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For any question about this dataset please contact Laurent Boualit at laurent.boualit(at)protonmail.com The dataset is under a CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/) The data were collected during a PhD work at University of Lausanne directed by Dr Nathalie Chèvre, co-supervised by Dr Hugo Cayuela. Laurent Boualit was the PhD candidate. The dataset contains the results of 2 projects, The Amphibian Short Term Assay and the Amphibian Chronic Assay. ##################################################################################### # The Amphibian Short Term Assay # ##################################################################################### In the first project, we develop a new ecotoxicological method for assessing neurotoxicity of organophosphate pesticides on early stages in Xenopus laevis. The two pesticides were tested in this project were the Diazinon and the Chlorpyrifos. The exposure scenario and the biochemical, morphometrical, life history and behavioral measurements are described in the following open-access articles: Boualit, L., Cayuela, H., Cattin, L., & Chèvre, N. (2022). The Amphibian Short‐Term Assay: Evaluation of a New Ecotoxicological Method for Amphibians Using Two Organophosphate Pesticides Commonly Found in Nature—Assessment of Biochemical, Morphological, and Life‐History Traits. Environmental Toxicology and Chemistry, 41(11), 2688-2699. The dataset regarding this project is made of two files, and each file correspond to a tested pesticide, Tad_vs_DZN.xlsx for the diazinon and Tad_vs_CPF.xlsx for the chlorpyrifos. Additionally, the repository contains a Read_Me.txt file containing the very same information you are reading, a "boite_lumineuse.STEP file containing a 3D-model of the item conceived for the behavioral test and a tracking_app.py file containing the Python code that was used to track larvae trajectories. ########## Tad_vs_DZN.xls - DIAZINON ########## The cells containing the value "dead" means that the individual was dead at the date of the trait measurement The cells containing the value "cont." means that there was a handling error during the plate wells filling during the biochemical measurement. Here is the convention for the column names in the Tad_vs_DZN.xls file : "name" contains the unique names of each individual composed of three indications ------- the dejellying condition (D for dejellied and ND for non-dejellied) | | ------- the exposure condition (CTL for the control condition, C1 to C5 for the DZN concentration ordered by the lowest to the highest) | | ------- the number randomly assign to the tadpole (from 1 to 10) "jell" contains the dejellying condition (D for dejellied and ND for non-dejellied) "conc" contains the exposure condition (CTL for the control condition, C1 to C5 for the DZN concentration ordered by the lowest to the highest) "conc_num" contains the mean pesticides concentration actually measured in individual 250 mL plastic containers (3 samples per concentration at H0 and H24) "AChE_activity" contains the acetylcholinesterase activity in nmol/min/mg protein "EROD_activity" contains the ethoxyresorufin‐O‐deethylase activity in nmol/min/mg protein "GST_activity" contains the glutathione‐S‐transferase activity in nmol/min/mg protein "duration_activity_period_Day6" contains the total time the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 6. The value is in seconds "nb_activity_period_Day6" contains the number of periods the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 6. The value is in periods "mean_speed_Day6" contains the larva swimming mean speed during behavioral test at day 6. The value is in centimeter per second "mean_speed_change_Day6" contains the larva swimming mean speed change during behavioral test at day 6. The value is in centimeter per squared second "mean_DC_Day6" contains the larva swimming direction change during behavioral test at day 6. The value is in degree per second "mean_SD_DC_Day6" contains the larva swimming direction change standard deviation during behavioral test at day 6. The value is in degree per second "well_Day6" contain the well position in the recording item where larva was placed for the test at day 6. No unit. "duration_activity_period_Day7" contains the total time the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 7. The value is in seconds "nb_activity_period_Day7" contains the number of periods the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 7. The value is in periods "mean_speed_Day7" contains the larva swimming mean speed during behavioral test at day 7. The value is in centimeter per second "mean_speed_change_Day7" contains the larva swimming mean speed change during behavioral test at day 7. The value is in centimeter per squared second "mean_DC_Day7" contains the larva swimming direction change during behavioral test at day 7. The value is in degree per second "mean_SD_DC_Day7" contains the larva swimming direction change standard deviation during behavioral test at day 7. The value is in degree per second "well_Day7" contain the well position in the recording item where larva was placed for the test at day 7. No unit. "duration_activity_period_Day8" contains the total time the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 8. The value is in seconds "nb_activity_period_Day8" contains the number of periods the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 8. The value is in periods "mean_speed_Day8" contains the larva swimming mean speed during behavioral test at day 8. The value is in centimeter per second "mean_speed_change_Day8" contains the larva swimming mean speed change during behavioral test at day 8. The value is in centimeter per squared second "mean_DC_Day8" contains the larva swimming direction change during behavioral test at day 8. The value is in degree per second "mean_SD_DC_Day8" contains the larva swimming direction change standard deviation during behavioral test at day 8. The value is in degree per second "well_day8" contain the well position in the recording item where larva was placed for the test at day 8. No unit. ########## Tad_vs_CPF - CHLORPYRIFOS ########## Here is the convention for the column names in the Tad_vs_CPF.xls file: "name" contains the unique names of each individual composed of three indications ------- the dejellying condition (D for dejellied and ND for non-dejellied) | | ------- the exposure condition (CTL for the control condition, DMSO for the solvent control and C1 to C4 for the CPF concentration ordered by the lowest to the highest) | | ------- the number randomly assign to the tadpole (from 1 to 10) "jell" contains the dejellying condition (D for dejellied and ND for non-dejellied) "conc" contains the exposure condition (CTL for the control condition, C1 to C5 for the DZN concentration ordered by the lowest to the highest) "conc_num" contains the mean pesticides concentration actually measured in individual 250 mL plastic containers (3 samples per concentration at H0 and H24) "AChE_activity" contains the acetylcholinesterase activity in nmol/min/mg protein "EROD_activity" contains the ethoxyresorufin‐O‐deethylase activity in nmol/min/mg protein "GST_activity" contains the glutathione‐S‐transferase activity in nmol/min/mg protein "STL_emb" contains the embryo snout-to-tail length at day 4. The value is in mm "SVL_emb" contains the embryo snout-to-vent length at day 4. The value is in mm "Muscle" contains the embryo tail muscle width at day 4. The value is in mm "Fin" contains the embryo fin width at day 4. The value is in mm "STL_Tad" contains the larva snout-to-tail length width at day 8. The value is in mm "SVL_Tad" contains the larva snout-to-vent length width at day 8. The value is in mm "STL_SVL_emb" contains the embryo snout-to-tail/snout-to-vent lengths ratio at day 4. No unit "ratio tail" contains the embryo fin width/tail muscle widths ratio at day 4. No unit "STL_SVL_tad" contains the larva snout-to-tail/snout-to-vent lengths ratio width at day 8. No unit "GR" contains the day 4 to day 8 growth ratio. No unit "duration_activity_period_Day6" contains the total time the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 6. The value is in seconds "nb_activity_period_Day6" contains the number of periods the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 6. The value is in periods "mean_speed_Day6" contains the larva swimming mean speed during behavioral test at day 6. The value is in centimeter per second "mean_speed_change_Day6" contains the larva swimming mean speed change during behavioral test at day 6. The value is in centimeter per squared second "mean_DC_Day6" contains the larva swimming direction change during behavioral test at day 6. The value is in degree per second "mean_SD_DC_Day6" contains the larva swimming direction change standard deviation during behavioral test at day 6. The value is in degree per second "well_Day6" contain the well position in the recording item where larva was placed for the test at day 6. No unit. "duration_activity_period_Day7" contains the total time the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 7. The value is in seconds "nb_activity_period_Day7" contains the number of periods the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 7. The value is in periods "mean_speed_Day7" contains the larva swimming mean speed during behavioral test at day 7. The value is in centimeter per second "mean_speed_change_Day7" contains the larva swimming mean speed change during behavioral test at day 7. The value is in centimeter per squared second "mean_DC_Day7" contains the larva swimming direction change during behavioral test at day 7. The value is in degree per second "mean_SD_DC_Day7" contains the larva swimming direction change standard deviation during behavioral test at day 7. The value is in degree per second "well_Day7" contain the well position in the recording item where larva was placed for the test at day 7. No unit. "duration_activity_period_Day8" contains the total time the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 8. The value is in seconds "nb_activity_period_Day8" contains the number of periods the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 8. The value is in periods "mean_speed_Day8" contains the larva swimming mean speed during behavioral test at day 8. The value is in centimeter per second "mean_speed_change_Day8" contains the larva swimming mean speed change during behavioral test at day 8. The value is in centimeter per squared second "mean_DC_Day8" contains the larva swimming direction change during behavioral test at day 8. The value is in degree per second "mean_SD_DC_Day8" contains the larva swimming direction change standard deviation during behavioral test at day 8. The value is in degree per second "well_day8" contain the well position in the recording item where larva was placed for the test at day 8. No unit. ##################################################################################### # The Amphibian Short Term Assay # ##################################################################################### In this last project, we aimed at testing the neurotoxicity of Diazinon on X. laevis behavior all along the metamorphosis. Unfortunately, numerous larvae from all exposure conditions demonstrated scoliosis forcing us to stop the experiment after 44 days. Nevertheless, we we obtained behavioral data on larvae at days 6, 7, 8 and 16. The exposure scenario and the behavioral measurements are described in the following open-access Ph.D. thesis available at: The cells containing the value "dead" means that the individual was dead at the date of the trait measurement Here is the convention for the column names in the Tad_vs_DZN.xls file : "name" contains the unique names of each individual composed of three indications ------- the dejellying condition (D for dejellied and ND for non-dejellied) | | ------- the number randomly assign to the tadpole (from 1 to 10) "conc" contains the exposure condition (CTL for the control condition, C1 to C5 for the DZN concentration ordered by the lowest to the highest) "conc_num" contains the mean pesticides concentration actually measured in individual 250 mL plastic containers (3 samples per concentration at H0 and H24) "duration_activity_period_Day6" contains the total time the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 6. The value is in seconds "nb_activity_period_Day6" contains the number of periods the larva was swimming at a speed higher than 0 cm/sec during behavioral test at day 6. The value is in periods "mean_speed_Day6" contains the larva swimming mean speed during behavioral test at day 6. The value is in centimeter per second "mean_speed_change_Day6" contains the larva swimming mean speed change during behavioral test at day 6. The value is in centimeter per squared second "mean_DC_Day6" contains the larva swimming direction change during behavioral test at day 6. The value is in degree per second "mean_SD_DC_Day6" contains the larva swimming direction change standard deviation during behavioral test at day 6. The value is in degree per second "well_Day6" contain the well position in the recording item where larva was placed for the test at day 6. No unit. "duration_activity_period_Day7" con

Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g., lifespan, reproduction) are still scarce, likely due to the recent application of methylome resequencing methods to non-model species. In this study, we examined associations between whole genome DNA methylation and environmentally driven life history variation in 2 lineages of a marine fish, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbor 2 contrasting life history tactics (demersal vs. beach-spawning). Performing whole genome and methylome sequencing, we showed that life history tactics are associated with epigenetic changes in both lineages, though the effect was stronger in European capelin. Genetic differentiation between the capelin harboring different life history tactics was negligible, but we found genome-wide methylation changes in both lineages. We identified 9,125 European and 199 North American differentially methylated regions (DMRs) due to life history. Gene ontology (GO) enrichment analysis for both lineages revealed an excess of terms related to neural function. Our results suggest that environmental variation causes important epigenetic changes that are associated with contrasting life history tactics in lineages with divergent genetic backgrounds, with variable importance of genetic variation in driving epigenetic variation. Our study emphasizes the potential role of genome-wide epigenetic variation in adaptation to environmental variation.

Habitat anthropization is a major driver of global biodiversity decline. Although most species are negatively affected, some benefit from anthropogenic habitat modifications by showing intriguing life-history responses. For instance, increased recruitment through higher allocation to reproduction or improved performance during early-life stages could compensate for reduced adult survival, corresponding to “compensatory recruitment”. To date, evidence of compensatory recruitment in response to habitat modification is restricted to plants, limiting understanding of its importance as a response to global change. We used the yellow-bellied toad ( Bombina variegata ), an amphibian occupying a broad range of natural and anthropogenic habitats, as a model species to test for and to quantify compensatory recruitment. Using an exceptional capture–recapture dataset composed of 21,714 individuals from 67 populations across Europe, we showed that adult survival was lower, lifespan was shorter, and actuarial senescence was higher in anthropogenic habitats, especially those affected by intense human activities. Increased recruitment in anthropogenic habitats fully offset reductions in adult survival, with the consequence that population growth rate in both habitat types was similar. Our findings indicate that compensatory recruitment allows toad populations to remain viable in human-dominated habitats and might facilitate the persistence of other animal populations in such environments.

Actuarial senescence, the increase in adult mortality risk with increasing age, is a widespread phenomenon across the animal kingdom. Although between-species variation in the rate of increase in mortality as organisms age (i.e. ageing rate) is now well documented, the occurrence of variation in ageing rate within a given species remains much more debatable. We evaluated the level of within-species variation in ageing rate in four populations of the southern Darwin’s frog (Rhinoderma darwinii) from Chile. Our results revealed strong among-population variation in ageing rates, and these were correlated with the population-specific generation time. A higher ageing rate occurred in populations where individuals exhibited a faster pace of life. Our results, along with recent studies in evolutionarily distant amphibian species, indicate that there can be substantial within-species variation in the rate of ageing, highlighting amphibians as emerging models to study the patterns and mechanisms of intraspecific variation in ageing rate.

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4,190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA. As typical for most marine species, we observed a weak, albeit highly significant genetic structure. We also found that adaptive genetic variation allows detecting fine-scale population structure not resolved by neutral genetic variation alone. Using the recent genome assembly of the American lobster, we were able to map and annotate several SNPs located in functional genes potentially implicated in adaptive processes such as thermal stress response, salinity tolerance and growth metabolism pathways. Taken together, our study indicates that weak population structure in high gene flow systems can be resolved at various spatial scales, and that putatively adaptive genetic variation can substantially enhance the delineation of biological management units of marine exploited species.

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.

Evolutionary theories relating to aging predict that patterns of actuarial and reproductive senescence should be aligned, with a common onset of senescence set at the age of first reproduction. However, a few empirical studies reported asynchrony between actuarial and reproductive senescence. This asynchrony is expected to be particularly pronounced in organisms with indeterminate growth. Yet, this process is still poorly documented due to the lack of long-term demographic data on known-aged individuals. We investigated the asynchrony of actuarial and reproductive senescence in the European whip snake, Hierophis viridiflavus, an oviparous colubrid with indeterminate growth. Using demographic data collected over a 29-year period, we showed that females did not experience any fecundity loss late in life. In contrast, they suffered from an early, severe actuarial senescence. Our findings thus revealed a pronounced asynchrony in actuarial and reproductive senescence processes, a phenomenon that could be widespread across the tree of life.

Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced-representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (Homarus americanus) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs accounts for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic-environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in non-model species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.

Amphibia is the most threatened class among vertebrates, with40% of the species threatened with extinction. Pollution is thought to alter amphibian population dynamics. With the growing interest in behavioral ecotoxicology, the neurotoxic organophosphate pesticides are of special concern. Understanding how exposure to neurotoxics leads to behavioral alterations is of crucial importance, and mechanistic endpoints should be included in ecotoxicological methods. In the present study, we tested an 8-day assay to evaluate the toxicity of two organophosphates, diazinon and chlorpyrifos, on Xenopus laevis, that is, on biochemical, morphological, and life-history traits related to locomotion capacities. The method involves measuring biomarkers such as glutathione-S-transferase (GST) and ethoxyresorufin-O-deethylase (EROD; two indicators of the detoxifying system) in the 8-day-old larvae as well as acetylcholinesterase (AChE) activity (involved in the nervous system) in 4-day-old embryos and 8-day-old larvae. Snout-to-vent length and snout-to-tail length of 4-day-old embryos and 8-day larvae were recorded as well as the corresponding growth rate. Fin and tail muscle widths were measured as well for testing changes in tail shape. Both tests showed effects of both organophosphates on AChE activity; however, no changes were observed in GST and EROD. Furthermore, exposure to chlorpyrifos demonstrated impacts on morphological and life-history traits, presaging alteration of locomotor traits. In addition, the results suggest a lower sensitivity to chlorpyrifos of 4-day-old embryos compared to 8-day-old larvae. Tests on other organophosphates are needed to test the validity of this method for the whole organophosphate group. Environ Toxicol Chem 2022;41:2688-2699. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Human activities and resource exploitation led to a massive decline of wild salmonid populations, consequently, numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Sequencing of hatchery and wild-born adult Coho salmon (Oncorhynchus kisutch) originating from two previously studied river systems, we show that early-life hatchery-rearing environment-induced significant and parallel gene expression differentiation is maintained until Coho come back to their natal river for reproduction. A total of 3,643 genes differentially expressed and 859 coexpressed genes were downregulated in parallel in hatchery-born fish from both rivers relative to their wild congeners. Among those genes, 26 displayed a significant relationship between gene expression and the median gene body methylation and 669 single CpGs displayed a significant correlation between methylation level and the associated gene expression. The link between methylation and gene expression was weak suggesting that DNA methylation is not the only player in mediating hatchery-related expression differences. Yet, significant gene expression differentiation was observed despite 18 months spent in a common environment (i.e., the sea). Finally, the differentiation is observed in parallel in two different river systems, highlighting the fact that early-life environment may account for at least some of the reduced fitness of the hatchery salmon in the wild. These results illustrate the relevance and importance of considering both epigenome and transcriptome to evaluate the costs and benefits of large-scale supplementation programs.

Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. Here, we examined how genotype determines the TGP of phenotypic traits related to dispersal, a fundamental process in ecology and evolution. We used an experimental approach in Tetrahymena thermophila, a ciliate model-species, to determine if and how phenotypic changes expressed following a dispersal treatment are inherited over multiple generations. Our results show that morphological and movement traits associated with dispersal are plastic, and that these modifications are inherited over at least 35 generations. The fitness costs and benefits associated with these plastic changes are also transmitted to further generations. We highlight that the genotype modulates the expression and reversibility of transgenerational plasticity of dispersal-related traits and its fitness outcomes. Our study thus suggests that genotype-dependent TGP could play an important role in eco-evolutionary dynamics as dispersal determines gene flow and the long-term persistence of natural populations.

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determinationsystems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due toan apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females)systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY andZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sexdifferences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and notlifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but agingrates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome systemon sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleteriousmutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat-rich Y/W chromosome (the “toxic Y/W effect”) couldaccelerate aging in the heterogametic sex in some vertebrate clades., C was supported asa postdoctoral researcher by the Vanier-Banting postdoctoral fellowship program and the Swiss National Science Foundation (SNF grant number 31003A_182265).

International audience; Variation in temperature is known to influence mortality patterns in ectotherms. Even though a few experimental studies on model organisms have reported a positive relationship between temperature and actuarial senescence (i.e., the increase in mortality risk with age), how variation in climate influences the senescence rate across the range of a species is still poorly understood in free-ranging animals. We filled this knowledge gap by investigating the relationships linking senescence rate, adult lifespan, and climatic conditions using long-term capture–recapture data from multiple amphibian populations. We considered two pairs of related anuran species from the Ranidae ( Rana luteiventris and Rana temporaria ) and Bufonidae ( Anaxyrus boreas and Bufo bufo ) families, which diverged more than 100 Mya and are broadly distributed in North America and Europe. Senescence rates were positively associated with mean annual temperature in all species. In addition, lifespan was negatively correlated with mean annual temperature in all species except A. boreas . In both R. luteiventris and A. boreas , mean annual precipitation and human environmental footprint both had negligible effects on senescence rates or lifespans. Overall, our findings demonstrate the critical influence of thermal conditions on mortality patterns across anuran species from temperate regions. In the current context of further global temperature increases predicted by Intergovernmental Panel on Climate Change scenarios, a widespread acceleration of aging in amphibians is expected to occur in the decades to come, which might threaten even more seriously the viability of populations and exacerbate global decline.

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range, and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed flyCoelopa frigidaalong a bioclimatic gradient stretching across 10° of latitude, a salinity gradient and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyse 1,446 low-coverage whole genomes collected along those gradients. We found several large non-recombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.

Kin selection and dispersal play a critical role in the evolution of cooperative breeding systems. Limited dispersal dramatically increases relatedness in spatially structured populations (population viscosity), with the result that neighbours tend to be genealogical relatives. Yet the increase in neighbours’ performance through altruistic interaction may also result in habitat saturation and thus exacerbate local competition between kin. Our goal was to detect the footprint of kin selection and competition by examining the spatial structure of relatedness and by comparing non-effective and effective dispersal in a population of a lekking bird,Tetrao urogallus. For this purpose, we analysed capture–recapture and genetic data collected over a 6-year period on a spatially structured population ofT. urogallusin France. Our findings revealed a strong spatial structure of relatedness in males. They also indicated that the population viscosity allowed male cooperation through two non-exclusive mechanisms. First, at their first lek attendance, males aggregate in a lek composed of relatives. Second, the distance corresponding to non-effective dispersal dramatically outweighed effective dispersal distance, which suggests that dispersers incur high post-settlement costs. These two mechanisms result in strong population genetic structuring in males. In females, our findings revealed a lower level of spatial structure of relatedness and genetic structure in respect to males. Additionally, non-effective dispersal and effective dispersal distances in females were highly similar, which suggests limited post-settlement costs. These results indicate that kin-dependent dispersal decisions and costs are factors driving the evolution of cooperative courtship and have a genetic footprint in wild populations.

Life‐history theory states that, during the lifetime of an individual, resources are allocated to either somatic maintenance or reproduction. Resource allocation tradeoffs determine the evolution and ecology of life‐history strategies and determine an organisms’ position along the fast–slow continuum. Theory predicts that environmental stochasticity is an important driver of resource allocation and therefore life‐history evolution. Highly stochastic environments are expected to increase uncertainty in reproductive success and select for iteroparity and a slowing down of the life history. To date, most empirical studies have used comparisons among species to examine these theoretical predictions. By contrast, few have investigated how environmental stochasticity affects life‐history strategies at the intraspecific level. In this study, we examined how variation in breeding site stochasticity (among‐year variability in pond volume and hydroperiod) promotes the co‐occurrence of different life‐history strategies in a spatially structured population, and determines life‐history position along the fast–slow continuum in the yellow‐bellied toad Bombina variegata. We collected mark–recapture data from a metapopulation and used multievent capture–recapture models to estimate survival, recruitment and breeding probabilities. We found higher survival and longer lifespans in populations inhabiting variable sites compared to those breeding in stable ones. In addition, probabilities of recruitment and skipping a breeding event were higher in variable sites. The temporal variance of survival and recruitment probabilities, as well as the probability to skip breeding, was higher in variable sites. Taken together, these findings indicate that populations breeding in variable sites experienced a slowing down of the life‐history. Our study thus revealed similarities in the macroevolutionary and microevolutionary processes shaping life‐history evolution.

Dispersal is a central mechanism in ecology and evolution. Dispersal evolution is driven by a trade-off between costs and benefits, which is influenced by inter-individual variability and local environmental conditions (context-dependent dispersal). Many studies have investigated how dispersal decisions may be influenced by environmental factors, including density, predation, and interspecific competition. Yet few have attempted to examine how habitat disturbance may affect the dispersal process in spatially structured populations. In early successional species, one might expect individuals to adjust their dispersal decisions based on two main factors that potentially have an influence on reproductive success: patch size and the level of patch disturbance. In this study, we examined how these two factors affect breeding success and dispersal decisions in an early successional amphibian, the yellow-bellied toad (Bombina variegata). To this end, we used capture–recapture data collected on a spatially structured population occupying 28 breeding patches. We took advantage of recent developments in multievent capture–recapture models to detect signs of context-dependent dispersal. The results revealed that the probability of successful reproduction and the number of newly metamorphosed individuals increased with both the size and the proportion of disturbance of a patch. In addition, our results showed that the factors affecting breeding success also influenced breeding dispersal probability. Large patch size negatively influenced emigration probability; in contrast, it positively influenced immigration probability. Equally, higher disturbance (in terms of the proportion of the patch’s surface area disturbed each year) had a strong negative influence on emigration probability and slightly positively affected immigration probability. These findings strongly suggest that individuals make context-dependent dispersal decisions, adjusted to maximize future fitness prospects in a patch, allowing them to better cope with rapid changes in environmental conditions resulting from the ecological succession process. This opens new areas of potential research into the role of dispersal in organism specialization along an ecological succession gradient.

Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance and direction, these individual-level decisions further modulate the demography, relatedness and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a great crested newt (Triturus cristatus) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across an SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.

Temperature is a critical driver of ectotherm life-history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life-history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) can help uncover the molecular mechanisms of temperature-driven variation in growth, longevity and senescence. However, our understanding of these mechanisms is still limited, which reduces our ability to predict the response of non-model ectotherms to global temperature change. In this study, we examined the potential role of thermal adaptation in clinal shifts of life-history traits (i.e. life span, senescence rate and recruitment) in the Columbia spotted frog Rana luteiventris along a broad temperature gradient in the western United States. We took advantage of extensive capture-recapture datasets of 20,033 marked individuals from eight populations surveyed annually for 14-18 years to examine how mean annual temperature and precipitation influenced demographic parameters (i.e. adult survival, life span, senescence rate, recruitment and population growth). After showing that temperature was the main climatic predictor influencing demography, we used RAD-seq data (50,829 SNPs and 6,599 putative CNVs) generated for 352 individuals from 31 breeding sites to identify the genomic signatures of thermal adaptation. Our results showed that temperature was negatively associated with annual adult survival and reproductive life span and positively associated with senescence rate. By contrast, recruitment increased with temperature, promoting the long-term viability of most populations. These temperature-dependent demographic changes were associated with strong genomic signatures of thermal adaptation. We identified 148 SNP candidates associated with temperature including three SNPs located within protein-coding genes regulating resistance to cold and hypoxia, immunity and reproduction in ranids. We also identified 39 CNV candidates (including within 38 transposable elements) for which normalized read depth was associated with temperature. Our study indicates that both SNPs and structural variants are associated with temperature and could eventually be found to play a functional role in clinal shifts in senescence rate and life-history strategies in R. luteiventris. These results highlight the potential role of different sources of molecular variation in the response of ectotherms to environmental temperature variation in the context of global warming.

The interplay between recombination rate, genetic drift and selection modulates variation in genome-wide ancestry. Understanding the selective processes at play is of prime importance toward predicting potential beneficial or negative effects of supplementation with domestic strains (i.e., human-introduced strains). In a system of lacustrine populations supplemented with a single domestic strain, we documented how population genetic diversity and stocking intensity produced lake-specific patterns of domestic ancestry by taking the species’ local recombination rate into consideration. We used 552 Brook Charr (Salvelinus fontinalis) from 22 small lacustrine populations, genotyped at ~32,400 mapped SNPs. We observed highly variable patterns of domestic ancestry between each of the 22 populations without any consistency in introgression patterns of the domestic ancestry. Our results suggest that such lake-specific ancestry patterns were mainly due to variable associative overdominance (AOD) effects among populations (i.e., potential positive effects due to the masking of possible deleterious alleles in low recombining regions). Signatures of AOD effects were also emphasized by highly variable patterns of genetic diversity among and within lakes, potentially driven by predominant genetic drift in those small isolated populations. Local negative effects such as negative epistasis (i.e., potential genetic incompatibilities between the native and the introduced population) potentially reflecting precursory signs of outbreeding depression were also observed at a chromosomal scale. Consequently, in order to improve conservation practices and management strategies, it became necessary to assess the consequences of supplementation at the population level by taking into account both genetic diversity and stocking intensity when available.

Aim When modelling future or past geographic distributions of a species, attention should be paid to the possible differentiated responses to climate changes between lineages. Dispersal also plays an important role in the capacity of species to track suitable climate, which is particularly relevant for amphibians with limited dispersal ability. In this study, we included different lineages and dispersal distances into species distribution models to make them more biologically relevant in face of climate change scenarios. Location Europe. Taxa Bombina variegata and its lineages. Methods Using MaxEnt, we fitted correlative niche models for B. variegata lineages and also for the species level (B. variegata sensu lato) that we projected under Last Glacial Maximum (LGM) and future climate scenarios (RCP2.6, RCP8.5). A comparison of projections was conducted considering both unlimited and limited dispersal abilities. Results We found that the B. variegata lineages differed in their bioclimatic niches. In general, models run without discriminating the lineages showed reduced suitable areas compared to models run at each lineage, especially those for B. variegata pachypus and B. variegata scabra (southern lineages). Suitable areas identified for the LGM match with the climatic refugia identified in phylogeographic studies. Projections for the mid‐Holocene showed the increase of suitable areas for the lineages B. variegata variegata “Carpathians” and “Western” while they decreased for the southern lineages. In the future (2040–2080), only models under limited dispersal predict the extinction of the Carpathian lineage and a reduction in suitable areas for the other lineages, regardless of periods and scenarios. Main conclusions We demonstrated important shifts in habitat suitability in Europe suggesting range‐shifts about hundreds of kilometres in response to past climate changes. However, rapid and unprecedented changes in suitability are expected in the future due to the accelerated climate warming during the 21st. According to their limited dispersal abilities, the persistence of all B. variegata lineages over time appears uncertain. We further recommend to integrate the intraspecific levels, when available, in modelling process to catch local variations and obtain more accurate results.

The molecular mechanisms underlying intraspecific variation in life history strategies are still poorly understood, despite the importance of this question for understanding of organism’s responses to environmental variability. Theoretical work proposed that epigenetic mechanisms such as DNA methylation might regulate intraspecific variation in life history strategies, however this assumption has rarely been verified empirically in wild populations. We examined associations between genome-wide methylation changes and environmentally-driven life history variation in two lineages of a marine fish that diverged approximatively 2.5 Mya, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbour two contrasted life history strategies: some are strictly semelparous, experience fast actuarial senescence, but benefit from high hatching success by spawning on demersal sites where water temperature is low and relatively stable. In contrast, others are facultative iteroparous, have slower actuarial senescence, and suffer from lower hatching success by breeding in the intertidal zone where temperature is warmer, thermohaline parameters are less stable, and egg desiccation risk is high. Performing whole genome and epigenome sequencing, we showed that these contrasted life history strategies are more likely governed by epigenetic changes than by differences in DNA sequence. While genetic differentiation between the capelin harbouring different life history strategies was negligible, we detected parallel genome-wide methylation changes across lineages. We identified 1,067 differentially methylated regions (DMRs) comprising 15,818 CpGs, with 22% of them located within 5-kb around genes comprising promotor regions. We found that all DMRs were hypermethylated in demersal-spawning individuals. This striking result suggests that lower water temperature at demersal sites leads to an overall hypermethylation of the genome determined during the epigenetic reprogramming occurring over embryonic development. Our study emphasizes that parallel epigenetics changes in lineages with divergent genetic background could have a functional role in the regulation of intraspecific life history variation.

When facing an emerging infectious disease of conservation concern, we often have little information on the nature of the host-parasite interaction to inform management decisions. However, it is becoming increasingly clear that the life-history strategies of host species can be predictive of individual- and population-level responses to infectious disease, even without detailed knowledge on the specifics of the host-parasite interaction. Here, we argue that a deeper integration of life-history theory into disease ecology is timely and necessary to improve our capacity to understand, predict and mitigate the impact of endemic and emerging infectious diseases in wild populations. Using wild vertebrates as an example, we show that host life-history characteristics influence host responses to parasitism at different levels of organisation, from individuals to communities. We also highlight knowledge gaps and future directions for the study of life-history and host responses to parasitism. We conclude by illustrating how this theoretical insight can inform the monitoring and control of infectious diseases in wildlife.

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic region and transposable elements (TEs) may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be important drivers of population genetic structure, whose study is generally restricted to the use of SNPs. Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local thermal conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene amplification. We also identified 175 CNVs associated with the divergence of three parapatric glacial lineages, of which 24% were located within protein-coding genes, which might contribute to genetic incompatibilities and ultimately, reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, that was very different from that inferred based on SNPs in a previous study. Our findings underscore the complementarity of those two types of markers in population genomics studies.

Patterns of actuarial senescence can be highly variable among species. Previous comparative analyses revealed that both age at the onset of senescence and rates of senescence are linked to position of a species along the fast–slow life‐history continuum. As there are few long‐term datasets of wild populations with known‐age individuals, intraspecific (i.e. between‐population) variation in senescence is understudied and limited to comparisons of wild and captive populations of the same species, mostly birds and mammals. In this paper, we examined how population position along the fast–slow life‐history continuum affects intraspecific variation in senescence in an amphibian, Bombina variegata. We used capture–recapture data collected in four populations with contrasting life‐history strategies. Senescence trajectories were analysed using Bayesian capture–recapture models. We show that in populations with fast life histories the onset of actuarial senescence was earlier and individuals aged at a faster rate than individuals in populations with slow life histories. Our study provides one of the few empirical examples of among‐population variation in actuarial senescence patterns in the wild and confirms that the fast–slow life‐history gradient is associated with both macroevolutionary and microevolutionary patterns of actuarial senescence.

International audience; There is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human‐driven variation in patch persistence affects dispersal rates and distances, determines dispersal‐related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture–recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e., several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e., a few years), created by logging operations in intensively harvested woodland. Our capture–recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intrapatch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long‐term viability and genetic structure of wild populations.

Dispersal is a central process in ecology and evolution. It strongly influences the dynamics of spatially structured populations and affects evolutionary processes by shaping patterns of gene flow. For these reasons, dispersal has received considerable attention from ecologists, evolutionary biologists, and conservationists. Although it has been studied extensively in taxa such as birds and mammals, much less is known about dispersal in vertebrates with complex life cycles such as pond-breeding amphibians. Over the past two decades, researchers have taken an ever-increasing interest in amphibian dispersal and initiated both basic and applied studies, using a broad range of experimental and observational approaches. This body of research reveals complex dispersal patterns, causations, and syndromes, with dramatic consequences for the demography and genetics of amphibian populations. In this review, our goals are to: redefine and clarify the concept of amphibian dispersal; review current knowledge about the effects of individual (i.e., condition-dependent dispersal) and environmental (i.e., context-dependent dispersal) factors during the three stages of dispersal (i.e., emigration, transience, and immigration); identify the demographic and genetic consequences of dispersal in spatially structured amphibian populations; and propose new research avenues to extend our understanding of amphibian dispersal., Hugo Cayuela warmly thanks the Banting Postdoctoral Fellowships program for its financial support. Further-more, Mathieu Denoël is Research Director at Fonds dela Recherche Scientifique—FNRS. During manuscript writing, Andrés Valenzuela-Sánchez was supported bya FONDECYT de postdoctorado No. 3180107. Any useof trade, firm, and product names is for descriptive purposes only and does not imply endorsement by the U.S.Government. Íñigo Martínez-Solano acknowledges funding by FEDER/Ministerio de Ciencia, Innovación y Universidades—Agencia Estatal de Investigación, Spain,grant CGL2017-83131-P.

Understanding the mechanisms underlying population decline is a critical challenge for conservation biologists. Both deterministic (e.g. habitat loss, fragmentation, and Allee effect) and stochastic (i.e. demographic and environmental stochasticity) demographic processes are involved in population decline. Simultaneously, a decrease of population size has far-reaching consequences for genetics of populations by increasing the risk of inbreeding and the strength of genetic drift, which together inevitably results in a loss of genetic diversity and a reduced effective population size ( $$N_{{\text{e}}}$$ ). These genetic factors may retroactively affect vital rates (a phenomenon coined ‘inbreeding depression’), reduce population growth, and accelerate demographic decline. To date, most studies that have examined the demographic and genetic processes driving the decline of wild populations have neglected their spatial structure. In this study, we examined demographic and genetic factors involved in the decline of a spatially structured population of a lekking bird, the western capercaillie (Tetrao urogallus). To address this issue, we collected capture-recapture and genetic data over a 6-years period in the Vosges Mountains (France). Our study showed that the population of T. urogallus experienced a severe decline between 2010 and 2015. We did not detect any Allee effect on survival and recruitment. By contrast, individuals of both sexes dispersed to avoid small subpopulations, thus suggesting a potential behavioral response to a mate finding Allee effect. In parallel to this demographic decline, the population showed low levels of genetic diversity, high inbreeding and low effective population sizes at both subpopulation and population levels. Despite this, we did not detect evidence of inbreeding depression: neither adult survival nor recruitment were affected by individual inbreeding level. Our study underlines the benefit from combining demographic and genetic approaches to investigate processes that are involved in population decline.

International audience; Dispersal is a central process in ecology and evolution. At the individual level, the three stages of the dispersal process (i.e., emigration, transience and immigration) are affected by complex interactions between phenotypes and environmental factors. Condition‐ and context‐dependent dispersal have far‐reaching consequences, both for the demography and the genetic structuring of natural populations and for adaptive processes. From an applied point of view, dispersal also deeply affects the spatial dynamics of populations and their ability to respond to land‐use changes, habitat degradation and climate change. For these reasons, dispersal has received considerable attention from ecologists and evolutionary biologists. Demographic and genetic methods allow quantifying non‐effective (i.e., followed or not by a successful reproduction) and effective (i.e., with a successful reproduction) dispersal and to investigate how individual and environmental factors affect the different stages of the dispersal process. Over the past decade, demographic and genetic methods designed to quantify dispersal have rapidly evolved but interactions between researchers from the two fields are limited. We here review recent developments in both demographic and genetic methods to study dispersal in wild animal populations. We present their strengths and limits, as well as their applicability depending on study objectives and population characteristics. We propose a unified framework allowing researchers to combine methods and select the more suitable tools to address a broad range of important topics about the ecology and evolution of dispersal and its consequences on animal population dynamics and genetics.

Assessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and between chromosomes. Here, we used an exploited freshwater fish, the Brook Charr (Salvelinus fontinalis) for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped SNPs genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early and late-generation hybrids using admixture tracts information. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2Mb windows. This allowed us to detect the signature of varied evolutionary mechanisms, as reflected by the finding of genomic regions where the introgression of domestic haplotypes are favored or disfavored. Among these, the main factor modulating local ancestry was likely the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and chromosomal variation in local ancestry toward better understanding post-hybridization evolutionary outcomes.

There is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human-driven variation in patch persistence affects dispersal rates and distances, determines dispersal-related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture–recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e. several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e. a few years), created by logging operations in intensively harvested woodland. Our capture–recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intra-patch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long-term viability and genetic structure of wild populations.

Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species’ response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. Here, we examined how genotype determines the TGP of dispersal, a fundamental process in ecology and evolution. We used an experimental approach involving ~200 clonal generations in a model-species of ciliate to determine if and how TGP influences the expression of dispersal-related traits in several genotypes. Our results show that morphological and movement traits associated with dispersal are plastic, and that these modifications are inherited over at least 35 generations. We also highlight that genotype modulates the fitness costs and benefits associated with plastic dispersal strategies. Our study suggests that genotype-dependent TGP could play a critical role in eco-evolutionary dynamics as dispersal determines gene flow and the long-term persistence of natural populations. More generally, it outlines the tremendous importance that genotype-dependent TGP could have in the ability of organisms to cope with current and future environmental changes.SignificanceThe genetic control of the transgenerational plasticity is still poorly understood despite its critical role in species responses to environmental changes. We examined how genotype determines transgenerational plasticity of a complex trait (i.e., dispersal) in a model-species of ciliate across ~200 clonal generations. Our results provide evidence that plastic phenotypic variation linked to dispersal is stably inherited over tens of generations and that cell genotype modulates the expression and fitness cost of transgenerational plasticity.

Population genetic theory states that adaptation most frequently occurs from standing genetic variation, which results from the interplay between different evolutionary processes including mutation, chromosomal rearrangements, drift, gene flow and selection. To date, empirical work focusing on the contribution of standing genetic variation to local adaptation in the presence of high gene flow has been limited to a restricted number of study systems. Marine organisms are excellent biological models to address this issue since many species have to cope with variable environmental conditions acting as selective agents despite high dispersal abilities. In this study, we examined how, demographic history, standing genetic variation linked to chromosomal rearrangements and shared polymorphism among glacial lineages contribute to local adaptation to environmental conditions in the marine fish, the capelin (Mallotus villosus). We used a comprehensive dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,359 individuals collected from 31 spawning sites in the northwest Atlantic (North America and Greenland waters). First, we reconstructed the history of divergence among three glacial lineages and showed that they diverged from 3.8 to 1.8 MyA. Depending on the pair of lineages considered, historical demographic modelling provided evidence for divergence with gene flow and secondary contacts, shaped by barriers to gene flow and linked selection. We next identified candidate loci associated with reproductive isolation of these lineages. Given the absence of physical or geographic barriers, we thus propose that these lineages may represent three cryptic species of capelin. Within each of these, our analyses provided evidence for largeNeand high gene flow at both historical and contemporary time scales among spawning sites. Furthermore, we detected a polymorphic chromosomal rearrangement leading to the coexistence of three haplogroups within the Northwest Atlantic lineage, but absent in the other two clades. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Altogether, our study shows that standing genetic variation associated with both chromosomal rearrangements and ancestral polymorphism contribute to local adaptation in the presence of high gene flow.

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus). We first assembled a 490-Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large data set of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8 million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large Ne and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.

Actuarial senescence appears to be a common process, and senescence patterns are highly variable across the tree of life. To date, studies on animal senescence have largely focused on model species, such as as fruit flies, humans and a few other endotherms. In contrast, our knowledge about ageing remains fragmentary in ectotherm vertebrates, such as reptiles. Here, we examined life history and age-dependent mortality patterns in three tropical tortoises (Kinixys erosa, Kinixys homeana and Kinixys nogueyi) and snakes (Bitis gabonica, Bitis nasicornis and Causus maculatus). Our study revealed that tortoises of the genus Kinixys had a higher survival and a lower recruitment than snakes of the genera Bitis and Causus, indicating a slower life history. Furthermore, we confirmed that survival decreased more slowly with age in tortoises than in snakes. In addition, we highlighted contrasting patterns of age-dependent mortality among the three genera. In Kinixys, the relationship between mortality rate and age was positive and linear, suggesting gradual senescence over tortoise lifetime. In contrast, the relationship between mortality rate and age was negative and sharp in Bitis and Causus, possibly owing to a ‘negative senescence’. Our study is one of the few to have examined and compared the demography and age-dependent mortality patterns of tropical reptiles. Among other things, our results suggest that although negative senescence has never been reported in endotherm vertebrates, it could be a common phenomenon in ectotherms.

Understanding the mechanisms underlying biological extinctions is a critical challenge for conservation biologists. Both deterministic (e.g. habitat loss, fragmentation) and stochastic (i.e. demographic stochasticity, Allee effect) demographic processes are involved in population decline. Simultaneously, a decrease of population size has far-reaching consequences for genetics of populations by increasing the risk of inbreeding and the effects of genetic drift, which together inevitably results in a loss of genetic diversity and a reduced effective population size (Ne). These genetic factors may retroactively affect vital rates (a phenomenon coined ‘inbreeding depression’), and therefore reduce population growth and accelerate the extinction process of small populations. To date, few studies have simultaneously examined the demographic and genetic mechanisms driving the extinction of wild populations, and have most of the time neglected the spatial structure of populations. In this study, we examined demographic and genetic factors involved in the extinction process of a spatially structured population of a lekking bird, the western capercaillie (Tetrao urogallus). To address this issue, we collected capture-recapture and genetic data over a 6-years period in Vosges mountains, France. Our study showed that the population ofT.urogallusexperienced a severe decline between 2010 and 2015. We did not detect any Allee effect on survival and recruitment. By contrast, individuals of both sexes dispersed to avoid small leks, suggesting a behavioral response to a mate finding Allee effect. In parallel to this demographic decline, the population showed a low genetic diversity and high inbreeding. In addition, the effective population sizes at both lek and population levels was low. Despite this, we did not detected evidence of inbreeding depression: neither survival nor recruitment were affected by individual inbreeding level. Our study underlines the benefit from combining demographic and genetic approaches to investigate processes that are involved in biological extinctions.

International audience; Dispersal is a key process in ecology and evolution. Both theoretical and empirical evidence in actively dispersing organisms support the general notion that the use of nearly straight dispersal paths is a highly ef␣cient way to maximize dispersal success in heterogenous landscapes. In homogeneous landscapes, in contrast, the bene␣ts of a straighter dispersal path could be outweighed by an increase in risk costs, favouring the evolution of tortuous dispersal paths resulting in a relatively slow dispersal. Empirical support for this theoretical prediction, however, has remained elusive. To explore this theoretical pre- diction, we studied the movement behaviour of the southern Darwin's frog, Rhinoderma darwinii, a fully terrestrial amphibian inhabiting a highly homogeneous environment (i.e. South American temperate forest). Using spatial captureerecapture data collected over a 4-year period in wild populations, in combination with statistical and simulation modelling, we found evidence of a slow natal dispersal lasting one year or more. In contrast, adults exhibited high site ␣delity, having a median annual displacement of 3.64 m. A correlated random walk model produced synthetic distributions of juvenile annual displacement that were nearly identical to the empirical data, suggesting that a plausible explanation of juvenile dispersal is the use of routine movements (with high path tortuosity) over short temporal scales (

Identifying the drivers of population fluctuations in spatially distinct populations remains a significant challenge for ecologists. Whereas regional climatic factors may generate population synchrony (i.e., Moran effect), local factors including the level of density-dependence may reduce the level of synchrony. Although divergences in the scaling of population synchrony and spatial environmental variation have been observed, the regulatory factors that underlie such mismatches are poorly understood.No previous studies have investigated how density-dependent processes and population-specific responses to weather variation influence spatial synchrony at both local and continental scales. We addressed this issue in a pond-breeding amphibian, the great crested newt (Triturus cristatus). We used capture-recapture data collected through long-term surveys in five T. cristatus populations in Western Europe.We found a low level of demographic synchrony at both local and continental levels. Weather has weak and spatially variable effects on survival, recruitment and population growth rate. In contrast, density-dependence was a common phenomenon (at least for population growth) in almost all populations and subpopulations.Our findings support the idea that Moran’s effect is low in species where the population dynamics more closely depends on local factors (e.g. population density and habitat characteristics) than on large-scale environmental fluctuation (e.g. regional climatic variation). Those demographic feature likely have far-reaching consequences for the long-term viability of the spatially structured populations and their ability to response to large-scale climatic anomalies.

Understanding age-dependent mortality processes is a critical challenge for population biologists. Actuarial senescence appears to be a common process across the tree of life. Senescence patterns are highly variable in pluricellular organisms: senescence can be gradual or sharp and its onset may be early or delayed. By contrast, studies revealed that organisms may also not experience senescence at all while others display a “negative senescence”; i.e. a decrease of mortality rate with age. To date, studies on senescence have largely focused on human and other endotherm vertebrates, limiting our understanding of senescence in amniotes as a whole. By contrast, few have examined the diversity of senescence patterns in ectotherm vertebrates as reptiles. Here, we examined population dynamics and age-dependent mortality patterns in three tropical tortoises (Kinixys erosa, Kinixys homeana, Kinixys nogueyi) and snakes (Bitis gabonica, Bitis nasicornis, Causus maculatus). Our study revealed that tortoises ofKinixysgenus had a higher survival and a lower recruitment than snakes of the generaBitisandCausus, indicating that they have a slower life history. Furthermore, we showed that survival more slowly decreased with age in tortoises than in snakes. In addition, we highlighted contrasted patterns of age-dependent mortality in the three genera. InKinixys, the relationship between mortality rate and age was positive and linear, suggesting gradual senescence over tortoise lifetime. By contrast, the relationship between mortality rate and age was negative and sharp inBitisandCausus, possibly due to a “negative senescence” starting early in life. Our study highlighted various age-dependent mortality patterns in tropical reptiles. It also contributed to extend our knowledge of senescence in ectotherm vertebrates whose the demography is still poorly understood. In addition, while negative senescence has never been reported in endotherm vertebrates, our results showed that it can be common phenomenon in ectotherms.

Transport infrastructure such as roads has been reported to negatively affect dispersal. Their effects on dispersal are thought to be complex, depending on the characteristics of the structure and the intensity of the traffic using it. In addition, individual factors, such as age, may strongly affect dispersal decisions and success when individuals are confronted with transport infrastructure. Despite the importance of this topic for wildlife conservation, few studies have investigated the effect of transport infrastructure on individuals’ dispersal decisions before and after sexual maturity. We examined the effects on two kinds of infrastructure, gravel tracks and paved roads, on the dispersal of an endangered amphibian, the yellow-bellied toad (Bombina variegata). We used capture–recapture data collected during a five-year period on a large, spatially structured population of B. variegata. Our study revealed that emigration rates increased with an individual’s age, while dispersal distance decreased. It also showed that both tracks and roads had negative effects on immigration. The negative effect of roads was stronger than that of tracks. We additionally found that the effect of tracks on dispersal slightly decreased with a toad’s age. In contrast, the negative effect of roads was severe and relatively similar across age classes.

International audience; 1. Understanding the mechanisms that regulate the dynamics of spatially structured populations (SSP) is a critical challenge for ecologists and conservation managers. Internal population processes such as births and deaths occur at a local level, while external processes such as dispersal take place at an inter-population level. At both levels, density dependence is expected to play a critical role. At a patch scale, demographic traits (e.g., survival, breeding success) and the population growth rate can be influenced by density either negatively (e.g., competition effect) or positively (e.g., Allee effects). At the scale of an SSP, although positive density-dependent dispersal has been widely reported, an increasing number of studies have highlighted negative density-dependent dispersal. 2. While many studies have investigated the effects of density on population growth or on dispersal, few have simultaneously examined density-dependent effects at the scale of both the local population and the entire SSP. In this study, we examine how density is related to demographic processes at both the pond level (survival and population growth) and the SSP level (between-pond dispersal) in a pondbreeding amphibian, the great crested newt (Triturus cristatus). The study was based on 20 years of individual capture–recapture (CR) data (from 1996 to 2015) gathered from an SSP made up of 12 experimental ponds (“patches”). 3. We first used a CR multievent model to estimate both survival and dispersal rates in specific ponds as a function of distance between ponds. Then, using a second CR multievent model, we examined whether survival and recapture rates were influenced by population density in a pond. Lastly, we used state-space time series models to investigate whether density affected population growth in each pond. 4. Our results found a positive density-dependent effect on survival and a negative density-dependent effect on departure. In addition, the findings indicate that population growth was negatively related to density in all 12 ponds. 5. These results support the hypothesis that in SSPs, density may have multiple and contrasting effects on demographic parameters and growth rates within local populations as well as on dispersal. This study underlines the need to better understand how density dependence may influence potential trade-offs between life-history strategies and life-history stages.

Actuarial senescence (hereafter “senescence”) has been viewed for a long time as an inevitable and uniform process. However, the work on senescence has mainly focused on endotherms (especially mammals) with deterministic growth and low regeneration capacity at adult stages, leading to a strong taxonomic bias in the study of aging. Recent studies have highlighted that senescence could indeed display highly variable trajectory shape that correlates with species life history traits. Slow life histories and indeterminate growth seem to be associated with weak and late senescence. Furthermore, a few studies have suggested that high regenerative abilities could make senescence negligible in several ectotherms (e.g., hydra and salamanders). However, demographic data for species that would allow testing of these hypotheses are scarce and fragmented. Here, we investigated senescence patterns in a group of salamanders (i.e. “true salamanders”) from the Western Palearctic using capture-recapture data and Bayesian modeling. Our results showed that salamanders have slow life histories and that they experience negligible senescence. This pattern was consistent at both intra- and interspecific levels, suggesting that the absence of senescence may be a phylogenetically conserved trait. The regenerative capacities of true salamanders, and urodeles in general, likely explains why these small ectotherms have lifespans similar to that of large endotherms (e.g., ungulates, large birds) and undergo negligible senescence contrary to most amniotes including humans. Our study seriously challenges the idea that senescence is a ubiquitous phenomenon in the living world.

Relocations are increasingly popular among wildlife managers despite sharp debate and low rate of relocation success in vertebrates. In this context, understanding the influence of extrinsic (e.g., relocation design, habitat characteristics) and intrinsic factors (e.g., age and sex) on demographic parameters such as survival that regulate the dynamics of relocated populations is critical to improve relocation protocols and better predict relocation success.We investigated survival in naturally established and relocated populations of yellow-bellied toads (Bombina variegata), an amphibian that was nearly extinct in Belgium by the late 1990s. We quantified survival at three ontogenetic stages (juvenile, subadult, and adult) in the relocated population, the source population, and a control population. In the relocated population, we quantified survival in captive bred individuals and their locally born descendants.We showed that survival at juvenile and subadult stages was relatively similar in all populations. In contrast, relocated adult survival was lower than adult survival in the source and control populations. Despite this, offspring of relocated animals (the next generation, regardless of life stage) survived at similar rates to offspring in the source and control populations. Our simulations revealed that the relocated population was self-sustaining under different scenarios and that the fate (e.g., stability or finite rate of increase) of the simulated populations was highly dependent on the fecundity of relocated adults and their offspring.Policy implications. Our results indicate that survival in relocated individuals is lower than in non-relocated individuals but that this cost (= reduced survival) disappears in the second generation. A finer understanding of how relocation affects demographic processes is an important step in improving relocation success of amphibians and other animals.

Life-history theory states that, during the lifetime of an individual, resources are allocated to either somatic maintenance or reproduction. Resource allocation trade-offs determine the evolution and ecology of life-history strategies and determine an organism position along the fast-slow continuum. Theory predicts that environmental stochasticity is an important driver of resource allocation and therefore life-history evolution. Highly stochastic environments are expected to increase uncertainty in reproductive success and select for iteroparity and a slowing down of the life history. To date, most empirical studies have used comparisons among species to examine these theoretical predictions. By contrast, few have investigated how environmental stochasticity affects life-history strategies at the intraspecific level. In this study, we examined how variation in breeding site stochasticity (among-year variability in pond volume and hydroperiod) promotes the co-occurrence of different life-history strategies in a spatially structured population, and determines life-history position along the fast-slow continuum in the yellow-bellied toad (Bombina variegata). We collected mark-recapture data from a metapopulation and used multievent capture-recapture models to estimate survival, recruitment and breeding probabilities. We found higher survival and longer lifespans in populations inhabiting variable sites compared to those breeding in stable ones. In addition, probabilities of recruitment and skipping a breeding event were higher in variable sites. The temporal variance of survival and recruitment probabilities as well as the probability to skip breeding was higher in variable sites. Taken together, these findings indicate that populations breeding in variable sites experienced a slowing down of the life-history. Our study thus revealed similarities in the macroevolutionary and microevolutionary processes shaping life-history evolution.

International audience; Dispersal is one of the main processes that determine community structure. Individuals make dispersal decisions according to environmental and/or social cues that reflect the fitness prospects in a given patch. The presence and abundance of heterospecifics within the same ecological guild, and/or their breeding success, may act as public information that influences movement decisions. To date, most studies investigating the role of heterospecific attraction have focused on habitat choice, using both experimental and correlational approaches. The present study is the first to examine how long-term variation in heterospecific density in breeding patches may affect dispersal patterns in spatially structured populations. We investigate how the dispersal decisions of the great crested newt (Triturus cristatus) are related to the variable density of two other newt species, the alpine newt (Ichthyosaura alpestris) and the palmate newt (Lissotriton helveticus). To examine this issue, we used capture–recapture data collected in an experimental pond network over a 20-year period. The results revealed that the great crested newt’s dispersal is context dependent and is affected by variation in heterospecific density: individuals were less likely to emigrate from ponds with high heterospecific density and were more likely to immigrate to ponds with high heterospecific density. These findings suggest that individuals adjust their dispersal decisions at least partly based on public information provided by heterospecifics. This mechanism may play a critical role in the dynamics of spatially structured populations and community functioning.

International audience; Dispersal (i.e. movement from a natal or breeding site to another breeding site) is a central process in ecology and evolution as it affects the eco-evolutionary dynam- ics of spatially structured populations. Dispersal evolution is regulated by the bal- ance between costs and benefits, which is influenced by the individual phenotype (i.e. phenotype-dependent dispersal) and environmental factors (i.e. condition-dependent dispersal). Even though these processes have been extensively studied in species with simple life cycles, our knowledge about these mechanisms in organisms displaying complex life cycles remains fragmentary. In fact, little is specifically known about how the interplay between individual and environmental factors may lead to alternative dispersal strategies that, in turn, lead to the coexistence of contrasted site fidelity phe- notypes. In this paper, we examined breeding dispersal in a pond-breeding amphibian, the great crested newt Triturus cristatus, within usual walking distances for a newt. We took advantage of recent developments in multi-event capture–recapture models and used capture–recapture data (946 newts marked) collected in a spatially structured population occupying a large pond network (73 ponds). We showed a high rate of breeding site infidelity (i.e. pond use) and the coexistence of two dispersal phenotypes, namely, a highly pond faithful phenotype and a dispersing phenotype. Individuals that were site faithful at time t – 1 were therefore more likely to remain site faithful at time t. Our results also demonstrated that the probability that individuals belong to one or the other dispersal phenotypes depended on environmental and individual factors. In particular, we highlighted the existence of a dispersal syndrome implying a covariation pattern among dispersal behavior, body size, and survival. Our work opens new research prospects in the evolution of dispersal in organisms displaying complex life cycles and raises interesting questions about the evolutionary pathways that contribute to the diversification of movement strategies in the wild.

Transport infrastructure such as roads has been reported to negatively affect dispersal. Their effects on dispersal are thought to be complex, depending on the characteristics of the structure and the intensity of the traffic using it. In addition, individual factors, such as age, may strongly affect dispersal decisions and success when individuals are confronted with transport infrastructure. Despite the importance of this topic for wildlife conservation, few studies have investigated the effect of transport infrastructure on individuals’ dispersal decisions before and after sexual maturity. We examined the effects on two kinds of infrastructure, gravel tracks and paved roads, on the dispersal of an endangered amphibian, the yellow-bellied toad (Bombina variegata). We used capture-recapture data collected during a five-year period on a large, spatially structured population of B. variegata. Our study revealed that emigration rates increased with an individual’s age, while dispersal distance decreased. It also showed that both tracks and roads had negative effects on dispersal. The negative effect of roads was stronger than that of tracks. We additionally found that the effect of tracks on dispersal slightly decreased with a toad’s age. In contrast, the negative effect of roads was severe and relatively similar across age classes.