Assessing the influence of the amount of reachable habitat on genetic structure using landscape and genetic graphs.

Genetic structure, i.e. intra-population genetic diversity and inter-population genetic differentiation, is influenced by the amount and spatial configuration of habitat. Measuring the amount of reachable habitat (ARH) makes it possible to describe habitat patterns by considering intra-patch and inter-patch connectivity, dispersal capacities and matrix resistance. Complementary ARH metrics computed under various resistance scenarios are expected to reflect both drift and gene flow influence on genetic structure. Using an empirical genetic dataset concerning the large marsh grasshopper (Stethophyma grossum), we tested whether ARH metrics are good predictors of genetic structure. We further i…

Social interactions modulate the virulence of avian malaria infection

There is an increasing understanding of the context-dependent nature of parasite virulence. Variation in parasite virulence can occur when infected individuals compete with conspecifics that vary in infection status; virulence may be higher when competing with uninfected competitors. In vertebrates with social hierarchies, we propose that these competition-mediated costs of infection may also vary with social status. Dominant individuals have greater competitive ability than competing subordinates, and consequently may pay a lower prevalence-mediated cost of infection. In this study we investigated whether costs of malarial infection were affected by the occurrence of the parasite in compet…

Quand et comment utiliser les graphes génétiques pour analyser la connectivité écologique dans des paysages hétérogènes ?

National audience; Lorsque les espèces occupent des taches d’habitat au sein de paysages hétérogènes, la connectivité écologique est influencée par la topologie du réseau de populations qu’elles forment. Dans ce contexte, les méthodes basées sur les graphes génétiques permettent i) de révéler cette topologie en identifiant les chemins de dispersion directs et ii) de quantifier la résistance des éléments paysagers à la dispersion. Compte-tenu de l’intérêt croissant pour ces méthodes en génétique du paysage, il est nécessaire de mieux comprendre quand et comment il faut utiliser les graphes génétiques. Pour cela, nous avons simulé le flux génétique entre 50 populations dans différents paysage…

Diversité génétique au sein et entre populations.

10 pages; National audience

Effect of repeated exposure to Plasmodium relictum (lineage SGS1) on infection dynamics in domestic canaries.

7 pages; International audience; Parasites are known to exert strong selection pressures on their hosts and, as such, favour the evolution of defence mechanisms. The negative impact of parasites on their host can have substantial consequences in terms of population persistence and the epidemiology of the infection. In natural populations, however, it is difficult to assess the cost of infection while controlling for other potentially confounding factors. For instance, individuals are repeatedly exposed to a variety of parasite strains, some of which can elicit immunological memory, further protecting the host from subsequent infections. Cost of infection is, therefore, expected to be partic…

Predictions of avian Plasmodium expansion under climate change.

International audience; Vector-borne diseases are particularly responsive to changing environmental conditions. Diurnal temperature variation has been identified as a particularly important factor for the development of malaria parasites within vectors. Here, we conducted a survey across France, screening populations of the house sparrow (Passer domesticus) for malaria (Plasmodium relictum). We investigated whether variation in remotely-sensed environmental variables accounted for the spatial variation observed in prevalence and parasitemia. While prevalence was highly correlated to diurnal temperature range and other measures of temperature variation, environmental conditions could not pre…

Can landscape resistance to gene flow be inferred by genetic distances? A simulation study to evaluate the performances of landscape surface optimization

Assessing the influence of the amount of reachable habitat on genetic structure using graphs.

The genetic structure of populations is made of two components: the genetic diversity of every population (intra-population) and the genetic differentiation between every pair of populations (inter-population). These two components are influenced by genetic drift and gene flow, which are driven by the joint influence of the amount of habitat and of its spatial configuration in the landscape. Habitat amount and configuration are highly interdependent and together determine habitat connectivity, i.e. the amount of reachable habitat (ARH) at several scales. Adopting such a conception of habitat connectivity makes it possible to describe habitat patterns by considering simultaneously intra-patc…

Formes urbaines, connectivité des habitats et diversité génétique des aires urbaines européennes

Ce rapport s’inscrit dans le cadre d’une étude ayant pour objectif de comprendre le lien entre lesformes urbaines et tissus urbains, la connectivité écologique des habitats au sein des aires urbaines et les réponses biologiques potentielles des espèces à ces environnements. Les réflexions initiées en 2019 lors du projet REFUGE financé par le CNRS et impliquant les laboratoires ThéMA (UMR 6049 - Université de Bourgogne Franche-Comté - CNRS, Besançon) et Biogéosciences (UMR 6282 - Université de Bourgogne Franche-Comté - CNRS, Dijon) se sont poursuivies au premier semestre 2022 et ont donné lieu à deux volets d’analyse complémentaires. Cette étude a été financée par l’entreprise ARP-Astrance e…

Quand et comment utiliser des graphes génétiques pour analyser le flux génétique dans des paysages hétérogènes ?

La connectivité écologique des habitats dépend de la topologie du réseau formé par les populations qui les occupent. Les graphes génétiques permettent i) d’identifier les chemins de dispersion directs en révélant cette topologie et ii) de quantifier la résistance des éléments paysagers à la dispersion. Nous avons étudié comment l’équilibre migration-dérive affecte les choix de construction de ces graphes et les inférences qui en découlent. Nous avons simulé le flux génétique entre 50 populations dans différents paysages et construit des graphes pondérés avec plusieurs distances génétiques et élagués selon différents critères. Nous avons ensuite comparé la capacité de ces graphes à i) représ…

Microsatellite DNA markers for two endemic ground beetles: Carabus punctatoauratus and C. solieri

We isolated and characterized nine and five polymorphic microsatellite loci in the respective ground beetles Carabus punctatoauratus and C. solieri. We tested cross-species amplification of all these loci plus six isolated in C. solieri and for which primers sequences were soon published. From these combined analyses, we obtained 14 and 17 polymorphic markers, respectively, for C. punctatoauratus and C. solieri.

Diversifying selection on MHC class I in the house sparrow (Passer domesticus).

10 pages; International audience; Genes of the major histocompatibility complex (MHC) are the most polymorphic loci known in vertebrates. Two main hypotheses have been put forward to explain the maintenance of MHC diversity: pathogen-mediated selection and MHC-based mate choice. Host-parasite interactions can maintain MHC diversity via frequency-dependent selection, heterozygote advantage, and diversifying selection (spatially and/or temporally heterogeneous selection). In this study, we wished to investigate the nature of selection acting on the MHC class I across spatially structured populations of house sparrows (Passer domesticus) in France. To infer the nature of the selection, we comp…

Expanding genetic graphs' potential to analyse ecological connectivity: assessment of graphs construction methods

International audience; Dispersal movements are often constrained in human-shaped landscapes, thereby threatening species survival. Landscape genetics approaches are commonly used to analyse ecological connectivity because genetic data well reflect dispersal capacities. When species occupy discrete habitat patches, graph-theoretic methods are a particularly relevant approach to study dispersal-driven gene flow. The links of a genetic graph can be weighted using different genetic distances between populations (nodes). Similarly, graph pruning (link set selection) can rely on different criteria. However, despite growing interest in genetic graphs, the influence of these parameters remains mos…

Inférence de la résistance du paysage au flux de gènes à l'aide de modèles gravitaires intégrant des variables intra-populationnelles

International audience; Modéliser les mouvements de dispersion nécessite d'associer aux éléments paysagers des valeurs de coût caractérisant leur résistance aux déplacements. En landscape genetics, l'inférence de ces valeurs se fait à partir de mesures de différenciation génétique entre populations. Bien que l'hétérogénéité spatiale des tailles de populations puisse aussi influencer de façon significative la différenciation génétique, les variables intra-populationnelles sont rarement prises en compte dans ce type d'inférence. Nous avons étudié à quel point la prise en compte de ces variables pouvait améliorer l'inférence des coûts. Pour cela, nous avons simulé des flux de gènes entre 60 po…

New polymorphic microsatellite loci in the house sparrow, Passer domesticus.

3 pages; International audience; We developed 13 new polymorphic microsatellite loci in the house sparrow (Passer domesticus), which exhibited from 2 to 15 alleles. Observed and expected heterozygosities ranged from 0.17 to 0.77 and from 0.35 to 0.85, respectively. We detected no linkage disequilibrium between loci. Allele frequencies supported Hardy–Weinberg equilibrium for 8 loci out of 13 after Bonferroni correction. Combined with loci previously isolated in the house sparrow, these new microsatellite markers provide valuable tools to study population genetics of this species.

Hybridization, developmental stability, and functionality of morphological traits in the ground beetle Carabus solieri (Coleoptera, Carabidae).

Correspondance.: stephane.garnier@u-bourgogne.fr; International audience; The assessment of developmental stability in hybrids can provide valuable information in the study of species formation because it allows an evaluation of the degree of incompatibility of genetic systems that control developmental processes. The present study assessed the impact of two hybridization events, assumed to have occurred at different times, on developmental instability in the ground beetle Carabus solieri . Developmental instability was estimated in 678 individuals from 27 populations from the fluctuating asymmetry (FA) levels of four morphological traits: the tibia length of middle and hind legs, which are…

Les contraintes.

Isolation by distance and sharp discontinuities in gene frequencies: implications for the phylogeography of an alpine insect species, Carabus solieri

Analysis of genetic isolation by distance (IBD) is of prime importance for the study of processes responsible for spatial population genetic structure and is thus frequently used in case studies. However, the identification of a significant IBD pattern does not necessarily imply the absence of sharp discontinuities in gene frequencies. Therefore, identifying barriers to gene flow and/or secondary contact between differentiated entities remains a major challenge in population biology. Geographical genetic structure of 41 populations (1080 individuals) of an alpine insect species, Carabus solieri , was studied using 10 microsatellite loci. All populations were significantly differentiated and…

Validating graph-based connectivity models using independent presence/absence and genetic datasets.

Analyse de sensibilité des modèles de connectivité écologique

Le succès des mesures de conservation de la biodiversité basées sur le maintien de la connectivité écologique dépend de la qualité de la modélisation spatiale des mouvements des espèces. Le calcul de chemins de moindre coût est censé identifier les trajets qui minimisent les coûts de déplacement à travers la matrice paysagère. Il apporte deux types d’information : (i) la localisation spatiale des chemins de moindre coût et (ii) le coût accumulé le long de ces chemins, aussi appelé distance-coût. Cette modélisation spatiale nécessite qu’un coût soit attribué à chaque type d’occupation du sol, constituant alors un scénario de coût. L’influence de ces scénarios sur la localisation des chemins …

When morphometry meets genetics: inferring the phylogeography of Carabus solieri using Fourier analyses of pronotum and male genitalia

Population differentiation is a crucial step in the speciation process and is therefore a central subject in studies of microevolution. Assessing divergence and inferring its dynamics in space and time generally require a wide array of markers. Until now however, most studies of population structure are based on molecular markers and those concerning morphological traits are more scarce. In the present work, we studied morphological differentiation among populations of the ground beetle Carabus solieri, and tested its congruence with genetic population structure. The shape of pronotum and aedeagus was assessed using Dual Axis Fourier Shape Analysis. manova on Fourier coefficients revealed h…

Analysing gene flow in heterogeneous landscapes: why and how to use genetic graphs?

International audience; In heterogeneous landscapes, when species occupy discrete habitat patches, ecological connectivity is influenced by populations’ topology. Graph-theoretic methods constitute a relevant tool to reveal this topology and better analyse gene flow. Despite growing interest in genetic graphs, a better understanding of when and how to use them is lacking.To fill this gap, we simulated gene flow between 50 populations in different landscape configurations and constructed genetic graphs using various genetic distances and pruning (link selection) methods. We then compared metrics derived from these graphs to analogous metrics describing the topology and connectivity of the di…

Les contraintes.

Validation des modèles de connectivité issus de la théorie des graphes en utilisant des données génétiques

National audience; Modéliser la connectivité fonctionnelle des habitats est déterminant pour la conservation de la biodiversité. Les graphes paysagers, en modélisant des taches d’habitat reliées par des chemins de dispersion potentiels, permettent de quantifier la connectivité du paysage. Si cette approche semble prometteuse, sa validité écologique reste à démontrer. Tester sa validité implique de confronter des données de connectivité issues d’un graphe à des données reflétant la dispersion des individus, telles que des données génétiques. Dans cet objectif, nous avons modélisé la connectivité de l’habitat d’une espèce d’oiseau forestière, la Paruline caféiette (Setophaga plumbea), en Guad…

Antagonistic effects of a Mhc class I allele on malaria-infected house sparrows.

8 pages; International audience; Genes of the Major Histocompatibility Complex (Mhc) play a fundamental role during the immune response because MHC molecules expressed on cell surface allow the recognition and presentation of antigenic peptides to T-lymphocytes. Although Mhc alleles have been found to correlate with pathogen resistance in several host-parasite systems, several studies have also reported associations between Mhc alleles and an accrued infection risk or an accelerated disease progression. The existence of these susceptibility alleles is puzzling, as the cost generated by the infection should rapidly eliminate them from the population. Here, we show that susceptibility alleles…

Validation of graph-based connectivity models using genetic data.

Modelling the functional connectivity of habitats is crucial for biodiversity conservation. By modelling potential dispersal paths among habitat patches, landscape graphs are often used to quantify landscape connectivity. While this approach seems promising, it often lacks biological validation. To ensure its ecological relevance, we assessed the ability of connectivity metrics calculated from landscape graphs to predict population genetic structure that closely reflects the dispersal of individuals, and thus functional connectivity. We modelled the habitat network of a forest bird species (Plumbeous warbler, Setophaga plumbea) in Guadeloupe using three graphs constructed either from expert…

Females tend to prefer genetically similar mates in an island population of house sparrows.

11 pages; International audience; BACKGROUND: It is often proposed that females should select genetically dissimilar mates to maximize offspring genetic diversity and avoid inbreeding. Several recent studies have provided mixed evidence, however, and in some instances females seem to prefer genetically similar males. A preference for genetically similar mates can be adaptive if outbreeding depression is more harmful than inbreeding depression or if females gain inclusive fitness benefits by mating with close kin. Here, we investigated genetic compatibility and mating patterns in an insular population of house sparrow (Passer domesticus), over a three-year period, using 12 microsatellite mar…

EPIDEMIOLOGY OF PLASMODIUM RELICTUM INFECTION IN THE HOUSE SPARROW.

International audience; : Abstract In vertebrates, multiple host characteristics and environmental factors are known to influence infectious disease dynamics. Here, we investigated variability in prevalence and parasitemia of Plasmodium relictum in the house sparrow (Passer domesticus), across a large number of rural and urban populations (n = 16). We found that prevalence was not predicted by any of the host traits investigated (age, sex, body mass or wing length). However, parasitemia was significantly higher in females when compared to males and in 1-yr-olds as compared to older individuals. Neither prevalence nor parasitemia differed according to habitat type (urban vs. rural). These re…

Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri.

12 pages; International audience; Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40-50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zone…

Evolution of parasitism.

Data from: Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri

Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40–50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zones of the island of Guadeloupe was …