Social copying drives a tipping point for nonlinear population collapse.

Sudden changes in populations are ubiquitous in ecological systems, especially under perturbations. The agents of global change may increase the frequency and severity of anthropogenic perturbations, but complex populations' responses hamper our understanding of their dynamics and resilience. Furthermore, the long-term environmental and demographic data required to study those sudden changes are rare. Fitting dynamical models with an artificial intelligence algorithm to population fluctuations over 40 y in a social bird reveals that feedback in dispersal after a cumulative perturbation drives a population collapse. The collapse is well described by a nonlinear function mimicking social copying, whereby dispersal made by a few individuals induces others to leave the patch in a behavioral cascade for decision-making to disperse. Once a threshold for deterioration of the quality of the patch is crossed, there is a tipping point for a social response of runaway dispersal corresponding to social copying feedback. Finally, dispersal decreases at low population densities, which is likely due to the unwillingness of the more philopatric individuals to disperse. In providing the evidence of copying for the emergence of feedback in dispersal in a social organism, our results suggest a broader impact of self-organized collective dispersal in complex population dynamics. This has implications for the theoretical study of population and metapopulation nonlinear dynamics, including population extinction, and managing of endangered and harvested populations of social animals subjected to behavioral feedback loops.

Differential adult survival at close seabird colonies: The importance of spatial foraging segregation and bycatch risk during the breeding season.

Marine megafauna, including seabirds, are critically affected by fisheries bycatch. However, bycatch risk may differ on temporal and spatial scales due to the uneven distribution and effort of fleets operating different fishing gear, and to focal species distribution and foraging behavior. Scopoli's shearwater Calonectris diomedea is a long-lived seabird that experiences high bycatch rates in longline fisheries and strong population-level impacts due to this type of anthropogenic mortality. Analyzing a long-term dataset on individual monitoring, we compared adult survival (by means of multi-event capture-recapture models) among three close predator-free Mediterranean colonies of the species. Unexpectedly for a long-lived organism, adult survival varied among colonies. We explored potential causes of this differential survival by (1) measuring egg volume as a proxy of food availability and parental condition; (2) building a specific longline bycatch risk map for the species; and (3) assessing the distribution patterns of breeding birds from the three study colonies via GPS tracking. Egg volume was very similar between colonies over time, suggesting that environmental variability related to habitat foraging suitability was not the main cause of differential survival. On the other hand, differences in foraging movements among individuals from the three colonies expose them to differential mortality risk, which likely influenced the observed differences in adult survival. The overlap of information obtained by the generation of specific bycatch risk maps, the quantification of population demographic parameters, and the foraging spatial analysis should inform managers about differential sensitivity to the anthropogenic impact at mesoscale level and guide decisions depending on the spatial configuration of local populations. The approach would apply and should be considered in any species where foraging distribution is colony-specific and mortality risk varies spatially.

Varying demographic impacts of different fisheries on three Mediterranean seabird species.

Fisheries have an enormous economic importance, but reconciling their socio-economic features with the conservation and sustainability of marine ecosystems presents major challenges. Bycatch mortality from fisheries is clearly among the most serious global threats for marine ecosystems, affecting a wide range of top predators. Recent estimates report ca. 200,000 seabirds killed annually by bycatch in European waters. However, there is an urgent need to rigorously estimate actual mortality rates and quantify effects of bycatch on populations. The Mediterranean Sea is one of the most impacted regions. Here, we estimate for the first time both bycatch mortality rates and their population-level effects on three endemic and vulnerable Mediterranean taxa: Scopoli's shearwater, Mediterranean shag, and Audouin's gull, that die in different types of fishing gears: longlines, gillnets and sport trolling, respectively. We use multi-event capture-recapture modelling to estimate crucial demographic parameters, including the probabilities of dying in different fishing gears. We then build stochastic demography models to forecast the viability of the populations under different management scenarios. Longline bycatch was particularly severe for adults of Scopoli's shearwaters and Audouin's gulls (ca. 28% and 23% of total mortality, respectively) and also for immature gulls (ca. 90% of mortality). Gillnets had a lower impact, but were still responsible for ca. 9% of juvenile mortality on shags, whereas sport trolling only slightly influenced total mortality in gulls. Bycatch mortality has high population-level impacts in all three species, with shearwaters having the highest extinction risk under current mortality rates. Different life-history traits and compensatory demographic mechanisms between the three species are probably influencing the different bycatch impact: for shearwaters, urgent conservation actions are required to ensure the viability of their populations. Results will be very useful for guiding future seabird conservation policies and moving towards an ecosystem-based approach to sustainable fisheries management.

Climate-driven vital rates do not always mean climate-driven population.

Current climatic changes have increased the need to forecast population responses to climate variability. A common approach to address this question is through models that project current population state using the functional relationship between demographic rates and climatic variables. We argue that this approach can lead to erroneous conclusions when interpopulation dispersal is not considered. We found that immigration can release the population from climate-driven trajectories even when local vital rates are climate dependent. We illustrated this using individual-based data on a trans-equatorial migratory seabird, the Scopoli's shearwater Calonectris diomedea, in which the variation of vital rates has been associated with large-scale climatic indices. We compared the population annual growth rate λi , estimated using local climate-driven parameters with ρi , a population growth rate directly estimated from individual information and that accounts for immigration. While λi varied as a function of climatic variables, reflecting the climate-dependent parameters, ρi did not, indicating that dispersal decouples the relationship between population growth and climate variables from that between climatic variables and vital rates. Our results suggest caution when assessing demographic effects of climatic variability especially in open populations for very mobile organisms such as fish, marine mammals, bats, or birds. When a population model cannot be validated or it is not detailed enough, ignoring immigration might lead to misleading climate-driven projections.

Evaluating mortality rates with a novel integrated framework for nonmonogamous species.

The conservation of wildlife requires management based on quantitative evidence, and especially for large carnivores, unraveling cause-specific mortalities and understanding their impact on population dynamics is crucial. Acquiring this knowledge is challenging because it is difficult to obtain robust long-term data sets on endangered populations and, usually, data are collected through diverse sampling strategies. Integrated population models (IPMs) offer a way to integrate data generated through different processes. However, IPMs are female-based models that cannot account for mate availability, and this feature limits their applicability to monogamous species only. We extended classical IPMs to a two-sex framework that allows investigation of population dynamics and quantification of cause-specific mortality rates in nonmonogamous species. We illustrated our approach by simultaneously modeling different types of data from a reintroduced, unhunted brown bear (Ursus arctos) population living in an area with a dense human population. In a population mainly driven by adult survival, we estimated that on average 11% of cubs and 61% of adults died from human-related causes. Although the population is currently not at risk, adult survival and thus population dynamics are driven by anthropogenic mortality. Given the recent increase of human-bear conflicts in the area, removal of individuals for management purposes and through poaching may increase, reversing the positive population growth rate. Our approach can be generalized to other species affected by cause-specific mortality and will be useful to inform conservation decisions for other nonmonogamous species, such as most large carnivores, for which data are scarce and diverse and thus data integration is highly desirable.

Climate change overruns resilience conferred by temperature-dependent sex determination in sea turtles and threatens their survival.

Temperature-dependent sex determination (TSD) is the predominant form of environmental sex determination (ESD) in reptiles, but the adaptive significance of TSD in this group remains unclear. Additionally, the viability of species with TSD may be compromised as climate gets warmer. We simulated population responses in a turtle with TSD to increasing nest temperatures and compared the results to those of a virtual population with genotypic sex determination (GSD) and fixed sex ratios. Then, we assessed the effectiveness of TSD as a mechanism to maintain populations under climate change scenarios. TSD populations were more resilient to increased nest temperatures and mitigated the negative effects of high temperatures by increasing production of female offspring and therefore, future fecundity. That buffered the negative effect of temperature on the population growth. TSD provides an evolutionary advantage to sea turtles. However, this mechanism was only effective over a range of temperatures and will become inefficient as temperatures rise to levels projected by current climate change models. Projected global warming threatens survival of sea turtles, and the IPCC high gas concentration scenario may result in extirpation of the studied population in 50 years.

Neighbouring populations, opposite dynamics: influence of body size and environmental variation on the demography of stream-resident brown trout (Salmo trutta).

In organisms such as fish, where body size is considered an important state variable for the study of their population dynamics, size-specific growth and survival rates can be influenced by local variation in both biotic and abiotic factors, but few studies have evaluated the complex relationships between environmental variability and size-dependent processes. We analysed a 6-year capture-recapture dataset of brown trout (Salmo trutta) collected at 3 neighbouring but heterogeneous mountain streams in northern Spain with the aim of investigating the factors shaping the dynamics of local populations. The influence of body size and water temperature on survival and individual growth was assessed under a multi-state modelling framework, an extension of classical capture-recapture models that considers the state (i.e. body size) of the individual in each capture occasion and allows us to obtain state-specific demographic rates and link them to continuous environmental variables. Individual survival and growth patterns varied over space and time, and evidence of size-dependent survival was found in all but the smallest stream. At this stream, the probability of reaching larger sizes was lower compared to the other wider and deeper streams. Water temperature variables performed better in the modelling of the highest-altitude population, explaining over a 99 % of the variability in maturation transitions and survival of large fish. The relationships between body size, temperature and fitness components found in this study highlight the utility of multi-state approaches to investigate small-scale demographic processes in heterogeneous environments, and to provide reliable ecological knowledge for management purposes.

From recruitment to senescence: food shapes the age-dependent pattern of breeding performance in a long-lived bird.

We used a long-term data set (26 years) from Audouin's Gull (Larus audouinii), a long-lived seabird, to address the relationship between the age-dependent pattern of reproductive performance and environmental conditions during breeding. Although theoretical models predict that the youngest and oldest breeders (due to inexperience and senescence, respectively) will perform less well than intermediate age classes, few empirical data exist regarding how this expected pattern varies with food availability. To assess the influence of age and food availability (corrected by population size of the main consumers to take into account density dependence) on a number of breeding parameters (laying dates, egg volume, clutch size, and hatching success), we modeled mean and variances of these parameters by incorporating heterogeneity into generalized linear models. All parameters varied with age and to different degrees, depending on food availability. As expected, performance improved with increased food supply, and the observed age pattern was quadratic, with poorer breeding performances occurring in extreme ages. For most parameters (except for laying dates, for which age and food did not interact), the pattern changed with food somewhat unexpectedly; the differences in performance between age classes were higher (i.e., the quadratic pattern was more noticeable) when food was more readily available than when food availability was lower. We suggest that, under poor environmental conditions, only high-quality individuals of the younger and older birds bred and that the differences in breeding performance between age classes were smaller. Although variances for egg volume were constant, variances for laying dates were highest for the youngest breeders and tended to decrease with age, either due to the selection of higher-quality individuals or to a greater frequency of birds skipping breeding with age, especially when food was in low supply. Our results show that mean and variances of breeding parameters changed with age, but that this pattern was different for each parameter and also varied according to food availability. It is likely that, other than food, certain additional factors (e.g., sex, cohort effects, density dependence) also influence changes in breeding performance with age, and this may preclude the finding of a common pattern among traits and among studies on different taxa.

Determinants of extinction-colonization dynamics in Mediterranean butterflies: the role of landscape, climate and local habitat features.

Many species are found today in the form of fragmented populations occupying patches of remnant habitat in human-altered landscapes. The persistence of these population networks requires a balance between extinction and colonization events assumed to be primarily related to patch area and isolation, but the contribution of factors such as the characteristics of patch and matrix habitats, the species' traits (habitat specialization and dispersal capabilities) and variation in climatic conditions have seldom been evaluated simultaneously. The identification of environmental variables associated with patch occupancy and turnover may be especially useful to enhance the persistence of multiple species under current global change. However, for robust inference on occupancy and related parameters, we must account for detection errors, a commonly overlooked problem that leads to biased estimates and misleading conclusions about population dynamics. Here, we provide direct empirical evidence of the effects of different environmental variables on the extinction and colonization rates of a rich butterfly community in the western Mediterranean. The analysis was based on a 17-year data set containing detection/nondetection data on 73 butterfly species for 26 sites in north-eastern Spain. Using multiseason occupancy models, which take into account species' detectability, we were able to obtain robust estimates of local extinction and colonization probabilities for each species and test the potential effects of site covariates such as the area of suitable habitat, topographic variability, landscape permeability around the site and climatic variability in aridity conditions. Results revealed a general pattern across species with local habitat composition and landscape features as stronger predictors of occupancy dynamics compared with topography and local aridity. Increasing area of suitable habitat in a site strongly decreased local extinction risks and, for a number of species, both higher amounts of suitable habitat and more permeable landscapes increased colonization rates. Nevertheless, increased topographic variability decreased the extinction risk of bad dispersers, a group of species with significantly lower colonization rates. Our models predicted higher sensitivity of the butterfly assemblages to deterministic changes in habitat features rather than to stochastic weather patterns, with some relationships being clearly dependent on the species' traits.

Spatiotemporal organization of ant foraging from a complex systems perspective.

We use complex systems science to explore the emergent behavioral patterns that typify eusocial species, using collective ant foraging as a paradigmatic example. Our particular aim is to provide a methodology to quantify how the collective orchestration of foraging provides functional advantages to ant colonies. For this, we combine (i) a purpose-built experimental arena replicating ant foraging across realistic spatial and temporal scales, and (ii) a set of analytical tools, grounded in information theory and spin-glass approaches, to explore the resulting data. This combined approach yields computational replicas of the colonies; these are high-dimensional models that store the experimental foraging patterns through a training process, and are then able to generate statistically similar patterns, in an analogous way to machine learning tools. These in silico models are then used to explore the colony performance under different resource availability scenarios. Our findings highlight how replicas of the colonies trained under constant and predictable experimental food conditions exhibit heightened foraging efficiencies, manifested in reduced times for food discovery and gathering, and accelerated transmission of information under similar conditions. However, these same replicas demonstrate a lack of resilience when faced with new foraging conditions. Conversely, replicas of colonies trained under fluctuating and uncertain food conditions reveal lower efficiencies at specific environments but increased resilience to shifts in food location.

Ecological and evolutionary implications of food subsidies from humans.

Human activities are the main current driver of global change. From hunter-gatherers through to Neolithic societies-and particularly in contemporary industrialised countries-humans have (voluntarily or involuntarily) provided other animals with food, often with a high spatio-temporal predictability. Nowadays, as much as 30-40% of all food produced in Earth is wasted. We argue here that predictable anthropogenic food subsidies (PAFS) provided historically by humans to animals has shaped many communities and ecosystems as we see them nowadays. PAFS improve individual fitness triggering population increases of opportunistic species, which may affect communities, food webs and ecosystems by altering processes such as competition, predator-prey interactions and nutrient transfer between biotopes and ecosystems. We also show that PAFS decrease temporal population variability, increase resilience of opportunistic species and reduce community diversity. Recent environmental policies, such as the regulation of dumps or the ban of fishing discards, constitute natural experiments that should improve our understanding of the role of food supply in a range of ecological and evolutionary processes at the ecosystem level. Comparison of subsidised and non-subsidised ecosystems can help predict changes in diversity and the related ecosystem services that have suffered the impact of other global change agents.

Contrasting effects of climatic variability on the demography of a trans-equatorial migratory seabird.

Large-scale seasonal climatic indices, such as the North Atlantic Oscillation (NAO) index or the Southern Oscillation Index (SOI), account for major variations in weather and climate around the world and may influence population dynamics in many organisms. However, assessing the extent of climate impacts on species and their life-history traits requires reliable quantitative statistical approaches. We used a new analytical tool in mark-recapture, the multi-event modelling, to simultaneously assess the influence of climatic variation on multiple demographic parameters (i.e. adult survival, transient probability, reproductive skipping and nest dispersal) at two Mediterranean colonies of the Cory's shearwater Calonectris diomedea, a trans-equatorial migratory long-lived seabird. We also analysed the impact of climate in the breeding success at the two colonies. We found a clear temporal variation of survival for Cory's shearwaters, strongly associated to the large-scale SOI especially in one of the colonies (up to 66% of variance explained). Atlantic hurricane season is modulated by the SOI and coincides with shearwater migration to their wintering areas, directly affecting survival probabilities. However, the SOI was a better predictor of survival probabilities than the frequency of hurricanes; thus, we cannot discard an indirect additive effect of SOI via food availability. Accordingly, the proportion of transients was also correlated with SOI values, indicating higher costs of first reproduction (resulting in either mortality or permanent dispersal) when bad environmental conditions occurred during winter before reproduction. Breeding success was also affected by climatic factors, the NAO explaining c. 41% of variance, probably as a result of its effect in the timing of peak abundance of squid and small pelagics, the main prey for shearwaters. No climatic effect was found either on reproductive skipping or on nest dispersal. Contrarily to what we expect for a long-lived organism, large-scale climatic indexes had a more pronounced effect on survival and transient probabilities than on less sensitive fitness parameters such reproductive skipping or nest dispersal probabilities. The potential increase in hurricane frequency because of global warming may interact with other global change agents (such as incidental bycatch and predation by alien species) nowadays impacting shearwaters, affecting future viability of populations.

Drivers of resource allocation for breeding under variable environments in a bet hedger.

The evolutionary theory of life histories predicts that there is a trade-off between survival and reproduction: since adult survival in long-lived organisms is high, then breeding investment is more variable and more dependent on conditions (e.g. food availability and individual experience). Clutch features influence fitness prospects, but how a bet hedger builds its clutch in temporally varying environments is quite unknown. Using 27-year data on 2847 clutches of known-age breeders, we analyse how Audouin's gulls (Larus audouinii), a species showing a combination of conservative and adaptive bet-hedging breeding strategies, can allocate energy by laying clutches and eggs of different sizes. Results show that both food availability and age influenced clutch size and total egg volume in a clutch. Interestingly, we found an interaction between food and age on egg parameters: total volume in two-egg clutches, laid mostly by younger breeders, did not significantly change with food availability and the quadratic pattern in clutch size over the range of ages was less marked as long as food conditions became harsher. With increased food, females invested more by building larger first eggs, whereas they were more conservative on second and third eggs. Furthermore, asymmetries in egg volume within three-egg clutches increased with food availability for old females. Egg size profiles of two-egg clutches suggest that gulls should exhibit progressive reduction of the size of the third egg before shifting to a two-egg clutch size. Food availability influenced all parameters studied, whereas age affected the amount of energy allocated for producing eggs (their size and number) but not the way of allocating those energies (i.e. asymmetries within the clutch). Despite the range of factors affecting the clutch, results suggest that females can allocate the amount of resources in a clutch optimally to increase their fitness under variable environments via bet-hedging.

Exploiting uncertain ecological fieldwork data with multi-event capture--recapture modelling: an example with bird sex assignment.

1. Sex plays a crucial role in evolutionary life histories. However, the inclusion of sex in demographic analysis may be a challenge in fieldwork, particularly in monomorphic species. Although behavioural data may help us to sex individuals in the field, this kind of data is unlikely to be error free and is usually discarded. 2. Here we propose a multi-event capture-recapture model that enables us to exploit uncertain field observations regarding the sex of individuals based on behavioural or morphological criteria. The multi-event capture-recapture model allows us to account for sex uncertainty not restricting our ability to estimate the parameters of interest. In this case, by adding the confirmed sex of just a few individuals, we greatly improve the efficiency of the optimization algorithm. 3. Using such an approach, we analysed sex differences in demographic parameters (e.g. survival, transience and sex ratio) in a population of Audouin's gulls using observations from long-term fieldwork monitoring (1988-2007). We also assessed the probability of ascertaining sex over time and the probability of error for each field-sexing criterion. 4. We detected no strong effect of sex on either survival or transience probabilities, and both sexes showed a decreasing trend in survival over time and transience probability after recruitment increased with age and over time. The probability of ascertaining sex over time depended on observers' experience. Strikingly, courtship feeding (but not copulation) emerged as the most reliable clue for sexing individuals, which would suggest that Audouin's gulls engage in same-sex sexual behaviour such as same-sex mounting. 5. The present modelling emerged as a reliable method for estimating demographic parameters and state transition parameters in ecological studies in which field observations of sex or other individual states are assigned erroneously and uncertainly. This approach could also be useful for applied ecologists for assessing the reliability of their criteria for assigning sex or other individual covariates in the field, thereby permitting them to optimizing their field ecological protocols.

Genetic and phenotypic differentiation between the critically endangered Balearic shearwater and neighboring colonies of its sibling species.

Understanding the demographic and evolutionary processes within and between populations is essential for developing effective management strategies. Thus, for establishing good conservation policies both genetic and phenotypic studies are crucial. We carried out an integrated analysis of genetic and phenotypic characters of the critically endangered Balearic shearwater Puffinus mauretanicus (182 individuals) and compared them with those of 2 nearby colonies of Yelkouan shearwater P. yelkouan (40 individuals), a species for which hybridization has been hypothesized. The results of the microsatellite analyses were compared with previous mitochondrial DNA analyses. Genetic variability was low in the Balearic shearwater and high levels of inbreeding were revealed at local scale. Most dispersal in Balearic shearwaters was to neighboring sites, even though low levels of population structure were found. The admixture between the 2 species was much higher at nuclear than at mitochondrial level, but phenotypic characters would seem to indicate that a lower level of admixture exists. Individual nuclear DNA, mtDNA, and phenotype did not match at individual level, showing that migration alone cannot explain this phenomenon. We suggest that these 2 young shearwater species could have been involved in processes of divergence and admixing. However, due to the longer coalescence times in nuclear markers, incomplete lineage sorting cannot be ruled out.

Inferring the age of breeders from easily measurable variables.

Age drives differences in fitness components typically due to lower performances of younger and senescent individuals, and changes in breeding age structure influence population dynamics and persistence. However, determining age and age structure is challenging in most species, where distinctive age features are lacking and available methods require substantial efforts or invasive procedures. Here we explore the potential to assess the age of breeders, or at least to identify young and senescent individuals, by measuring some breeding parameters partially driven by age (e.g. egg volume in birds). Taking advantage of a long-term population monitored seabird, we first assessed whether age influenced egg volume, and identified other factors driving this trait by using general linear models. Secondly, we developed and evaluated a machine learning algorithm to assess the age of breeders using measurable variables. We confirmed that both younger and older individuals performed worse (less and smaller eggs) than middle-aged individuals. Our ensemble training algorithm was only able to distinguish young individuals, but not senescent breeders. We propose to test the combined use of field monitoring, classic regression analysis and machine learning methods in other wild populations were measurable breeding parameters are partially driven by age, as a possible tool for assessing age structure in the wild.

Interspecific synchrony on breeding performance and the role of anthropogenic food subsidies.

Synchrony can have important consequences for long-term metapopulations persistence, community dynamics and ecosystems functioning. While the causes and consequences of intra-specific synchrony on population size and demographic rates have received considerable attention only a few factors that may affect inter-specific synchrony have been described. We formulate the hypothesis that food subsidies can buffer the influence of environmental stochasticity on community dynamics, disrupting and masking originally synchronized systems. To illustrate this hypothesis, we assessed the consequences of European policies implementation affecting subsidy availability on the temporal synchrony of egg volume as a proxy of breeding investment in two sympatric marine top predators with differential subsidy use. We show how 7-year synchrony appears on egg volume fluctuations after subsidy cessation suggesting that food subsidies could disrupt interspecific synchrony. Moreover, cross correlation increased after subsidy cessation and environmental buffering seems to act during synchronization period. We emphasize that subsidies dynamics and waste management provide novel insights on the emergence of synchrony in natural populations.

It's not all abundance: Detectability and accessibility of food also explain breeding investment in long-lived marine animals.

Large-scale climatic indices are extensively used as predictors of ecological processes, but the mechanisms and the spatio-temporal scales at which climatic indices influence these processes are often speculative. Here, we use long-term data to evaluate how a measure of individual breeding investment (the egg volume) of three long-lived and long-distance-migrating seabirds is influenced by i) a large-scale climatic index (the North Atlantic Oscillation) and ii) local-scale variables (food abundance, foraging conditions, and competition). Winter values of the North Atlantic Oscillation did not correlate with local-scale variables measured in spring, but surprisingly, both had a high predictive power of the temporal variability of the egg volume in the three study species, even though they have different life-history strategies. The importance of the winter North Atlantic Oscillation suggests carry-over effects of winter conditions on subsequent breeding investment. Interestingly, the most important local-scale variables measured in spring were associated with food detectability (foraging conditions) and the factors influencing its accessibility (foraging conditions and competition by density-dependence). Large-scale climatic indices may work better as predictors of foraging conditions when organisms perform long distance migrations, while local-scale variables are more appropriate when foraging areas are more restricted (e.g. during the breeding season). Contrary to what is commonly assumed, food abundance does not directly translate into food intake and its detectability and accessibility should be considered in the study of food-related ecological processes.

The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle.

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and a member of the most speciose group of pelagic seabirds, the order Procellariiformes, which exhibit extreme adaptations to a pelagic lifestyle. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the Balearic shearwater population size. Currently, populations of the species continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, with some studies predicting its extinction by 2070. Here, using a combination of short and long reads, we generate the first high-quality reference genome for the Balearic shearwater, with a completeness amongst the highest across available avian species. We used this reference genome to study critical aspects relevant to the conservation status of the species and to gain insights into the adaptation to a pelagic lifestyle of the order Procellariiformes. We detected relatively high levels of genome-wide heterozygosity in the Balearic shearwater despite its reduced population size. However, the reconstruction of its historical demography uncovered an abrupt population decline potentially linked to a reduction of the neritic zone during the Penultimate Glacial Period (∼194-135 ka). Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision, and the development of natriuresis. The reference genome obtained will be the crucial in the future development of genetic tools in conservation efforts for this Critically Endangered species.

Studying the reproductive skipping behavior in long-lived birds by adding nest inspection to individual-based data.

The frequency at which individuals breed is an important parameter in population, as well as in evolutionary, studies. However, when nonbreeding individuals are absent from the study area, the reproductive skipping is usually confounded with a recapture failure and cannot be estimated directly. Yet, there are situations in which external information may help to estimate reproductive skipping. Such a situation is found with nest-tenacious birds: the fact that an individual is not encountered in its previous nest is a good indication that it must be skipping reproduction. We illustrate here a general probabilistic framework in which we merged the classical individual capture-recapture information with nest-based information to obtain the simultaneous estimate of recapture, survival, reproductive skipping, and within-colony breeding dispersal probabilities using multi-event models. We applied this approach to Cory's Shearwater (Calonectris diomedea), a long-lived burrow-nesting seabird. By comparing results with those obtained from the analysis of the capture-recapture information alone, we showed that the model separates successfully the probabilities of recapture from those of temporal emigration. We found that the probabilities of future reproduction and breeding-site fidelity were lower for individuals temporarily absent from the colony, suggesting a lower intrinsic quality of intermittent breeders. The new probabilistic framework presented here allowed us to refine the estimates of demographic parameters by simply adding nest-based data, a type of information usually collected in the field but never included in the analysis of individual-based data. Our approach also provides a new and flexible way to test hypotheses on temporal emigration and breeding dispersal in longitudinal data.