Landscape genetics and gene flow in the banana pathogenic fungus Mycosphaerella fijiensis

Among the different evolutionary forces driving population genetics, gene flow related to dispersal plays a major role in local adaptation processes. However very few studies on plant pathogenic fungi focussed on deciphering gene flow patterns at the scale of a producing area. The causal agent of the black leaf streak disease on Banana crops, Mycosphaerella fijiensis, can be considered as a good biological model to study the adaptive potential of plant fungal pathogens: populations show relative demographic stability and panmixia so that most methods of population genetics can be properly applied. For gene flow analysis, we focussed on small farming production units which are scarcely distributed among large producing areas and rarely subjected to fungicide spraying. Previous population genetic studies of M. fijiensis allowed us to define the spatial scale to be considered and warned us about the effect of some putative barriers for gene flow analysis. Here we aimed at taking into account landscape in our population genetic analysis to i) delineate pathogen populations and determine the nature and importance of the barriers to gene flow and ii) assess M. fijiensis dispersal pattern within a continuous population. Around 850 isolates were sampled in a referenced area in Cameroon and genotyped using 22 microsatellite markers. The effect of landscape features on gene flow was investigated using a population genetics method explicitly taking spatial location of samples into account (Landscape genetics). Two distinct populations were detected across a 50x50 km area, but no landscape feature matches the observed genetic discontinuity. Within the largest of the two pathogen populations, the dispersal pattern of M. fijiensis was examined using the continuous model of isolation by distance. The observed dispersal pattern is further discussed in the light of simulation results predicting dispersal patterns according to some realistic demographic scenarios for this plant pathogenic fungus. (Texte intégral

Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen

Dispersal is a key parameter of adaptation, invasion and persistence. Yet standard population genetics inference methods hardly distinguish it from drift and many species cannot be studied by direct mark-recapture methods. Here, we introduce a method using rates of change in cline shapes for neutral markers to estimate contemporary dispersal. We apply it to the devastating banana pest Mycosphaerella fijiensis, a wind-dispersed fungus for which a secondary contact zone had previously been detected using landscape genetics tools. By tracking the spatio-temporal frequency change of 15 microsatellite markers, we find that σ, the standard deviation of parent–offspring dispersal distances, is 1.2 km/generation1/2. The analysis is further shown robust to a large range of dispersal kernels. We conclude that combining landscape genetics approaches to detect breaks in allelic frequencies with analyses of changes in neutral genetic clines offers a powerful way to obtain ecologically relevant estimates of dispersal in many species

Integrating the landscape epidemiology and genetics of RNA viruses: rabies in domestic dogs as a model

Landscape epidemiology and landscape genetics combine advances in molecular techniques, spatial analyses and epidemiological models to generate a more real-world understanding of infectious disease dynamics and provide powerful new tools for the study of RNA viruses. Using dog rabies as a model we have identified how key questions regarding viral spread and persistence can be addressed using a combination of these techniques. In contrast to wildlife rabies, investigations into the landscape epidemiology of domestic dog rabies requires more detailed assessment of the role of humans in disease spread, including the incorporation of anthropogenic landscape features, human movements and socio-cultural factors into spatial models. In particular, identifying and quantifying the influence of anthropogenic features on pathogen spread and measuring the permeability of dispersal barriers are important considerations for planning control strategies, and may differ according to cultural, social and geographical variation across countries or continents. Challenges for dog rabies research include the development of metapopulation models and transmission networks using genetic information to uncover potential source/sink dynamics and identify the main routes of viral dissemination. Information generated from a landscape genetics approach will facilitate spatially strategic control programmes that accommodate for heterogeneities in the landscape and therefore utilise resources in the most cost-effective way. This can include the efficient placement of vaccine barriers, surveillance points and adaptive management for large-scale control programmes

Landscape population genetics and the role of organic farming

This project aims at understanding the effect of different farming systems on the genetic diversity of common agricultural species. It is well known that organic farming generally improves the biodiversity and abundance of species in the agricultural landscape (Hole et al., 2005). A reduction in species number and abundance has been shown as a result of the intensification of farming suggesting a relationship between farming intensity and species abundance (e.g. Stoate et al., 2001). Anyway, none of the studies that investigated the effects of pesticides presence and farming intensity has investigated the effect on the genetic diversity and isolation of the populations. It has been shown that, despite the theoretical expectations, also very abundant species like Abax parallelepipedus can be divided in isolated and genetically distinct populations within very few years in response to human activity (e.g. construction of streets: Keller et al., 2004). Therefore, we chose two common agricultural species (field vole, Microtus agrestis, and a non-pest ground beetle, Bembidion lampros) belonging to different taxa and with different dispersal abilities, to investigate the effect of pesticide use and intensiveness of farming on their genetic structuring and diversity

Fluctuation Domains in Adaptive Evolution

We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains - parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource

Landscape genetics of highly disturbed arable systems : insights gained from investigating a small mammal species

A large proportion of the earth’s surface is dedicated to food production, and agriculture is widely acknowledged to influence local biodiversity via habitat loss and degradation. Landscape genetics is an emerging field which can provide detailed understanding of how wildlife populations are influenced by landscape configuration and composition but the approach is yet to be fully integrated with agroecology. When addressing landscape genetics questions, small mammals may provide insight; they may act as model organisms, they are abundant, they are relatively easy to sample and they may have important ecological roles within arable ecosystems. This thesis merged the study of arable landscapes, landscape genetics and small mammals, to develop what is known about the landscape genetics of wild species in this dynamic habitat type. To decide upon a study organism, small mammals were surveyed at an example arable field site. Wood mice (Apodemus sylvaticus) were found to be the most abundant species and a microsatellite marker multiplex was developed for genotyping individuals. Two aspects of their landscape genetics in arable habitat were investigated. First, the possibility of temporal patterns in fine scale genetic structure of arable populations was explored, since this had not been investigated previously. Next, inter-population genetic differentiation was examined to determine whether arable habitat acted as a barrier to gene flow for this species. At the fine scale, three genetically distinct clusters of wood mice were identified and temporal variation in the spatial pattern was confirmed. There was no evidence that arable habitat acted as a barrier to gene flow for this species in comparison to populations in urban habitat, which showed significant differentiation. It is hoped that the landscape genetic insights provided by this thesis will encourage greater momentum for conducting landscape genetics studies in agricultural habitat

A landscape genetics approach to unravel the complex evolutionary history of the Iberian honey bee hybrid zone

While landscape genetics is in its infancy, it is a rapidly growing research field in part owing to the increasing availability of powerful molecular and analytical tools. By integrating landscape ecology, spatial statistics and population genetics, landscape genetics is allowing an unprecedented understanding of the microevolutionary processes shaping genetic variation, which has important implications for the advance of ecological and evolutionary knowledge. The Iberian honey bee provides a great model system to address evolutionary questions using a landscape genetics framework. First, previous studies suggest that the Iberian honey bee has a hybrid origin and hybrid zones have been favored by evolutionary biologists as powerful natural laboratories to study evolutionary processes. Second, with the publication of the honey bee genome and development of high‐density SNP markers, powerful tools are now available to dissect the relative importance of neutral and adaptive forces in shaping the Iberian honey bee hybrid zone, a goal of central importance as it leads to more robust inferences of demographic history and to identification of adaptive divergence. Herein, we will present an ongoing research project on the Iberian honey bee hybrid zone where the tools of landscape genetics and population genomics will be combined to unravel the challenging evolutionary history of the Iberian honey bee

Application and refinement of molecular ecology techniques for amphibian conservation

Wildlife conservation has become increasingly difficult due to habitat loss habitat fragmentation and land use change. Thus conservationists have embraced advances in molecular ecology such as landscape genetics and microbial bioinformatics that employ genetic techniques to further understand the relationship between individuals and their environment. In landscape genetics model inferences can be used to identify features that facilitate or resist gene flow providing a framework for anticipating the impacts of land use changes on a species’ ability to disperse. However the factors that affect the transferability of landscape genetics inferences are poorly understood and little is known about the effect of sampling density and study area size on landscape genetics inferences. To address these understudied factors I performed a series of landscape genetics analyses using populations of the Mississippi slimy salamander (Plethodon mississippi) in Mississippi and Alabama. Regional replication revealed the importance of habitat configuration on the relationship between land use and gene flow among salamander populations and the transferability of landscape genetics inferences to neighboring areas. Analysis of hierarchically nested datasets of different sampling densities and study area sizes identified differences due to study area size however no clear effect was seen as a result of different sampling densities. Conservation practitioners can also use microbial ecology to better understand the relationship between wildlife species and their environment. The mutualistic relationship between amphibians and their cutaneous microbial community can strengthen the amphibian’s ability to fight fungal pathogens. However in order to inform management strategies such as probiotic inoculation researchers must first understand the method in which amphibian cutaneous microbiomes are shaped. I compared salamander relatedness salamander cutaneous microbiomes and the microbiomes of salamanders’ immediate soil environment which revealed no relationship between kinship and similarity of skin microbiomes. Further comparison of skin and soil microbiomes provided evidence that the presence of antifungal taxa in a salamander’s environment does not guarantee incorporation of the taxa into salamander cutaneous microbiomes. The results of this research fill knowledge gaps within the fields of landscape genetics and amphibian cutaneous microbial ecology and provide a greater understanding of the relationship between P. mississippi and its environment

Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response

Dramatic rise of mutators has been found to accompany adaptation of bacteria in response to many kinds of stress. Two views on the evolutionary origin of this phenomenon emerged: the pleiotropic hypothesis positing that it is a byproduct of environmental stress or other specific stress response mechanisms and the second order selection which states that mutators hitchhike to fixation with unrelated beneficial alleles. Conventional population genetics models could not fully resolve this controversy because they are based on certain assumptions about fitness landscape. Here we address this problem using a microscopic multiscale model, which couples physically realistic molecular descriptions of proteins and their interactions with population genetics of carrier organisms without assuming any a priori fitness landscape. We found that both pleiotropy and second order selection play a crucial role at different stages of adaptation: the supply of mutators is provided through destabilization of error correction complexes or fluctuations of production levels of prototypic mismatch repair proteins (pleiotropic effects), while rise and fixation of mutators occur when there is a sufficient supply of beneficial mutations in replication-controlling genes. This general mechanism assures a robust and reliable adaptation of organisms to unforeseen challenges. This study highlights physical principles underlying physical biological mechanisms of stress response and adaptation

Landscape Genetics: From Classic Molecular Markers to Genomics

Landscape genetics combines population genetics and landscape ecology to understand processes that shape the distribution and organization of human, animal, or plant populations. This field of genetics emerged from the availability of several studies with classical molecular markers, such as isozymes, RAPD, AFLP, and microsatellites. Population genetic studies enabled the detection of population structure with those markers, but a more comprehensive analysis of natural populations was only possible with the development of statistical methods that combined both molecular data and environmental variables. Ultimately, the rapid development of sequencing technologies allowed studies at the genomic level, augmenting the resolution of association with environment factors. This chapter outlines basic concepts in landscape genetics, the main statistical methods used so far, and the perspectives of this field of knowledge into strategies for conservation of natural populations of plant and animal species. Moreover, we briefly describe the application of the field to understand historical human migration processes as well as how some diseases are spread throughout the world