Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.

Playing "hide and seek" with the Mediterranean monk seal: a citizen science dataset reveals its distribution from molecular traces (eDNA).

Animal conservation relies on assessing the distribution and habitat use of species, but for endangered/elusive animals this can prove difficult. The Monk Seal, Monachus monachus, is one of the world's most endangered species of pinniped, and the only one endemic to the Mediterranean Sea. During recent decades, direct observations have been few and scattered, making it difficult to determine its distribution away from the Aegean Sea (core distribution area of the post-decline relict population). This study relies on environmental DNA (eDNA) analysis to detect the presence of the Monk Seal in 135 samples collected in 120 locations of the central/western Mediterranean Sea, spanning about 1500 km longitudinally and 1000 km latitudinally. A recently described species-specific qPCR assay was used on marine-water samples, mostly collected during 2021 by a Citizen Science (CS) project. Positive detections occurred throughout the longitudinal range, including the westernmost surveyed area (Balearic archipelago). The distribution of the positive detections indicated six "hotspots", mostly overlapping with historical Monk Seal sites, suggesting that habitat-specific characteristics play a fundamental role. We applied single-season occupancy models to correct for detection probability and to assess the importance of site-specific characteristics. The distance from small islets and protected (or access-restricted) areas was correlated negatively with the detection probability. This novel molecular approach, applied here for the first time in an extensive CS study, proved its potential as a tool for monitoring the distribution of this endangered/elusive species.

Active breeding seabirds prospect alternative breeding colonies.

Compared to other animal movements, prospecting by adult individuals for a future breeding site is commonly overlooked. Prospecting influences the decision of where to breed and has consequences on fitness and lifetime reproductive success. By analysing movements of 31 satellite- and GPS-tracked gull and tern populations belonging to 14 species in Europe and North America, we examined the occurrence and factors explaining prospecting by actively breeding birds. Prospecting in active breeders occurred in 85.7% of studied species, across 61.3% of sampled populations. Prospecting was more common in populations with frequent inter-annual changes of breeding sites and among females. These results contradict theoretical models which predict that prospecting is expected to evolve in relatively predictable and stable environments. More long-term tracking studies are needed to identify factors affecting patterns of prospecting in different environments and understand the consequences of prospecting on fitness at the individual and population level.

Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota.

Background: Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation. Methods: Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes. Results: All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover. Conclusions: These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards' metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems.

Life span, growth, senescence and island syndrome: Accounting for imperfect detection and continuous growth.

Small vertebrates on islands are expected to attain a larger body size, and a greater survival than their mainland counterparts. Comparative studies have questioned whether lizards exhibit this set of adaptations, referred to as the 'island syndrome'. We collected data on 730 individuals the endemic Lilford's lizard Podarcis lilfordi throughout a 10-year period on a small island of the Balearic archipelago (Spain). We coupled a growth function with a capture-mark-recapture model to simultaneously estimate size- and sex-dependent growth rate and survival. To put our results into a wider context, we conducted a systematic review of growth, life span and age at maturity in different Podarcis species comparing insular and mainland populations. We found a low average growth coefficient (0.56 and 0.41 year-1 for males and females to reach an asymptotic size of 72.3 and 65.6 mm respectively), a high annual survival probability of 0.81 and 0.79 in males and females, and a large variability between individuals in growth parameters. Survival probability decreased with body size in both sexes, indicating a senescence pattern typical of long-lived species or in populations with a low extrinsic mortality. Assuming a constant survival after sexual maturity, at about 2 years old, the average life span was 6.18 years in males and 8.99 in females. The oldest animal was a male last captured at an estimated age of ≥13 years and still alive at the end of the study. Our results agree with the predictions of the 'island syndrome' for survival, life span and growth parameters. A comparative analysis of these values across 29 populations of 16 different species of Podarcis indicated that insular lizards grow slower and live longer than their mainland counterparts. However, our data differed from other island populations of the same species, suggesting that island-specific characteristics play an additional role to isolation. Within this study we developed an analytical approach to study the body size-dependent survival of small reptiles. We discuss its applicability to contrast hypotheses on senescence in different sexes of this species, and provide the code used to integrate the growth and capture-mark-recapture models.

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.

Hardship at birth alters the impact of climate change on a long-lived predator.

Climate change is increasing the frequency of extreme events, such as droughts or hurricanes, with substantial impacts on human and wildlife communities. Extreme events can affect individuals through two pathways: by altering the fitness of adults encountering a current extreme, and by affecting the development of individuals born during a natal extreme, a largely overlooked process. Here, we show that the impact of natal drought on an avian predator overrode the effect of current drought for decades, so that individuals born during drought were disadvantaged throughout life. Incorporation of natal effects caused a 40% decline in forecasted population size and a 21% shortening of time to extinction. These results imply that climate change may erode populations more quickly and severely than currently appreciated, suggesting the urgency to incorporate "penalties" for natal legacies in the analytical toolkit of impact forecasts. Similar double impacts may apply to other drivers of global change.

Climate warming induced a stretch of the breeding season and an increase of second clutches in a passerine breeding at its altitudinal limits.

The increase in the average air temperature due to global warming has produced an early onset of the reproduction in many migratory birds of the Paleartic region. According to the "mismatch hypothesis" this response can lead to a decrease in the breeding output when the conditions that trigger the departure from the wintering areas do not match the availability of food resources in the breeding ground. We used 653 brooding events registered during the period 1991-2013 to investigate the link between climatic variables and individual breeding performance of a partially migratory passerine, the Rock Sparrow Petronia petronia, breeding at the altitude limit of its distribution. The laying date (LD) of the earliest first clutch was associated with local spring (minimum) temperatures but did not show a significant trend during the period considered. The LD of the latest first clutch had a positive and statistically significant trend, unrelated to local covariates and resulting in a longer breeding season (∼1.5 days/year). A longer breeding season allowed birds to produce more second clutches, which proportion increased from 0.14 to 0.25. The average breeding success was also positively correlated with the average temperature in July and with the duration of the breeding season. Contrary to expectations, the most important climate-dependent effect was a stretch of the breeding season due to a significant increase of the LD of the latest first-clutches rather than an earlier breeding onset. We show how climate changes act on bird populations through multiple paths and stress the need to assess the link between climatic variables and several aspects of the breeding cycle.

Demographic modeling to fine-tune conservation targets: importance of pre-adults for the decline of an endangered raptor.

Large, long-lived species with slow life histories and protracted pre-breeding stages are particularly susceptible to declines and extinction, often for unknown causes. Here, we show how demographic modeling of a medium-sized raptor, the Red Kite Milvus milvus, can aid to refocus conservation research and attention on the most likely mechanisms driving its decline. Red Kites' survival and reproduction increased through three sequential stages for 1-2, 3-6, and 7-30 yr of age, mainly corresponding to individuals that are dispersing, attempting to gain a territory, and breeding. As typical of long-lived species, elasticities were highest for adult (≥7 yr old) survival, but this was high, with little scope for improvement. Instead, the declines were driven by an extremely low survival of pre-adults in their first years of life, which weakened the whole demographic system by nullifying the offspring contribution of adults and curtailing their replacement by recruits. For example, 27 pairs were necessary to generate a single prime age adult. Simulation of management scenarios suggested that the decline could be halted most parsimoniously by increasing pre-adult survival to the mean levels recorded for other areas, while only the synergistic, simultaneous improvement of breeding success, adult and pre-adult survival could generate a recovery. We propose three actions to attain such goals through selective supplementary feeding of both breeding and non-breeding individuals, and through mortality improvement by GPS remote-sensing devices employed as surveillance monitoring tools. Our results show how improving demographic models by using real, local vital rates rather than "best guess" vital rates can dramatically improve model realism by refocusing attention on the actual stages and mortality causes in need of manipulation, thus building precious time and resources for conservation management. These results also highlight the frequent key role of pre-adult survival for the management of long-lived species, coherent with the idea of demographic systems as integrated chains only as strong as their weakest link.

Diet composition of the lizard Podarcis lilfordi (Lacertidae) on 2 small islands: an individual-resource network approach.

Despite it is widely accepted that intrapopulation variation is fundamental to ecological and evolutionary processes, this level of information has only recently been included into network analysis of species/population interactions. When done, it has revealed non-random patterns in the distribution of trophic resources. Nestedness in resource use among individuals is the most recurrent observed pattern, often accompanied by an absence of modularity, but no previous studies examine bipartite modularity. We use network analysis to describe the diet composition of the Balearic endemic lizard Podarcis lilfordi in 2 islets at population and individual levels, based on the occurrence of food items in fecal samples. Our objectives are to 1) compare niche structure at both levels, 2) characterize niche partition using nestedness and modularity, and 3) assess how size, sex, season, and spatial location influence niche structure. At population-level niche width was wide, but narrow at the level of the individual. Both islet networks were nested, indicating similar ranking of the food preferences among individuals, but also modular, which was partially explained by seasonality. Sex and body size did not notably affect diet composition. Large niche overlap and therefore possibly relaxed competition were observed among females in one of the islets and during spring on both islets. Likewise, higher modularity in autumn suggests that higher competition could lead to specialization in both populations, because resources are usually scarce in this season. The absence of spatial location influence on niche might respond to fine-grained spatio-temporally distribution of food resources. Behavioral traits, not included in this study, could also influence resource partitioning.

Contrasting size-dependent life history strategies of an insular lizard.

In many species with continuous growth, body size is an important driver of life-history tactics and its relative importance is thought to reflect the spatio-temporal variability of selective pressures. We developed a deterministic size-dependent integral projection model for 3 insular neighboring lizard populations with contrasting adult body sizes to investigate how size-related selective pressures can influence lizard life-history tactics. For each population, we broke down differences in population growth rates into contributions from size-dependent body growth, survival, and fecundity. A life table response experiment (LTRE) was used to compare the population dynamics of the 3 populations and quantify the contributions of intrinsic demographic coefficients of each population to the population growth rate (λ). Perturbation analyses revealed that the largest adults contributed the most to the population growth rate, but this was not true in the population with the smallest adults and size-independent fertility. Although we were not able to identify a single factor responsible for this difference, the combination of the demographic model on a continuous trait coupled with an LTRE analysis revealed how individuals from sister populations of the same species follow different life strategies and showed different compensatory mechanisms among survival, individual body growth, and fertility. Our results indicate that body size can play a contrasting role even in closely-related and closely-spaced populations.

When and where mortality occurs throughout the annual cycle changes with age in a migratory bird: individual vs population implications.

The annual cycle of most animals is structured into discrete stages, such as breeding, migration and dispersal. While there is growing appreciation of the importance of different stages of an organism's annual cycle for its fitness and population dynamics, almost nothing is known about if and how such seasonal effects can change through a species lifespan. Here, we take advantage of the opportunity offered by a long-term satellite/GPS-tracking study and a reliable method of remote death-detection to show that certain stages of both the annual and life cycle of a migratory long-lived raptor, the Black kite Milvus migrans, may represent sensitive bottlenecks for survival. In particular, migratory journeys caused bursts of concentrated-mortality throughout life, but the relative importance of stage-specific survival changed with age. On the other hand, the balance between short-stages of high mortality and long-stages of low mortality made population-growth similarly dependent on all portions of the annual cycle. Our results illustrate how the population dynamics of migratory organisms can be inextricably linked to ecological pressures balanced over multiple stages of the annual cycle and thus multiple areas of the globe, suggesting the frequent need for challenging conservation strategies targeting all portions of a species year-round range.

Unravelling the sex- and age-specific impact of poaching mortality with multievent modeling.

BACKGROUND: Poaching is a prominent source of 'hidden hurdles', cryptic impacts of human activities that may hinder the conservation of animal populations. Estimating poaching mortality is challenging, as the evidence for illegal killing is not outwardly obvious. Using resighting and recovery data collected on 141 marked red deer Cervus elaphus within the Stelvio National Park (central Italian Alps), we show how multievent models allow to assess the direct impacts of illegal harvesting on age- and sex-specific survival, accounting for uncertainty over mortality causes. RESULTS: Mortality caused by poaching was consistently higher for males than for females in all age classes. In males, the probability of dying from poaching was higher for extreme age classes, while in females all age classes showed fairly similar values of poaching mortality. The strong bias in sex-specific poaching mortality was possibly due to trophy killing in adult males and 'bushmeat-like' killing for private or commercial gain in young males and in females. CONCLUSIONS: A robust assessment of age- and sex-specific prevalence of poaching in wildlife populations is pivotal when illegal killing is of conservation concern. This provides timely information on what segment of the population is most likely to be affected. Besides obvious demographic consequences on small populations, age- and sex-biased poaching prevalence may contrast with the need to maintain ecosystem complexity and may alter behavioral responses to human presence. The information provided by multievent models, whose flexibility makes them adaptable to many systems where individual-based data is part of population monitoring, offers a support to design appropriate strategies for the conservation of wildlife populations.

Assessing the effect of density on population growth when modeling individual encounter data.

The relative role of density-dependent and density-independent variation in vital rates and population size remains largely unsolved. Despite its importance to the theory and application of population ecology, and to conservation biology, quantifying the role and strength of density dependence is particularly challenging. We present a hierarchical formulation of the temporal symmetry approach, also known as the Pradel model, that permits estimation of the strength of density dependence from capture-mark-reencounter data. A measure of relative population size is built in the model and serves to detect density dependence directly on population growth rate. The model is also extended to account for temporal random variability in demographic rates, allowing estimation of the temporal variance of population growth rate unexplained by density dependence. We thus present a model-based approach that enable to test and quantify the effect of density-dependent and density-independent factors affecting population fluctuations in a single modeling framework. More generally, we use this modeling framework along with simulated and empirical data to show the value of including density dependence when modeling individual encounter data without the need for auxiliary data.

Modelling the range expansion of the Tiger mosquito in a Mediterranean Island accounting for imperfect detection.

BACKGROUNDS: Aedes albopictus (Diptera; Culicidae) is a highly invasive mosquito species and a competent vector of several arboviral diseases that have spread rapidly throughout the world. Prevalence and patterns of dispersal of the mosquito are of central importance for an effective control of the species. We used site-occupancy models accounting for false negative detections to estimate the prevalence, the turnover, the movement pattern and the growth rate in the number of sites occupied by the mosquito in 17 localities throughout Mallorca Island. RESULTS: Site-occupancy probability increased from 0.35 in the 2012, year of first reported observation of the species, to 0.89 in 2015. Despite a steady increase in mosquito presence, the extinction probability was generally high indicating a high turnover in the occupied sites. We considered two site-dependent covariates, namely the distance from the point of first observation and the estimated yearly occupancy rate in the neighborhood, as predicted by diffusion models. Results suggested that mosquito distribution during the first year was consistent with what predicted by simple diffusion models, but was not consistent with the diffusion model in subsequent years when it was similar to those expected from leapfrog dispersal events. CONCLUSIONS: Assuming a single initial colonization event, the spread of Ae. albopictus in Mallorca followed two distinct phases, an early one consistent with diffusion movements and a second consistent with long distance, 'leapfrog', movements. The colonization of the island was fast, with ~90% of the sites estimated to be occupied 3 years after the colonization. The fast spread was likely to have occurred through vectors related to human mobility such as cars or other vehicles. Surveillance and management actions near the introduction point would only be effective during the early steps of the colonization.

Conspecific and not performance-based attraction on immigrants drives colony growth in a waterbird.

Local recruitment and immigration play an important part in the dynamics and growth of animal populations. However, their estimation and incorporation into open population models is, in most cases, problematic. We studied factors affecting the growth of a recently established colony of Eurasian spoonbill (Platalea leucorodia) and assessed the contribution of local recruits, i.e. birds born in the colony, and immigrants, i.e. birds of unknown origin, to colony growth. We applied an integrated population model that accounts for uncertainty in breeding state assignment and merges population surveys, local fecundity and individual longitudinal data of breeding and non-breeding birds, to estimate demographic rates and the relative role of recruitment and immigration in driving the local dynamics. We also used this analytical framework to assess the degree of support for the 'performance-based' and 'conspecific attraction' hypotheses as possible mechanisms of colony growth. Among the demographic rates, only immigration was positively and significantly correlated with population growth rate. In addition, the number of immigrants settling in the colony was positively correlated with colony size in the previous and current year, but was not correlated with fecundity of the previous year. Our results suggest that the variation in immigration affected colony dynamics and that conspecific attraction likely triggered the relevant role of immigration in the growth of a recently formed waterbird colony, supporting the need of including immigration in population analysis.

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.

Oceanographic drivers and mistiming processes shape breeding success in a seabird.

Understanding the processes driving seabirds' reproductive performance through trophic interactions requires the identification of seasonal pulses in marine productivity. We investigated the sequence of environmental and biological processes driving the reproductive phenology and performance of the storm petrel (Hydrobates pelagicus) in the Western Mediterranean. The enhanced light and nutrient availability at the onset of water stratification (late winter/early spring) resulted in annual consecutive peaks in relative abundance of phytoplankton, zooplankton and ichthyoplankton. The high energy-demanding period of egg production and chick rearing coincided with these successive pulses in food availability, pointing to a phenological adjustment to such seasonal patterns with important fitness consequences. Indeed, delayed reproduction with respect to the onset of water stratification resulted in both hatching and breeding failure. This pattern was observed at the population level, but also when confounding factors such as individuals' age or experience were also accounted for. We provide the first evidence of oceanographic drivers leading to the optimal time-window for reproduction in an inshore seabird at southern European latitudes, along with a suitable framework for assessing the impact of environmentally driven changes in marine productivity patterns in seabird performance.