Histoire évolutive, contexte spatial et écologique de la divergence de deux sous-espèces d'Antirrhinum majus

Identifier les mécanismes évolutifs impliqués dans la spéciation, i.e. formation des espèces, est crucial dans une époque de crise de la biodiversité. À ce jour, la classification dichotomique des mécanismes impliqués dans le processus de spéciation (i.e. allopatrie versus sympatrie, écologique versus non-écologique ...) n'intègrent pas l'interaction dynamique qui les régit. Dans cette thèse, nous avons cherché à intégrer au mieux les différentes composantes de la spéciation - isolement spatial, écologique et reproducteur - dans un cadre temporel. Pour cela, nous avons étudié la divergence de deux sous-espèces de plantes à fleurs, Antirrhinum majus pseudomajus et A. m. striatum aux fleurs respectivement rouges et jaunes. Nous avons intégré durant cette thèse des approches d'écologie (modélisation de niche) de génétique des populations (analyses de structuration génétique, inférence basée sur le coalescent, ajustement de clines) à différentes échelles spatiales, de l'aire de distribution globale à une zone hybride localisée, en pensant par le détail des zones de contact. Nos résultats montrent comment les processus historiques et démographiques agissent conjointement sur la distribution actuelle des populations des deux sous espèces d'A. majus. L'ensemble de nos résultats soutient l'hypothèse du rôle adaptatif de la couleur des fleurs dans le maintien de l'isolement à l'échelle de l'espèce. De plus, la divergence de niche que nous avons détectée entre les deux sous-espèces pourrait être à l'origine de leur divergence phénotypique. Dans les zones de contact, nous avons mis en évidence des échanges de gènes récurrents entre sous-espèces associés à des gradients d'expansion géographique dans des directions opposées. L'ensemble de nos résultats soulève l'hypothèse d'un maintien de la parapatrie entre sous-espèces assuré par leur exclusion compétitive dans les zones de contact. En conclusion, la divergence des deux sous-espèces semble résulter de la combinaison dans le temps de processus historiques neutres et démographiques actuels avec des processus sélectifs associés à l'écologie des sous espèces qui modèlent non indépendamment leur diversité.This thesis sought at understanding how evolutionary and ecological processes lead to population divergence and ultimately speciation. To this aim, i integrated the different components of speciation - ecological, spatial and matting isolation - ina temporal framework to gain a better understanding of their dynamicinteraction through time. I studied the ongoing divergence of two snapdragon subspecies of Antirrhiunum majus pseudomajus and A.m striatum. I tested the relative role of historical processes of colonasation (post-glacial colonisation scenario), contemporary barriers to gene flow and local adaptation to explain the current patterns of subspecies distribution and the distribution of their genetic diversity. I also investigated the extent of gene flaw between the two subspecies in the contact zones and the role of environmental factors on the direction of gene flow and the maintenance of disjunct distributions despite gene flow. Finally, i studied the relative roles of neutral processesof dispersal and selective processes in the maintenance of a stable hybrid zone between the two subspecies

Using metabarcoding to reveal and quantify plant-pollinator interactions.

12 pagesInternational audienceGiven the ongoing decline of both pollinators and plants, it is crucial to implement effective methods to describe complex pollination networks across time and space in a comprehensive and high-throughput way. Here we tested if metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions. Metabarcoding experiments on pollen DNA mixtures described a positive relationship between the amounts of DNA from focal species and the number of trnL and ITS1 sequences yielded. The study of pollen loads of insects captured in plant communities revealed that as compared to the observation of visits, metabarcoding revealed 2.5 times more plant species involved in plant-pollinator interactions. We further observed a tight positive relationship between the pollen-carrying capacities of insect taxa and the number of trnL and ITS1 sequences. The number of visits received per plant species also positively correlated to the number of their ITS1 and trnL sequences in insect pollen loads. By revealing interactions hard to observe otherwise, metabarcoding significantly enlarges the spatiotemporal observation window of pollination interactions. By providing new qualitative and quantitative information, metabarcoding holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole

Data from: Level of genetic differentiation affects relative performances of EST- and genomic SSRs

Microsatellites, also called simple sequence repeats (SSRs) are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers and highly conserved SSRs have recently been developed from Expressed Sequence Tags (EST) to improve SRR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multi-species approach on passerine birds. We tested whether patterns and levels of genetic diversity within- and between-populations assessed from EST- and from genomic SSRs are congruent and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SRRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency

Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs.

11 pagesInternational audienceMicrosatellites, also called simple sequence repeats (SSRs), are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers, and highly conserved SSRs have recently been developed from expressed sequence tags (EST) to improve SSR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multispecies approach on passerine birds. We tested whether patterns and levels of genetic diversity within and between populations assessed from EST- and from genomic SSRs are congruent, and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency

Raster maps for 29 environmental variables in three geographical regions

Aim: Greater understanding of the processes underlying biological invasions is required to determine and predict invasion risk. Two subspecies of olive (Olea europaea subsp. europaea and Olea europaea subsp. cuspidata) have been introduced into Australia from the Mediterranean Basin and southern Africa during the 19th century. Our aim was to determine to what extent the native environmental niches of these two olive subspecies explain the current spatial segregation of the subspecies in their non-native range. We also assessed whether niche shifts had occurred in the non-native range, and examined whether invasion was associated with increased or decreased occupancy of niche space in the non-native range relative to the native range. Location: South-eastern Australia, Mediterranean Basin and southern Africa. Methods: Ecological niche models (ENMs) were used to quantify the similarity of native and non-native realized niches. Niche shifts were characterized by the relative contribution of niche expansion, stability and contraction based on the relative occupancy of environmental space by the native and non-native populations. Results: Native ENMs indicated that the spatial segregation of the two subspecies in their non-native range was partly determined by differences in their native niches. However, we found that environmentally suitable niches were less occupied in the non-native range relative to the native range, indicating that niche shifts had occurred through a contraction of the native niches after invasion, for both subspecies. Main conclusions: The mapping of environmental factors associated with niche expansion, stability or contraction allowed us to identify areas of greater invasion risk. This study provides an example of successful invasions that are associated with niche shifts, illustrating that introduced plant species are sometimes readily able to establish in novel environments. In these situations the assumption of niche stasis during invasion, which is implicitly assumed by ENMs, may be unreasonable

Spatial segregation and realized niche shift during the parallel invasion of two olive subspecies in south-eastern Australia.

12 pagesInternational audienceAimGreater understanding of the processes underlying biological invasions is required to determine and predict invasion risk. Two subspecies of olive (Olea europaea subsp. europaea and Olea europaea subsp. cuspidata) have been introduced into Australia from the Mediterranean Basin and southern Africa during the 19th century. Our aim was to determine to what extent the native environmental niches of these two olive subspecies explain the current spatial segregation of the subspecies in their non-native range. We also assessed whether niche shifts had occurred in the non-native range, and examined whether invasion was associated with increased or decreased occupancy of niche space in the non-native range relative to the native range.LocationSouth-eastern Australia, Mediterranean Basin and southern Africa.MethodsEcological niche models (ENMs) were used to quantify the similarity of native and non-native realized niches. Niche shifts were characterized by the relative contribution of niche expansion, stability and contraction based on the relative occupancy of environmental space by the native and non-native populations.ResultsNative ENMs indicated that the spatial segregation of the two subspecies in their non-native range was partly determined by differences in their native niches. However, we found that environmentally suitable niches were less occupied in the non-native range relative to the native range, indicating that niche shifts had occurred through a contraction of the native niches after invasion, for both subspecies.Main conclusionsThe mapping of environmental factors associated with niche expansion, stability or contraction allowed us to identify areas of greater invasion risk. This study provides an example of successful invasions that are associated with niche shifts, illustrating that introduced plant species are sometimes readily able to establish in novel environments. In these situations the assumption of niche stasis during invasion, which is implicitly assumed by ENMs, may be unreasonable

Microsatellite data

EST- and genomic SSR dataset

Data from: Habitat fragmentation, not habitat loss, drives the prevalence of blood parasites in a Caribbean passerine

Habitat destruction due to human land-use activities is well recognized as a central threat to biodiversity. However, there is still debate about the relative influence of its two components, habitat loss and habitat fragmentation, mostly because few studies have been able to disentangle their respective effects. We studied mechanisms by which habitat destruction might influence the prevalence of vector-transmitted haemosporidian blood parasites of the genera Plasmodium and Haemoproteus the Lesser Antillean Bullfinch, Loxigilla noctis, on the Caribbean islands of Guadeloupe and Martinique . Starting from a large set of environmental descriptors (including metrics reflecting habitat loss, habitat fragmentation and landscape heterogeneity; as well as other variables not linked to habitat destruction, such as climatic conditions), we used PLS regression analyses to determine which variables were driving parasite prevalence on the islands. Our results showed that variables related to forest destruction were much more influential than other factors for all parasites analyzed on both islands. Remarkably, the effects documented were almost exclusively due to forest fragmentation, as opposed to habitat loss. This positive effect of forest fragmentation on blood parasite prevalence is proposed to happen through its effects on insect vectors and/or host biology. Increased understanding of the role of habitat fragmentation as a driver of parasitic diseases can help anticipate future effects and limit the risk of emergence and proliferation of wildlife pathogenic outbreaks and zoonosis through informed landscape planning

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

International audienc

Perez-Rodriguez et al. 2018. Ecography. DATASET

Excel file with data of parasite prevalence per sampling site, plus the climatic and habitat structure metrics associated to each sampling site