Research

We are interested in understanding how natural populations evolve and adapt at the genomic level. My group is particularly interested in the process of adaptation and speciation, through which clusters of individual genotypes become distinct and persist over time. This is the fundamental process that underlies the evolution and diversification of life.

How, when, and why did distinct populations or species split? What are the evolutionary footprints left in their genomes? What is the role of natural selection in shaping the diversity of natural populations and species? When sexual species hybridize and share genetic material, why don’t they eventually collapse into a single species? What are the consequences of the exchanges of genetic material between species, and how often is this process beneficial? These are some of the questions I work on.

The Fontaine’s Lab has been working on a broad range of organisms ranging from marine mammals to plant pathogens, and mosquitoes. Since 2012, my research interest has focused increasingly towards the diverse and highly adaptable Anopheles mosquitoes, well known as vectors of the deadly Plasmodium parasites responsible of malaria. Most anopheles species are complex of closely related species including races with distinct ecology (“ecotypes”) that hybridize in the wild.

My overall goal is to improve our understanding of speciation and adaptation by testing hypotheses about the mechanics of these processes. By better understanding the pattern of diversity, introgression, and adaptation, my work also contributes to design and assess the feasibility and impacts of new vector control strategies. I use genome sequencing of natural populations combined with both descriptive and model-based computational approaches, most of which are rooted in population-genetic theory. I am interested in developing creative ways of working with genomic data, so that we can get the most out of this tremendous resource.

Here is a list of the various research projects funded over the past years

Ongoing research projects

Evolutionary genomics & bioinformatics of vector Mosquitoes (Anopheles sp, Aedes albopictus, Aedes aegypti)

EyWA: Evolutionary genomics of the Aedes aegypti mosquitoe’s in the West indies: impact of transposable element in their Adaptation

PIs: AS Fiston-Lavier (ISEM), MC Fontaine (MIVEGEC), D. Couvin (U. Antilles), E Permal, A Vega-Rua, E. Calvbel (IP Guwadeloupe)
Funded by MITI-CNRS - “Pépinière interdisciplinaire des Antilles françaises” (PIAF) 2024

GALVA2DAPT_: Genomic Analyses based on Long-read Variation in Aedes albopictus ADAPTation

PIs: MC Fontaine, AS Fiston-Lavier, L Orlando, C Paupy, C Costantini
Funded by the “Défis cles Région Occitanie - Risque infectieux et vecteurs (RIVOC)- Occitanie”

KIM-RIVE INVALBO

PIs: MC Fontaine (MIVEGEC - U. Montpellier, CNRS, IRD ) & Sebastien Boyer (Pasteur Institute Cambodia)
Keywords: Aedes albopictus ; biological invasion ; genomics of local adaptation ; urban vs natural habitat; Phnom Penh (Cambodia)
Funded by the Key Initiative MUSE Risks & Vectors (U. Montpellier)

Evolutionary genomics of Plasmodium

ANR HAMLET: To Die, To Sleep: Biology and Evolution of Dormancy in Avian Malaria Parasites

PI: Ana Rivero (MIVEGEC)
Partners: C Loiseau (MIVEGEC), MC Fontaine (MIVEGEC), A Talman(MIVEGEC), S Gandon (CEFE)
Funded by the French National Research Agency (ANR)

ANR GENAD: Genetic adaptation of parasites to new environments: Plasmodium vivax in Americas

PI: V Rougeron
Partners: MC Fontaine, F Prugnol
Funded by the French National Research Agency (ANR)

OrA: Origin and Adaptation of parasites to new environments: the case of monkey malarial agents in French Guiana

PIs: Virginie Rougeron, Michael C. Fontaine, Olivier Duron, Benoit De Thoisy
Funded by the Laboratoire of excellence CEBA (Center for the study of biodiversity in Amazonia)

Evolutionary & Conservation genomics (Porpoises & Dolphins especially, but not only)

Porpoise Genome project

Past research projects

NWO

Adaptive Life Programme from GELIFES - U. Groningen

2017: How species of malaria vector mosquitoes emerged and evolved in the Anopheles gambiae complex

PIs: Michael Fontaine, Sander van Doorn, & Bregje Wertheim

Summary: Evidence of introgressive hybridization is widespread in the tree of life, occurring especially among closely related species in various clades such as hominids, Anopheline mosquitoes and Heliconius butterflies. High-resolution genomic-data have recently been produced and enabled scientists to perform in-depth investigation of the extent and evolutionary consequences of introgression on the adaptation and speciation processes. However, major challenges remain to redefine key biological concepts and our understating of speciation: How can species diverge and adapt to distinct ecological niches if their reproductive barriers are porous? What genomic features and processes keep species as separate entities if their genomes are a blend of private genomic sequences that have evolved within the species and genomic information borrowed from related organisms but with an independent evolutionary past? What are the adaptive implications of introgression and how to quantify them? This project explores the genetic architecture of divergence, adaptation and speciation with gene-flow in the medically important A. gambiae species complex, mosquito vectors of the deadly Plasmodium sp. parasite causing malaria. We will use state-of-the-art population genetic approaches to analyse mosquitoes’ genetic diversity using new comprehensive genomic data about the species complex. From a theoretical perspective, we will use mechanistic models to simulate conditions under which species of A. gambiae complex diverged and specialize ecologically in face of gene flow; we will also simulate introgression occurring between individuals to analyse the resilience of allele networks occurring in nature and, using agent-based models, we will aim to understand how patterns of gene flow can become established and be affected by changes in the environment. Finally, we will try to integrate the results produced in the previous three approaches in a definitive theory of speciation that incorporates the concept of gene exchange and porous reproductive barriers.

Related phd at GELIFES - U. Groningen by Jorge E. Amaya Romero (now post-doc at Harvard U.): Speciation and evolution in the Anopheles gambiae complex in the face of widespread introgressive hybridization. doi: 10.33612/diss.824282369. See project results.

2017: Adaptive diversity and eco-evolutionary dynamics

PIs: Rampal Etienne, Sander van Doorn & Michael Fontaine

Summary: While the genetic basis of more and more traits is being unravelled, the complexity of the genome has remained underappreciated in making theories on one of the most important questions in evolution, how do species form? Most of the models of speciation make simplistic assumptions with respect to the genomic basis of potential traits under disruptive selection, or leading to reproductive isolation. We know recombination is heterogeneous across the genome (linkage blocks are often present, separated by hot spots of recombination) and it is likely that most genes act in epistasis (the effect of an allele depends on its genetic background) in their contribution to individual fitness. These two fundamental properties are likely interacting with natural or sexual selection regimes to lead to divergence between populations and speciation, but their relative influence on the divergence process is unknown. In this study, we propose tackling the question of the relationship between genome structure and eco-evolutionary divergence using individual-based models to simulate speciation under various scenarios of genomic complexity and ecological interactions and investigate their impact on diversification, and diversity. We will empirically test the link between recombination and divergence across the genome in a case study of malaria mosquitoes Anopheles gambiae showing putative ecological speciation mediated by reduced recombination. This project will help build a more integrative theory of speciation as well as in enhancing further research in research on malaria vectors.

Related phd at GELIFES - U. Groningen by Raphaël Scherrer. See project results

2016: Reproductive parasitism in a love triangle – Wolbachia, master manipulator or microbe mediator?

PIs: Leo Beukeboom, Joana Falcao Salles & Michael Fontaine

Summary: We will study the triangular interactions between cytoplasmic incompatibility inducing Wolbachia bacteria, the host nuclear genome and the remainder of the microbiome in the parasitoid wasp genus Nasonia. Questions that will be addressed are how vertical inheritance and environmental acquisition shape microbiome composition in Wolbachia-infected and –uninfected individuals; how different microbiome compositions affect reproductive manipulation by Wolbachia; whether novel Wolbachia infections lead to shifts in microbiome composition; and how Wolbachia affects host gene expression in interaction with the microbiome.

Related phD at GELIFES - U. Groningen: Complex interactions in a host-symbiont-microbiome triangle: The wasp Asobara japonica, the endosymbiont Wolbachia and the remainder microbiome by Pina Brinker (now postdoc at the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig). doi: 10.33612/diss.240460364 See project results.

2016: Human induced eco-evolutionary feedbacks restructure ecosystems and limit their recovery

PIs: Klemens Eriksson, Michael Fontaine & Martine Maan

Summary: Declines in top-predators have enabled the threespine stickleback to increase hundred-fold in the Baltic Sea the past decade. Today, stickleback have reorganized the coastal food-web dramatically, causing algal overgrowth and decreased water quality. We hypothesize that the problems are caused by a benthic ecotype of stickleback that have adapted rapidly to the new biological conditions and thereby locked coastal areas in a societally undesirable state. The project will combine ecological field studies, behavioral experiments and population genetics to characterize the ecological and evolutionary impacts of the benthic ecotype and the underlying genetic mechanisms.

Related PhD at GELIFES by Casey Yanos: Eco-evolutionary dynamics in the Baltic Sea: Distribution and impact of threespine stickleback phenotypes in a changing environment. doi: 10.33612/diss.192995846. See project results