Biology subjects

Charmantier, A.

Publications and source records attributed to Charmantier, A..

16 recordsLinked to original sources

bioRxiv2026

Widespread circulation of West Nile and Usutu viruses in sedentary and migratory avifauna: A Two-Year Study (2024-2025) of active surveillance in South of France

West Nile virus (WNV) and Usutu virus (USUV) are neurotropic Orthoflaviviruses sharing a similar enzootic transmission cycle primarily involving Culex pipiens mosquitoes as vectors and birds as amplifying hosts. First identified in Africa, both viruses established endemicity across Europe over the past two decades, most likely introduced and spread by migratory bird species along Mediterranean flyways. In avian species, infection outcomes range from subclinical to fatal neuroinvasive disease, varying by viral strain, host immunity, and species susceptibility. Southern France emerges as a key hotspot for the circulation of these viruses, supported by diverse avian habitats conducive to year-round viral maintenance. This study investigated the prevalence of WNV and USUV in more than 2500 sedentary and migratory wild birds from these regions during 2024-2025 using molecular surveillance. Samples were collected using mist net and bird boxes, across multiple passerine and non-passerine taxa, spanning wetlands, urban fringes, and agricultural zones. Our analyses revealed widespread viral circulation across diverse species, mainly among passerines such as great tits, house sparrows, and barn swallows with USUV detected at higher rates than WNV in both study years. Overall prevalence was markedly higher in 2024 than in 2025, potentially reflecting climatic or ecological drivers. Migratory individuals likely seed viral introductions during seasonal passages, whereas resident populations sustain local enzootic cycles, facilitating overwintering persistence. These results highlight the pivotal role of mixed avifauna in arbovirus dynamics within Mediterranean Europe and emphasize the necessity for integrated, year-round surveillance targeting high-risk species and habitats. Enhanced monitoring will aid in predicting spillover risks and informing vector control strategies to mitigate zoonotic threats.

microbiology↗

bioRxiv2025

Disentangling urbanisation, climate effects and their interaction on ornamental colourations

Urbanisation and climate change can both affect phenotype expression across taxa. Most evidence collected so far has focused on exploring these two phenomena on isolation. Currently, the combined effects of climate change and urbanisation remain underexplored, despite being among the greatest challenges faced by biodiversity. Here, we use a decade-long, individual-based study of urban and forest great tits (Parus major) to analyse urbanisation, climate and their interactive effects on yellow breast colouration, a carotenoid-based trait. We find that urban birds exhibit duller colourations than forest counterparts, being 10-20% less chromatic, with first-year birds and males being more negatively impacted by cities. Additionally, birds in the city are more sexually dichromatic than in the forest. Over the decade, colouration differences between habitats remain stable, following a similar quadratic temporal pattern. Finally, while climate has a weak effect on colouration, urban birds appear more sensitive to its influence than forest birds. Our results indicate urbanisation has a stronger impact than last decade climatic variation on great tit colouration, though both factors may interact. The heightened sensitivity of first-year birds and increased sexual dichromatism in cities may alter the strength of natural and sexual selection on this trait in urban environments.

ecology↗

bioRxiv2024

Tit wit: environmental and genetic drivers of cognitive variation along an urbanization gradient

Cognitive abilities can promote acclimation and adaptation to life in cities. However, the genetic versus environmental drivers of cognition have rarely been studied in the wild and there exists a major gap concerning the role of cognition in adaptation to novel urban contexts. To address this, we evaluate cognitive variation in wild great tits (Parus major; N = 393) along an urban gradient, and decipher the genetic basis of this variation using a combination of a common garden experiment, quantitative genetic analyses, and genome-wide association studies. Specifically, we measure inhibitory control abilities which affect how animals respond to novel resources and challenges. We find that wild urban and forest tits do not clearly differ in inhibitory control performance (number of errors or the latency to escape) during a motor detour task; a result that was consistent in birds from urban and forest origins reared in a common garden (N = 73). Cognitive performance was repeatable (R = 0.35 - 0.38) and showed low to moderate heritability in the wild (h2= 0.16 - 0.28 using social and genomic pedigrees). We identified five SNPs that were significantly associated with the number of errors during the task, explaining 21% of the cognitive variation. These SNPs are linked to genes related to serotonergic and dopaminergic systems that are known to play important roles in cognition. Altogether, our study finds limited evidence that inhibitory control abilities have evolved under novel urban contexts, yet reveals a genetic basis of this cognitive trait in great tits.

animal behavior and cognition↗

bioRxiv2024

The city and forest bird flock together in a common garden: genetic and environmental effects drive urban phenotypic divergence

Urban phenotypic divergences are documented across diverse taxa, but the underlying genetic and environmental drivers behind these phenotypic changes are unknown in most wild urban systems. We conduct a common garden experiment using great tit (Parus major) eggs collected along an urbanization gradient to: 1) determine whether documented morphological, physiological, and behavioural shifts in wild urban great tits are maintained in birds from urban and forest origins reared in a common garden (N = 73) and 2) evaluate how different sources of genetic, early maternal investment, and later environmental variation contributed to trait variation in the experiment. In line with the phenotypic divergence in the wild, common garden birds from urban origins had faster breath rates (i.e., higher stress response) and were smaller than birds from forest origins, while wild differences in aggression and exploration were not maintained in the experiment. Differences between individuals (genetic and environmentally induced) explained the most trait variation, while variation among foster nests and captive social groups was limited. Our results provide trait-specific evidence of evolution in an urban species where genetic change likely underlies urban differences in morphology and stress physiology, but that urban behavioural divergences are more strongly driven by plasticity.

evolutionary biology↗

bioRxiv2024

Continent-wide drivers of spatial synchrony in age structure across wild great tit populations

Spatio-temporal variation in age structure influences population dynamics, yet we have limited understanding of the spatial scale at which its fluctuations are synchronised between populations. Using 32 great tit populations, spanning 3200km and >130,000 birds across 67 years, we quantify spatial synchrony in breeding age structure and its drivers. We show that larger clutch sizes, colder winters and summers, and larger beech crops lead to younger populations. We report distant-dependent spatial synchrony of age structure, which is maintained at approximately 650km. Despite covariation with age structure, reproductive and environmental variables do not influence the scale of synchrony, except for a moderate effect of beech masting. We suggest that local ecological and density-dependent dynamics impact how environmental variation interacts with age structure, influencing estimates of the environments effect on spatial synchrony. Our analyses demonstrate the operation of synchrony in age structure over large scales, with implications for age-dependent demography in populations.

ecology↗

bioRxiv2024

Global meta-analysis reveals urban-associated behavioral differences among wild populations

Urbanization is causing fundamental changes to natural environments, effecting rapid and substantial adaptive phenotypic change in wild populations. While a large body of work has investigated how urbanization may shape interspecific variation in behavioral traits, such as via urban environmental filtering, no study has yet quantitatively assessed global patterns of urban-associated intraspecific behavioral variation. Here, we conducted a phylogenetic meta-analysis to assess urban-associated behavioral differences in wild populations of birds, mammals, amphibians, reptiles, and insects. We focused on four commonly measured behaviors (boldness, aggression, activity, and exploration) and extracted paired urban-nonurban effect size estimates for phenotypic means and variances (k = 278), behavioral repeatability (k = 13), and behavioral correlations (k = 14) from 80 studies. We found clear evidence that urban populations exhibit heightened average boldness, aggression, exploration, and activity compared to nonurban conspecifics, a result that was robust among species, geographic region, and ecological niche. Further, our results suggested that "generalist" species have the strongest behavioral responses. Conversely, we did not find strong evidence linking urbanization to changes in phenotypic variation, behavioral repeatability, or behavioral correlations. Our results summarize data from a rapidly evolving field in urban ecology and demonstrate geographically and taxonomically widespread differences in behavior between urban and nonurban populations, suggesting parallel natural selection across urban species and populations.

animal behavior and cognition↗

bioRxiv2023

Cities as parasitic burden? Malaria prevalence and diversity along an urbanization gradient in great tits

Urbanization is a worldwide phenomenon that modifies the environment. By affecting the reservoirs of pathogens and the body and immune conditions of hosts, urbanization alters the epidemiological dynamics and diversity of diseases. Cities could act as areas of pathogen dilution or amplification, depending on whether urban features have positive or negative effects on vectors and hosts. In this study, we focused on a host species and investigated the prevalence and diversity of avian malaria parasites (Plasmodium/Haemoproteus sp. and Leucocytozoon sp.) in great tits (Parus major) living across an urbanization gradient. In general, we observed high prevalence in adult birds (from 95% to 100%), yet lower prevalence in fledglings (from 0% to 38%). We found a slight tendency for increased Plasmodium sp. prevalence with increasing urbanization in adults. Urban nestlings had higher Plasmodium sp. infection rates than non-urban nestlings. We found evidence of higher diversity of parasites in the most natural urban park; however, parasite diversity was similar across other urbanization levels (e.g. from a little artificialized park to a highly anthropized industrial area). Parasite lineages were not habitat specific. Only one Plasmodium sp. lineage (YWT4) was associated with urban areas and some rare lineages (e.g., AFR065) were present only in a zoo area, perhaps because of the presence of African birds. This study suggests that urbanization can lead to a parasite amplification effect and can favor different avian malaria lineages.

ecology↗

bioRxiv2021

A global meta-analysis reveals more variable life histories in urban birds compared to their non-urban neighbours

Cities pose a major ecological challenge for wildlife worldwide. Phenotypic variation, which can result from underlying genetic variation or plasticity, is an important metric to understand eco-evolutionary responses to environmental change. Recent work suggests that urban populations might have higher levels of phenotypic variation than non-urban counterparts. This prediction, however, has never been tested across species nor over a broad geographical range. Here, we conduct a meta-analysis of the avian literature to compare urban versus non-urban means and variation in phenology (i.e., lay date) and reproductive effort (i.e., clutch size, number of fledglings). First, we show that urban populations reproduce earlier and have smaller broods than non-urban conspecifics. Second, we show that urban populations have higher phenotypic variation in laying date than non-urban populations. This result arises from differences between populations within breeding seasons, conceivably due to higher landscape heterogeneity in urban habitats. These findings reveal a novel effect of urbanisation on animal life-histories with potential implications for species adaptation to urban environments (which will require further investigation). Higher variation in phenology in birds subjected to urban disturbance could result from plastic responses to a heterogeneous environment, or from higher genetic variation in phenology, possibly linked to higher evolutionary potential.

evolutionary biology↗

bioRxiv2021

Testing for parallel genomic and epigenomic footprints of adaptation to urban life in a passerine bird

Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in Evolutionary Biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a substantial role in rapid adaptation. In the context of rampant urbanization, joint examinations of genomic and epigenomic mechanisms are still lacking. Here, we investigated genomic (SNP) and epigenomic (CpG methylation) responses to urban life in a passerine bird, the Great tit (Parus major). To test whether urban evolution is predictable (i.e parallel) or involves mostly non-parallel molecular processes among cities, we analysed three distinct pairs of city and forest Great tit populations across Europe. Results reveal a polygenic response to urban life, with both many genes putatively under weak divergent selection and multiple differentially methylated regions (DMRs) between forest and city great tits. DMRs mainly overlapped transcription start sites and promotor regions, suggesting their importance in the modulation gene expression. Both genomic and epigenomic outliers were found in genomic regions enriched for genes with biological functions related to nervous system, immunity, behaviour, hormonal and stress responses. Interestingly, comparisons across the three pairs of city-forest populations suggested little parallelism in both genetic and epigenetic responses. Our results confirm, at both the genetic and epigenetic levels, hypotheses of polygenic and largely non-parallel mechanisms of rapid adaptation in new environments such as urbanized areas.

genomics↗

bioRxiv2021

Identifying drivers of spatio-temporal variation in survival in four blue tit populations

In a context of rapid climate change, the influence of large-scale and local climate on population demography is increasingly scrutinized, yet studies are usually focused on one population. Demographic parameters, including survival, can vary significantly across populations of a given species, depending on global or local climatic fluctuations but also on many other population-specific parameters such as breeding density, habitat naturalness, predation or parasitism. Such ecological differences between populations could lead to different paces-of-life (POL), whereby populations where individuals display higher reproductive investment and bolder behaviours would have lower survival probabilities. We use here long-term (19 to 38 years) monitoring datasets from four Mediterranean populations of blue tits (Cyanistes caeruleus) to investigate the effects of sex, age class, large-scale and local climate temporal variation and population breeding density, on adult survival, using Capture-Mark-Recapture modelling. Environment heterogeneity in these four populations (two in evergreen and two in deciduous forests) has been linked to strong multi-trait phenotypic variation, suggesting blue tits in deciduous forests display faster POL compared to their conspecifics in evergreen habitats. The present results show heterogeneity in average survival probabilities across the four populations, with, as predicted, lower survival in the fast blue tits occupying deciduous habitats. Interestingly, the year-to-year variation in survival probabilities was synchronous among populations. This suggests that regional environmental conditions could drive survival fluctuations across populations. However, breeding densities were not correlated across populations, and we found no evidence that adult survival is correlated with either large-scale or local, climate temporal variation in these four blue tit populations. Finally, two of the focal populations displayed a linear temporal decrease in adult survival over the study period, calling for further investigation to explain this decline. Overall, this multi-site study shows that blue tit parental survival from one spring to the next can vary substantially across years, in a synchronous way across populations, yet the climate indices we used are not correlated with the temporal variation. This calls for further investigations in other potential drivers such as resource (in particular insect) abundance, predation or parasitism.

ecology↗

bioRxiv2021

Is earlier reproduction associated with higher or lower survival? Antagonistic results between individual and population scales in the blue tit

Although it has been shown that phenology can respond to temporal environmental variation in free ranging populations of several species, little is known about the mechanisms of these responses and their effects on demography, and in particular on survival. Exploring phenological responses and their associated consequences on survival can be achieved at two distinct scales: the population scale, which focusses on a set of common responses to environmental conditions, and the individual scale, focusing on the relative position of each individual in the distribution of survival and phenology under particular conditions. In this study, we apply capture-mark-recapture multistate modelling on a 38-year monitoring dataset of blue tits (Cyanistes caeruleus) to investigate the effects of breeding phenology and some demographic covariates (breeding density, average and individual breeding success) on adult survival, at both population and individual scales. Our analysis revealed that (i) at the population scale, early breeding years are followed by lower average adult survival. (ii) At the individual level, earlier breeders within the population have higher subsequent survival than later breeders, although this relationship is reversed in years with very harsh conditions, e.g. warm spring and high breeding density. (iii) High individual relative breeding success is also associated with higher subsequent survival and explains more survival variation than relative phenology. Overall, our study indicates that, although earlier breeding is associated with a survival cost at the population level, substantial intrapopulation hererogeneity shapes a positive association between earlier breeding, breeding success and survival at the individual level.

ecology↗

bioRxiv2020

Bird populations most exposed to climate change are less responsive to climatic variation

The phenology of many species shows strong sensitivity to climate change; however, with few large scale intra-specific studies it is unclear how such sensitivity varies over a species range. We document large intra-specific variation in phenological sensitivity to temperature using laying date information from 67 populations of two European songbirds covering a large part of their breeding range. Populations inhabiting deciduous habitats showed stronger phenological sensitivity compared with those in evergreen and mixed habitats. Strikingly, however, the lowest sensitivity was seen in populations that had experienced the greatest change in climate. Therefore, we predict that the strongest phenological advancement will not occur in those populations with the highest sensitivity. Our results show that to effectively assess the impact of climate change on phenology across a species range it will be necessary to account for intra-specific variation in phenological sensitivity, climate change exposure, and the ecological characteristics of a population.

ecology↗

bioRxiv2019

Genomics of local adaptation in blue tit

Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.

evolutionary biology↗

bioRxiv2019

The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear "islands of differentiation" even among populations with very low levels of genome-wide differentiation. Low local recombination rate in the genome was a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.

evolutionary biology↗

bioRxiv2018

Parasite intensity is driven by temperature in a wild passerine bird

Increasing awareness that parasitism is an essential component of nearly all aspects of ecosystem functioning, as well as a driver of biodiversity, has led to rising interest in the consequences of climate change in terms of parasitism and disease spread. Yet empirical knowledge on the extent and ways in which climatic factors affect parasite prevalence and intensities remains scarce. In an 18-year, multi-site, correlative study we investigated the contributions of weather variables and other factors to spatio-temporal variation in infestation by blowfly parasitic larvae (Protocalliphora spp.) in nests of Corsican blue tits (Cyanistes caeruleus). We found that ambient temperature during the nestling stage is strongly and positively related to parasite load (number of parasites per chick), both across broods when controlling for year, and across years. In addition, annual mean parasite load also increased with minimal spring temperature, and decreased with increasing average temperature in the previous summer. There was no indication of a dependence of parasite dynamics on host dynamics in this system, likely due in part to the wide host range of blowflies that do not solely rely on blue tit hosts. This suggests a major effect of temperature during the blowfly life cycle, with potential implications for blowfly - host interactions across their geographical range as climate keeps warming up. Finally, given that ambient temperature increases throughout the breeding season and that blowflies negatively affect survival and recruitment of blue tits, these results also mean that parasites, along with caterpillar availability, can drive selection for breeding date in this system.

ecology↗

bioRxiv2018

On the timing of bill length evolution in British great tits: A comment on Bosse et al. 2017.

Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with strikingly rapid phenotypic changes in data series, it remains unpredictable in the long term. Second, while the temporal dynamics of some loci with large effect on phenotypic variation and fitness have been characterized, this task can be complicated in cases of highly polygenic trait architecture implicating numerous small effect size loci, or when statistical tests are sensitive to the heterogeneity of some key characteristics of the genome, like recombination rate variations. After introducing these aforementioned challenges, we discuss a recent investigation of the genomic architecture and spatio-temporal variation in great tit bill length, which was related to the recent use of bird feeders. We discuss how this case study illustrates the importance of considering different temporal scales and evolutionary mechanisms both while analyzing trait temporal trends and when searching for and interpreting the signals of putative genomic footprints of selection. More generally this commentary discusses interesting challenges for unraveling the time scale at which adaptive traits evolve and their genomic bases.\n\nImpact summaryAn important goal in evolutionary biology is to understand how individual traits evolve, leading to fascinating variations in time and space. Long-term field studies have been crucial in trying to understand the timing, extent, and ecological determinants of such trait variation in wild populations. In this context, recent genomic tools can be used to look for the genetic bases underlying such trait variation and can provide clues on the nature and timing of their evolution. However, the analysis and the interpretation of the time scales at which evolution occurs remain challenging. First, analyzing long-term data series can be tricky; short-term changes are highly predictable whereas long-term evolution is much less predictable. A second difficult task is to study the architecture of complex quantitative traits and to decipher the timing and roles of the several genomic mechanisms involved in their evolution. This commentary introduces these challenges and discusses a recent investigation of the nature and timing of ecological and genomic factors responsible for variation in great tit bill length. Overall, we raise cautionary warnings regarding several conceptual and technical features and limitations when coupling analyses of long-term and genomic data to study trait evolution in wild populations.

evolutionary biology↗