Biology subjects

Perrier, C.

Publications and source records attributed to Perrier, C..

18 recordsLinked to original sources

bioRxiv2026

Dispersal, gene flow and adaptive differentiation in hierarchically structured populations

The balance between local adaptation and gene flow is rarely quantified when populations are hierarchically differentiated across multiple spatial scales. We addressed this gap in Atlantic salmon (Salmo salar) at its southern range edge, using 1342 individuals from 21 rivers along the French Atlantic and Channel coasts with a 60k SNP array, and combining estimates of dispersal with genome-wide scans for adaptive differentiation across spatial scales. Population structure was hierarchical, resolving five genetic clusters with differentiation among groups five times higher than among populations within them. Assignment tests revealed a marked contrast between clusters, but unassigned individuals reached very high proportions within some clusters, indicating that gene flow has already blurred among-populations differences. Adaptive differentiation was detected among and within clusters, but the loci involved overlapped only partially across scales and among clusters, indicating that adaptation at each hierarchical level relies on distinct sets of variants. Dispersal was a poor guide to where this signal persisted: retaining putative dispersers reduced the candidate set more than threefold, showing that immigrant genotypes could dilute among-populations allele-frequency contrasts within a single generation. Yet differentiation among populations remained strong, as expected if dispersers reproduce poorly. Resolving the balance between local adaptation and gene flow therefore requires accounting for dispersal and adaptive differentiation at different spatial scales, with direct implications for conserving hierarchically structured populations at climatically vulnerable range edges.

evolutionary biology↗

bioRxiv2026

Genome-Environment Associations reveal shared and unique adaptive loci across multiple pollutants and populations of the eastern mosquitofish Gambusia holbrooki

Rapid adaptation to human-induced stressors is commonplace in the context of global change, including during biological invasions. Identifying the genomic bases and associated biological functions underlying such adaptation is hence crucial to understand and anticipate the response of populations and species to changing conditions. In particular, the extent to which genetic responses to multiple anthropogenic stressors vary between populations in the wild has been relatively unexplored. We addressed this question by leveraging whole-genome sequence data (both PoolSeq and IndSeq) in invasive populations of Gambusia holbrooki - a widespread invasive fish species - collected from 14 locations with different multi-pollutants exposure. We sought to identify adaptive loci associated with pollution tolerance by conducting Genome-Environment Association (GEA) analyses. Additionally, we investigated the degree of adaptive loci reuse between pollutants and their combinations as well as across populations. We found strong signals of association between allele frequency changes and pollutant exposure at several genomic locations, often overlapping with genes known for their functions in detoxification and immune response. We further showed that most adaptive loci are not shared among all populations, suggesting heterogeneous genomic response to each local selection. Interestingly, multiple tests looking for footprints of selection and association to pollutants yielded consistent results. Our results shed new light on the extent of genetic convergence in the genomic bases of rapid adaptation to different cocktails of human-induced pollution, and are important to our understanding of the fate of wild populations facing increasingly complex and stressful environments.

genomics↗

bioRxiv2025

Selection against dispersers: Sex, age and origin-dependent fitness differences in wild Atlantic salmon

Local adaptation is often portrayed as uniform fitness disadvantages of immigrants relative to residents. Yet dispersal costs vary with origin, sex, and life-history traits, shaping the balance between gene flow and adaptation. We quantified these heterogeneous costs by comparing the reproductive success of local and immigrant individuals using a 15-year genetic pedigree of Atlantic salmon (Salmo salar), including over 1,100 adults and 3,400 juveniles. Immigrants represented 19.5% of adults, showed male-biased dispersal, and averaged 15% lower reproductive success than locals. However, outcomes were strongly origin-dependent: immigrants from some populations suffered severe fitness costs while others matched or exceeded locals. Sex and life-history further modulated reproductive success: male immigrants underperformed local males, whereas multi-sea-winter females often equaled or outperformed female residents. Immigrant males partially compensated their fitness offset by acquiring more mates. These findings highlight that, while local adaptation promotes philopatry, immigrants origin effects should be considered in gene-flow adaptation dynamics.

evolutionary biology↗

bioRxiv2025

A major selective sweep likely linked to insecticide resistance identified along altitudinal gradients in the pine processionary moth

Understanding how natural populations adapt to complex environmental gradients is crucial for predicting evolutionary responses to global change. The pine processionary moth (Thaumetopoea pityocampa), a major forest pest expanding northward and upward in Europe, provides an ideal model to explore genomic adaptation along altitudinal and/or latitudinal gradients. We combined pooled and individual whole- genome resequencing of four pairs of low- and high-elevation populations from Spain, Italy and France (mainland and Corsica) to detect signatures of local adaptation. Population structure analyses revealed strong differentiation among distant populations but limited divergence within altitude pairs. Genome scans identified a few candidate regions under selection, and we notably uncovered a large (~1 Mbp) region showing reduced nucleotide diversity, negative Tajima's D, and fixed allele differences between high- and low-altitude populations, consistent with a recent selective sweep. This region includes a cluster of cytochrome P450 genes and the voltage-gated sodium channel gene para, both involved in detoxification and insecticide resistance. Although signatures of selection were observed at this locus in two distant population pairs, no definitive evidence of recent introgression was found between these distant populations, suggesting independent evolution. Altogether, our results do not show clear evidence for altitudinal adaptation in T. pityocampa, but suggest that xenobiotic exposure could exert a strong selective pressure locally. Our study highlights candidate genes and regions for further investigation of resistance evolution in an insect species in the wild.

evolutionary biology↗

bioRxiv2025

Population genomics of incipient allochronic divergence in the Pine Processionary Moth

Allochronic divergence is a key evolutionary mechanism that can frequently lead to incipient speciation. Although theoretical models suggest that such divergence is notably facilitated by small population size and genetic polymorphisms influencing reproductive timing, though constrained by genetic load, empirical validation remains limited. We investigated these predictions by re-analyzing a case of allochronic differentiation between two sympatric populations of pine processionary moth (Thaumetopoea pityocampa) in Portugal, using whole genome resequencing (IndSeq and PoolSeq) of those two populations and eight allopatric ones. We inferred the demographic history of those populations, assessed their genetic load, and searched for genomic regions associated with life cycle differences. Our analyses revealed a recent split between the sympatric allochronic populations, accompanied by a strong reduction in gene flow, bottlenecks, inbreeding, and accumulation of deleterious variants. Genome scans identified several loci associated with life cycle variation, including genes putatively involved in circadian rhythm regulation, predominantly located on the Z chromosome. We discuss how these empirical genomic findings support theoretical expectations that assortative mating driven by differences in reproductive timing, underpinned by polymorphisms in circadian genes, along with genetic drift and purge of genetic load at high-impact sites, can promote the onset and persistence of allochronic divergence.

evolutionary biology↗

bioRxiv2025

A Chromosome-Level Assembly of the Pine Processionary Moth (Thaumetopoea pityocampa) genome

We present a chromosome-level genome assembly and annotation of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae), a key forest pest that is a public health concern. The nuclear genome spans 615.9 Mb, scaffolded into 50 chromosome scale and 115 smaller scaffolds, with high completeness (BUSCO score: 98.9%) that provides a decisive improvement over the previous assembly (537 Mb; 68,292 contigs; BUSCO 83.6%). Coverage differences in resequenced males and females allowed identification of the Z chromosome and several W-linked contigs. As ex-pected from previous studies, we found that synteny was largely conserved with related Lepidoptera, although chromosomal fissions may explain the higher chromosome number of 49 autosomes com-pared to typical lepidopteran karyotypes. We also integrated into the assembly linkage map, allowing estimation of a genome-wide male recombination rate of 5.06 cM/Mb, varying from 11.6 cM/Mb to 1.98 cM/Mb from the smallest to the largest chromosomes. Repetitive elements represented 49.1% of this new assembly, dominated by LINEs (45.1% of classified repeats). Finally, gene prediction identified 12,898 gene models, among which 17 circadian rhythm genes were manually curated. Ex-pert annotation further allowed to identify 51 genes of the odorant receptor (OR) family as well as a total of 236 detoxification genes, including 78 CYPs, 56 CCEs, 30 GSTs, 23 UGTs and 49 ABCs. Overall, this assembly represents the first chromosome-level genome for a member of the Thaume-topoeinae subfamily, significantly expanding the currently limited set of genomic resources avail-able for Notodontidae. The fully annotated assembly is publicly accessible through the LepidoDB database (https://bipaa.genouest.org/is/lepidodb/) and will serve as a valuable resource for research on population genomics of this species.

genomics↗

bioRxiv2025

Avian promiscuity in the last European primeval forest

Primeval forests provide a reference baseline to understand the origins and evolution of mating systems because they offer a unique, undisturbed environment where ecological interactions and natural selection play out in their original context. We established rates of extra-pair paternity (EPP) for two bird species referential to evolutionary ecology: blue tits (Cyanistes caeruleus) and great tits (Parus major), breeding in natural cavities in Biaowie[z]a National Park, the sole remnant of European lowland primeval forests. Genotype-by-sequencing of 889 blue tits and 1,256 great tits revealed that 48% of blue tit broods and 39% great tit broods were of mixed paternity, with 15% blue tit and 14% great tit nestlings not sired by their social father. These referential levels align with median values of EPP reported in nestbox studies in secondary and managed forests, suggesting that certain reproductive strategies are advantageous across diverse environments. Observed promiscuity levels did not affect reproductive success or parental investment, indicating no or limited adaptive value for promiscuity in the context of a primeval forest ecosystem. Our study underscores how primeval habitats provide unparalleled insights into natural selection and mating strategies in wild populations, highlighting the stability and resilience of these strategies across different environmental contexts.

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

Transposable element accumulation drives genome size increase in Hylesia metabus (Lepidoptera: Saturniidae), an urticating moth species from South America

We present the first nuclear genome assembly and a complete mitogenome for Hylesia metabus (Arthropoda; Insecta; Lepidoptera; Saturniidae). The assembled nuclear genome sequence is 1,271 Mb long, which is among the 10 largest lepidopteran genome assemblies published to date. It is scaffolded in 31 pseudo chromosomes, has a BUSCO score of 99.5%, and has a highly conserved synteny compared to phylogenetically close species. Repetitive elements make up 67% of the nuclear genome and are mainly located in intergenic regions, among which LINEs were predominant, with CR1-Zenon being the most abundant. Phylogenetic and comparative analyses of H. metabus assembly and 17 additional Saturniidae and Sphingidae assemblies suggested that an accumulation of repetitive elements likely led to the increased size of H. metabus genome. Gene annotation using Helixer identified 26,122 transcripts. The Z scaffold was identified using both a synteny analysis and variations of coverage for two resequenced male and female H. metabus. The H. metabus nuclear genome and mitogenome assemblies can be found and browsed on the BIPAA website and constitute useful resources for future population and comparative genomics studies.

genomics↗

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↗

bioRxiv2023

The worldwide invasion history of a pest ambrosia beetle inferred using population genomics

Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geographical areas, and did not include Europe. Our first goal was to determine the worldwide genetic structure of this species based on both mitochondrial and genomic markers. Our second goal was to study X. crassiusculus invasion history on a global level and identify the origins of the invasion in Europe. We used a COI and RAD sequencing design to characterize 188 and 206 specimens worldwide, building the most comprehensive genetic dataset for any ambrosia beetle to date. The results were largely consistent between markers. Two differentiated genetic clusters were invasive, albeit in different regions of the world. The two markers were inconsistent only for a few specimens found exclusively in Japan. Mainland USA could have acted as a source for further expansion to Canada and Argentina through stepping-stone expansion and bridgehead events. We showed that Europe was only colonized by Cluster 2 through a complex invasion history including several arrivals from multiple origins in the native area, and possibly including bridgehead from the USA. Our results also suggested that Spain was colonized directly from Italy through intracontinental dispersion. It is unclear whether the mutually exclusive allopatric distribution of the two Clusters is due to neutral effects or due to different ecological requirements.

zoology↗

bioRxiv2021

Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex

Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species populations and their hybridization should be carefully considered while implementing conservation programs.

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↗

bioRxiv2019

Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype

Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) admixture with the closely related anadromous L. fluviatilis ecotype having a positive effect on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled in 81 sites upstream and downstream from barriers to migration, in 29 West-European rivers. Linear modelling revealed a strong positive relationship between the distance to the source and genetic diversity, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal following water flow. Downstream L. planeri populations in sympatry with L. fluviatilis displayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow mainly drive the genetic make up of upstream L. planeri populations whereas admixture between ecotypes maintains higher levels of genetic diversity in L. planeri populations sympatric with L. fluviatilis. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks.

evolutionary biology↗

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↗

bioRxiv2018

Effect of riverscape and exotic introgression on the genetic structure and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

evolutionary biology↗

bioRxiv2018

RAD-sequencing for estimating GRM-based heritability in the wild: a case study in roe deer

Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree-free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long-term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD-sequencing for estimating heritability in a free-ranging roe deer population for which no prior genomic resources were available. We propose a step-by-step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the SNP calling and filtering processes on the GRM structure and GRM-based heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7000). GRM-based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP dataset. We also showed that quality filters, such as the removal of low-frequency variants, affect the relatedness structure of the GRM, generating lower h2 estimates. Our work illustrates the huge potential of RAD-sequencing for estimating GRM-based heritability in virtually any natural population.

genomics↗

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↗