Emmanuelle Cam

Individual Covariation in Life‐History Traits: Seeing the Trees Despite the Forest

We investigated the influence of age on survival and breeding rates in a long‐lived species Rissa tridactyla using models with individual random effects permitting variation and covariation in fitness components among individuals. Differences in survival or breeding probabilities among individuals are substantial, and there was positive covariation between survival and breeding probability; birds that were more likely to survive were also more likely to breed, given that they survived. The pattern of age‐related variation in these rates detected at the individual level differed from that observed at the population level. Our results provided confirmation of what has been suggested by other investigators: within‐cohort phenotypic selection can mask senescence. Although this phenomenon has been extensively studied in humans and captive animals, conclusive evidence of the discrepancy between population‐level and individual‐level patterns of age‐related variation in life‐history traits is extremely rare in wild animal populations. Evolutionary studies of the influence of age on life‐history traits should use approaches differentiating population level from the genuine influence of age: only the latter is relevant to theories of life‐history evolution. The development of models permitting access to individual variation in fitness is a promising advance for the study of senescence and evolutionary processes.

Of bugs and birds: Markov Chain Monte Carlo for hierarchical modeling in wildlife research

Markov chain Monte Carlo (MCMC) is a statistical innovation that allows researchers to fit far more com- plex models to data than is feasible using conventional methods. Despite its widespread use in a variety of scien- tific fields, MCMC appears to be underutilized in wildlife applications. This may be due to a misconception that MCMC requires the adoption of a subjective Bayesian analysis, or perhaps simply to its lack of familiarity among wildlife researchers. We introduce the basic ideas of MCMC and software BUGS (Bayesian inference using Gibbs sampling), stressing that a simple and satisfactory intuition for MCMC does not require extraordinary mathemat- ical sophistication. We illustrate the use of MCMC with an analysis of the association between latent factors gov- erning individual heterogeneity in breeding and survival rates of kittiwakes (Rissa tridactyla). We conclude with a discussion of the importance of individual heterogeneity for understanding population dynamics and designing management plans.

RELATIVE SPECIES RICHNESS AND COMMUNITY COMPLETENESS: BIRDS AND URBANIZATION IN THE MID‐ATLANTIC STATES

The idea that local factors govern local richness has been dominant for years, but recent theoretical and empirical studies have stressed the influence of regional factors on local richness. Fewer species at a site could reflect not only the influence of local factors, but also a smaller regional pool. The possible dependency of local richness on the regional pool should be taken into account when addressing the influence of local factors on local richness. It is possible to account for this potential dependency by comparing relative species richness among sites, rather than species richness per se. We consider estimation of a metric permitting assessment of relative species richness in a typical situation in which not all species are detected during sampling sessions. In this situation, estimates of absolute or relative species richness need to account for variation in species detection probability if they are to be unbiased. We present a method to estimate relative species richness based on capture–recapture models. This approach involves definition of a species list from regional data, and estimation of the number of species in that list that are present at a site–year of interest. We use this approach to address the influence of urbanization on relative richness of avian communities in the Mid-Atlantic region of the United States. There is a negative relationship between relative richness and landscape variables describing the level of urban development. We believe that this metric should prove very useful for conservation and management purposes because it is based on an estimator of species richness that both accounts for potential variation in species detection probability and allows flexibility in the specification of a “reference community.” This metric can be used to assess ecological integrity, the richness of the community of interest relative to that of the “original” community, or to assess change since some previous time in a community.

Influence of food availability on demography and local population dynamics in a long-lived seabird.

Few studies have addressed the effects of food availability as a proximate factor affecting local adult survival in long–lived organisms and their consequences at local population dynamics. We used capture–recapture analysis of resightings of 10 birth cohorts of ringed Audouins gulls, Larus audouinii, to estimate adult survival and dispersal (both emigration and immigration). For the first time, permanent emigration (the transient effect in capture–recapture analysis) was modelled for the whole population and not only for the newly marked birds. Gulls exploit to a large extent fishes discarded from trawlers, and a trawling moratorium established since 1991 has decreased food supply for the colony. This was used as a natural experiment of food availability to assess its effects on adult survival and emigration. These and other demographic parameters were used in a projection modelling to assess the probabilities of extinction of the colony under two scenarios of lower and higher food availability. Food availability (together with the age of individuals) influenced emigration probabilities, but not adult survival, which was estimated at 0.91 (s.e. = 0.02). When food was in shorter supply during the chick–rearing period, emigration was very high (ca. 65%) for younger breeders, although this rate decreased sharply with age. Probabilities of extinction were very high when food availability was low, and when environmental stochasticity was introduced, and only stochastic immigration from the outside seemed to prevent extinction. The results highlight the importance of dispersal processes in the population dynamics of long–lived organisms.

Disentangling sampling and ecological explanations underlying species-area relationships

We used a probabilistic approach to address the influence of sampling ar- tifacts on the form of species-area relationships (SARs). We developed a model in which the increase in observed species richness is a function of sampling effort exclusively. We assumed that effort depends on area sampled, and we generated species-area curves under that model. These curves can be realistic looking. We then generated SARs from avian data, comparing SARs based on counts with those based on richness estimates. We used an approach to estimation of species richness that accounts for species detection probability and, hence, for variation in sampling effort. The slopes of SARs based on counts are steeper than those of curves based on estimates of richness, indicating that the former partly reflect failure to account for species detection probability. SARs based on estimates reflect eco- logical processes exclusively, not sampling processes. This approach permits investigation of ecologically relevant hypotheses. The slope of SARs is not influenced by the slope of the relationship between habitat diversity and area. In situations in which not all of the species are detected during sampling sessions, approaches to estimation of species richness integrating species detection probability should be used to investigate the rate of increase in species richness with area.

The Risk of Flawed Inference in Evolutionary Studies When Detectability Is Less than One

Addressing evolutionary questions in the wild remains a challenge. It is best done by monitoring organisms from birth to death, which is very difficult in part because individuals may or may not be resighted or recaptured. Although the issue of uncertain detection has long been acknowledged in ecology and conservation biology, in evolutionary studies of wild populations it is often assumed that detectability is perfect. We argue that this assumption may lead to flawed inference. We demonstrate that the form of natural selection acting on body mass of sociable weavers is altered and that the rate of senescence of roe deer is underestimated when not accounting for a value of detectability that is less than one. Because mark‐recapture models provide an explicit way to integrate and reliably model the detection process, we strongly recommend their use to address questions in evolutionary biology.

Hierarchical modeling of an invasive spread: the Eurasian Collared-Dove Streptopelia decaocto in the United States

Invasive species are regularly claimed as the second threat to biodiversity. To apply a relevant response to the potential consequences associated with invasions (e.g., emphasize management efforts to prevent new colonization or to eradicate the species in places where it has already settled), it is essential to understand invasion mechanisms and dynamics. Quantifying and understanding what influences rates of spatial spread is a key research area for invasion theory. In this paper, we develop a model to account for occupancy dynamics of an invasive species. Our model extends existing models to accommodate several elements of invasive processes; we chose the framework of hierarchical modeling to assess site occupancy status during an invasion. First, we explicitly accounted for spatial structure and how distance among sites and position relative to one another affect the invasion spread. In particular, we accounted for the possibility of directional propagation and provided a way of estimating the direction of this possible spread. Second, we considered the influence of local density on site occupancy. Third, we decided to split the colonization process into two subprocesses, initial colonization and recolonization, which may be ground-breaking because these subprocesses may exhibit different relationships with environmental variations (such as density variation) or colonization history (e.g., initial colonization might facilitate further colonization events). Finally, our model incorporates imperfection in detection, which might be a source of substantial bias in estimating population parameters. We focused on the case of the Eurasian Collared-Dove (Streptopelia decaocto) and its invasion of the United States since its introduction in the early 1980s, using data from the North American BBS (Breeding Bird Survey). The Eurasian Collared-Dove is one of the most successful invasive species, at least among terrestrial vertebrates. Our model provided estimation of the spread direction consistent with empirical observations. Site persistence probability exhibits a quadratic response to density. We also succeeded at detecting differences in the relationship between density and initial colonization vs. recolonization probabilities. We provide a map of sites that may be colonized in the future as an example of possible practical application of our work.

Test for age-specificity in survival of the common tern

Much effort in life-history theory has been addressed to the dependence of life-history traits on age, especially the phenomenon of senescence and its evolution. Although senescent declines in survival are well documented in humans and in domestic and laboratory animals, evidence for their occurrence and importance in wild animal species remains limited and equivocal. Several recent papers have suggested that methodological issues may contribute to this problem, and have encouraged investigators to improve sampling designs and to analyse their data using recently developed approaches to modelling of capture-mark-recapture data. Here we report on a three-year, two-site, mark-recapture study of known-aged common terns (Sterna hirundo) in the north-eastern USA. The study was nested within a long-term ecological study in which large numbers of chicks had been banded in each year for > 25 years. We used a range of models to test the hypothesis of an influence of age on survival probability. We also tested for a possible influence of sex on survival. The cross-sectional design of the study (one years parameter estimates) avoided the possible confounding of effects of age and time. The study was conducted at a time when one of the study sites was being colonized and numbers were increasing rapidly. We detected two-way movements between the sites and estimated movement probabilities in the year for which they could be modelled. We also obtained limited data on emigration from our study area to more distant sites. We found no evidence that survival depended on either sex or age, except that survival was lower among the youngest birds (ages 2-3 years). Despite the large number of birds included in the study (1599 known-aged birds, 2367 total), confidence limits on estimates of survival probability were wide, especially for the oldest age-classes, so that a slight decline in survival late in life could not have been detected. In addition, the cross-sectional design of this study meant that a decline in survival probability within individuals (actuarial senescence) could have been masked by heterogeneity in survival probability among individuals (mortality selection). This emphasizes the need for the development of modelling tools permitting separation of these two phenomena, valid under field conditions in which the recapture probabilities are less than one.

Model-based estimation of individual fitness

Fitness is the currency of natural selection, a measure of the propagation rate of genotypes into future generations. Its various definitions have the common feature that they are functions of survival and fertility rates. At the individual level, the operative level for natural selection, these rates must be understood as latent features, genetically determined propensities existing at birth. This conception of rates requires that individual fitness be defined and estimated by consideration of the individual in a modelled relation to a group of similar individuals; the only alternative is to consider a sample of size one, unless a clone of identical individuals is available. We present hierarchical models describing individual heterogeneity in survival and fertility rates and allowing for associations between these rates at the individual level. We apply these models to an analysis of life histories of Kittiwakes ( Rissa tridactyla ) observed at several colonies on the Brittany coast of France. We compare Bayesian estimation of the population distribution of individual fitness with estimation based on treating individual life histories in isolation, as samples of size one (e.g. McGraw & Caswell, 1996).

OpinionArchiving Primary Data: Solutions for Long-Term Studies

The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.