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Group Vuilleumier
Metapopulation ecology and genetics

Our aim is to answer fundamental theoretical questions on the genetics, ecology and evolution of populations. Our research focuses on understanding

(i) Dynamics of genetic diversity: evolutionary and species management consequences and genomic signatures, e.g. impact of large scale environmental changes on genetic diversity, implications for the reconstruction of populations’ demographic and evolutionary history from genomic data

(ii) Gene dynamics and fixation in heterogeneous environments, e.g. fixation when selection, population sizes, extinction and migration rates are heterogeneous, age and sojourn time of allele in populations

(iii) Dispersal in heterogeneous environment e.g. dispersal and behaviour, dispersal asymmetries, coexistence of dispersal strategies, evolution of metapopulation structure

(iv) Persistence in heterogeneous and disturbed environments e.g. disturbance and habitat aggregation, control of invasive species

(v) Metacommunity compositions in heterogeneous environment, e.g. mechanisms mediating specialists and generalists coexistence given species traits, environmental heterogeneity and spatial autocorrelation

(vi) Evolution of reproductive systems e.g. male to female heterogamety, parthenogenesis from sexual population, transition in number of self-incompatible loci.

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(i) Dynamics and evolution of genetic and genomic diversity

Work in collaboration with N.Alcala, Prof J. Goudet and Prof. J.D. Jensen

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g. bottleneck and expansion) and spatial structure (e.g. migration, number and size of populations) are known to shape the patterns of genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur, due for example to geological and climatic events. Those short and long-term environmental cycles in which habitat alternately contracts (with fragmentation) and expands (with defragmentation) have shaped nowadays species diversity and distributions. In this context, we are investigating their impact on the patterns of genetic diversity. The goals are to determine how many features of observed macro-evolutionary and macro-ecological patterns of genetic diversity can be explained using the standard assumptions of neutral theory, and to what extent other evolutionary mechanisms must be involved, for example, accelerated speciation during periods of habitat fragmentation.
Besides, we also investigate the genetic and genomic signature of population under migration fluctuations: The difference between observed and expected genetic diversity, is commonly used to infer population demographic history or to detect loci under selection (e.g. Ewens-Watterson test or Tajima’s D). For example, we disentangle the contribution of migration fluctuations to the observed excess or deficit of genetic diversity.

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(ii) Genes spread and fixation in heterogeneous environments

Work in collaboration with Prof. N. Perrin, Dr. J. Yearsley and Prof J. Goudet.

Understanding the dynamics of genetic components in biological compartments (individual, population, metapopulation) has direct relevance for understanding species adaptation to novel environments and changing environment. It is thus also of major interest for several present day health, agricultural or conservation challenges.
Vuilleumier et al. (2008) demonstrate that fixation of a novel mutant genotype can be strongly enhanced by spatial heterogeneities in selection (e.g. selective pressure) and be fastened by the occurrence of extinction processes (disturbances, control). Moreover, Vuilleumier et al. (2010) demonstrate that in structured population, assumptions on the pattern (stepping-stone, island) and type of migration models (e.g. source-sink, balanced) have drastic consequences on the fate of selected mutants. Spatial localization of newly arising mutations, patterns of selection and type of migration assumed (asymmetric, bottleneck) have been shown to have strong impacts on the likeliness of new genetic component fixation. Given the extreme sensitivity of fixation probability to characteristics of dispersal, they highlight the importance of making explicit the assumptions underlying migration models.

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(iii) Dispersal in heterogeneous environment

Work in collaboration with Dr. R. Metzger, Dr. Fontanillas and Prof. N. Perrin. Prof H.P. Possingham, Prof. B. Bolker and Dr. O. Levêque

Despite considerable evidence showing that dispersal between habitat populations is often asymmetric (e.g. river networks, directional dispersing agent, variation in habitat quality, spatial structure of the environment, social interaction) most models used to estimate population persistence assume symmetric dispersal. Dispersal strongly depends on how a species interacts with its environment and on its dispersal behaviour and strategies. With a spatially-explicit and individual-based dispersal model I have simulated complex interactions between individuals and the environment (Vuilleumier and Metzger 2006). Environmental heterogeneities and species behaviour have been shown to have a strong influence on dispersal pattern and resulting metapopulation dynamics (Vuilleumier and Perrin 2006, Vuilleumier and Fontanillas 2007). This has also strong consequences for the management of species. For example, assuming symmetric dispersal (between two populations the number of migrant exchanged is equal) when dispersal is actually asymmetric (between two populations only one population receive migrants) lead to a wrong estimation of metapopulation persistence in more than 50% (Vuilleumier and Possingham 2006, Vuilleumier et al. 2010a). Similarly, disturbance and related extinction pattern are not uniform in an environment; they can be spatially and temporarily aggregated (e.g. flooding, fire, pollution or human disturbance). Persistence of populations face to local extinction depends then not only on the regime of disturbance, but also on its spatial configurations and on the species recolonization pattern (Vuilleumier et al. 2007a, Vuilleumier and Possingham, 2012).

We are currently investigating how can evolve the rate of individual exchanges between populations (source-sink and the balanced migration) and delineate the conditions under which some metapopulation structures are more likely to emerge (the stepping-stone or island model) and which dispersal distance distributions are expected. Various forms of habitats distributions, heterogeneity in selection and fragmentation are investigated.

We also use network analysis to characterize and provide reliable management schemes for the control of an invasive African clawed frog, Xenopus laevis and the management of European beaver, Castor fiber in the Loire River.

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(iv) Persistence in spatial, heterogeneous and disturbed environments

Work in collaboration with Prof H.P. Possingham, Dr. C. Wilcox and Dr. B. Cairns

Disturbance and spatial aggregation: S. Vuilleumier has developed a stochastic, spatially-explicit model to analyze how metapopulation persistence is affected by different regimes of spread of disturbance looking at various spatial configurations and connectivity patterns (Vuilleumier et al. 2007a). With this model, S. Vuilleumier and H. Possingham also investigating how spatial and temporal variation in extinction risk and colonization impact the persistence of species and the conditions for which habitat aggregation or random distribution can favour species persistence (Vuilleumier and Possingham, 2012).

Work in collaboration with Dr. J. Yearsley and Prof. A Buttler

Invasive species: The effect of heterogeneous environments upon the dynamics of invasion and the eradication or control of an invasive species is poorly understood; S. Vuilleumier and co-workers investigated how the probability of eradication and the time for invasion or eradication are affected by spatial heterogeneity in a species' growth rate. Then, they studied the effect of control program strategies (e.g. species specificity, spatial scale, detection efficiency and local eradication efficiency) on the success and time of eradication (Vuilleumier et al., 2010).

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(v) Metacommunity compositions in heterogeneous environment

Work in collaboration with Dr. L. Büchi

The composition of metacommunity results from the combined effect of numerous evolutionary and ecological forces for example species life history traits, Kin and inter-species competition, dispersal strategies, the heterogeneity and structure of the environment. Using a unifying modeling approach, we determined the composition of metacommunity considering the combined effect of species traits (adult survival, specialization and dispersal strategies), environmental heterogeneity and structure (spatial autocorrelation, habitat availability and disturbance). In heterogeneous and disturbed environment, the type and number of dispersal strategies that coexist strongly depends on the strength of disturbance and on adult survival (Büchi and Vuilleumier, 2012). Several dispersal strategies coexist when disturbance and adult survival act in opposition. We also found that more specialized species coexisted when species have large dispersal abilities and when the number of interacting species is high (Büchi and Vuilleumier, in revision). Strong trait associations were found mostly for generalist species, while specialist species exhibited larger range of trait combinations. In most situations, generalists have low dispersal abilities, and high reproductive investment, but low competitiveness (Büchi and Vuilleumier, in prep).

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(vi) Evolution of reproduction systems: Evolutionary scenarii and genetic consequences

Work in collaboration with Prof. O. Seehausen and Prof. R. Lande.

Male to female heterogamety: In Vuilleumier et al. (2007b) we investigated the conditions under which dominant female-determining gene W can invade and become fixed in the population, changing the population from male to female heterogamety. We found that the interaction of sex-ratio selection and random genetic drift causes W to be fixed among females more often than a comparable neutral conditions (Vuilleumier et al. 2007b)

Work in collaboration with Prof. T. Schwander

To parthenogenesis from sexual population: Understanding how new phenotypes evolve is challenging because intermediate stages in transitions from ancestral to derived phenotypes often remain elusive. In Schwander et al. (2010), we describe and evaluate a new mechanism facilitating the transition from sexual reproduction to parthenogenesis. Using an analytical model, we show that if females are mate-limited, it can result in the loss of males through a positive feedback mechanism. Empirical data from Timema populations provide evidence for this simple mechanism through which parthenogenesis can evolve rapidly in a sexual population.

Work in collaboration with Dr. Hélène Niculita-Hirzel and Prof. Tatiana Giraud

Transition in number of mating type loci in fungi: Mating type self-incompatibility, is broadly present in plants, chordates, fungi and protists, incompatibility might be controlled by one or several multiallelic loci. We investigate how a transition in the number of SI loci can occur and the consequences of such event on population’s genetics and dynamics. We also analyzed the forces that drive the evolution and maintenance of these reproductive systems that are determined by mating compatibility.

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