a population is on the continuum. Based on variance-covariance formulae, I describe a simple metric for the rate of compensation-additivity. I synthesize the results from 10 wildlife capture-recapture monitoring programmes from the literature and online databases, reviewing current statistical methods and the treatment of common sources of bias. These results are used to test hypotheses regarding the effects of life-history strategy, population density, average cause-specific mortality and age class on the rate of compensation-additivity. This comparative analysis highlights that long-lived species compensate less than short-lived species and that populations below their carrying capacity compensate less than those above.

Integrated modeling of communities: parasitism, competition, and demographic synchrony in sympatric ducks.

Functionally similar species often co-occur within an ecosystem, and they can compete for or facilitate each other's access to resources. The coupled dynamics of such species play an important role in shaping biodiversity and an ecosystem's resilience to perturbations. Here we study two congeneric North American ducks: Redhead Aythya americana and Canvasback A. vaselineria. Both are largely sympatric during the breeding season, and in addition to competition, facultative parasitic egg-laying can lead to interspecific density dependence. Using multi-population integrated models, we combined capture-recovery data, population surveys, and age ratio data in order to simultaneously estimate the mechanistic drivers of fecundity, survival, and population dynamics for both species. Canvasback numbers positively affected Redhead fecundity, whereas Redhead numbers negatively affected Canvasback fecundity, as expected due to parasitism. This interaction was modulated by wetland habitat availability in a way that matched the observation that Redhead hens parasitize Canvasback nests under all conditions but exhibit typical nesting behavior more frequently during years with numerous ponds. Once these effects of density and habitat were statistically controlled for, we found high levels of interspecific synchrony in both fecundity and survival (respectively, 75% and 49% of remaining variation). Thus, both neutral and non-neutral mechanisms affected the dynamics of these functionally similar species. In this and other systems, our method can be used to test hypotheses about species coexistence and to gain insights into the demographic drivers of community dynamics.