The evolution of breeding systems
The evolution of breeding systems is of great importance for the ecology and evolution of natural organisms. In plants, variation in mating systems is often associated with different features of the life history or demography of populations. Yet, reproductive strategies themselves can evolve within a single species and transitions of breeding systems are commonly observed at the phylogenetic level. In flowering plants, the most common transition is the one from outcrossing to self-fertilization and a rich body of empirical and theoretical literature has accumulated describing the selective processes driving these transitions. Shifts to pre-dominant self-fertilization have a profound impact on developmental, demographic, genomics, and ecological features of the biology of a species. However, no statistical method exists that allows inferring the age of shifts in mating systems using genome-wide polymorphism data. In this project we develop a model-based approach that aims at jointly estimating changes in rates of self-fertilization and fluctuations in population sizes. Precise dating of transitions to self-fertilization will allow us to better understand the climatic conditions in which these major evolutionary changes occur and to evaluate how long self-fertilizing species manage to maintain themselves in fluctuating environments.
Reconstructing the demographic histories of natural populations using genetic variation
Population genetics theory provides theoretical models that establish a relation between genetic variation and major demographic features such as population sizes, population splits, and admixture events. Given empirical measures of genetic variation from natural populations, these theoretical results allow to calculate the likelihood of competing hypotheses regarding the evolutionary history of a species and to quantify important features of these histories such as the age of divergence or the intensity of gene flow between populations. These demographic reconstructions represent important ecological information about the history of natural populations but also provide valuable null hypotheses for studies aiming at identifying the effect of natural selection using genetic variation. In my group, we specialized in the reconstruction of demographic histories using large-scale genome-wide variation datasets. Besides developing pipelines and strategies to conduct population genomics analyses we are especially interested in understanding the impact of predominant self-fertilization and multiple merger on demographic inference. We apply these reconstruction approaches to Cardamine hirsuta, Drosophila melanogaster, and Copepods populations sampled in hydrothermal vents.
Estimating adaptive scenarios for recent selective sweeps
When a new beneficial mutation appears in a population, its swift increase in frequency creates a specific signal in the genetic variation surrounding the adaptive allele. This signal has been called a selective sweep and it remains measurable for a long period of time after the beneficial mutation has fixed. These signatures left by past molecular adaptations represent a unique opportunity to study the molecular changes that allowed populations to remain adapted to their environment. Several methods exist that can detect the signal of selective sweeps in genome-wide polymorphism datasets but they usually provide little or no information about the processes underlying the adaptive modification, such as the number of beneficial alleles involved, their respective contributions to fitness, their levels of dominance and epistatic interactions. Furthermore, positive selection typically acts in the context of complex demographic processes such as drift and migration, which should be taken into account when adaptive dynamics are quantified. In my group we develop simulation-based methods to describe the adaptive processes responsible for selective sweeps and pay particular attention to the effect of predominant self-fertilization and low-recombination.