Population genetics

Population genetics is the study of change of gene alleles frequencies in time and space. This allows making inferences about ecological (migration of individuals between populations) and evolutionary (mutation, selection, drift) processes at different spatial and temporal scales. Applied to genetic markers of infectious diseases agents, population genetics methods allow better understanding the mode of reproduction (clonal vs sexual) of infectious agents, the transmission network of infectious agents in host population or in a community of host species (between-host infectious disease transmission).

    • Notions of molecular biology and formal genetics
    • Population genetics
    • Genetic markers
    • Linkage disequilibrium
    • Alterations of Hardy-Weinberg proportions
    • Wright’s F-statistics
    • Inferences
    • Statistical procedures

  • Virginie Rougeron

    Virginie Rougeron received her PhD degree from the University of Montpellier in 2009. Her research focused on different aspects of the evolution and ecology of host-pathogen interactions, such as reproductive strategies of pathogens, human genetic polymorphisms involved in resistance to infectious diseases and genetic relationships between parasites infecting humans versus those infecting non-human great apes. Between 2012 and 2016, she has been working in Gabon first on the evolution of viruses, then, recruited in 2015 at the CNRS laboratory MIVEGEC , as a researcher, she is now developing a research project on the evolutionary history and genetic adaptation of Plasmodium vivax, the major cause of malaria outside Africa with tens of million of cases reported each year all over the world. The goal of this project is to study in details the evolutionary relationships between ape and human P. vivax clades, to characterize the mechanisms involved in the adaptation to their respective hosts and finally to evaluate the risk of transfer between these hosts in areas of contact.

    Anne-Laure Bañuls

    Anne-Laure Bañuls received a PhD in Biology and Health from the University of Montpellier in 1998. She has been a researcher at IRD since 2000 and has been posted in Hanoi, Vietnam since 2014. Specialist in population biology of pathogens and in molecular epidemiology, she seeks to deduce the modes of transmission, the virulence factors and / or drug resistance from molecular data. Her research focuses on several infectious diseases such as leishmaniases and tuberculosis, the latter one being at the center of her projects in Southeast Asia. The projects she develops in southeast Asia involve several countries and her main partners are the National Institute of Hygiene and Epidemiology (NIHE), the University of Science and Technology of Hanoi (USTH), the Pasteur Institute of Cambodia, the CICML (Centre d’Infectiologie Christophe Mérieux du Laos) and Fondation Mérieux. She is co-director of the International Joint Laboratory DRISA (Drug Resistance in Southeast Asia) studying the mechanisms of bacterial drug resistance emergence and their transmission at different spatial and temporal scales.

    Franck Prugnolle

    Franck Prugnolle is an evolutionary geneticist, specialist of host-parasite coevolution. He received his PhD in 2003 from the university of Montpellier (France). During his career, He worked in different institutions (University of Cambridge (UK), North Carolina state University (USA), University of Montpellier (France) and CIRMF (Gabon)) and worked on several aspects of the evolution of host / parasites interactions. For the last 10 years, he has studied the evolution of the agents of malaria in humans and great apes using the tools of population genetics, phylogenetics and comparative genomics.

    Thierry de Meeus

    Thierry de Meeûs received a PhD in population biology from the University of Montpellier (1991). He has been a researcher at CNRS in Montpellier, France, from 1993 to 2012 when he joined IRD as a director of research. He has been posted in Burkina Faso from 2009 to 2015. His research has focused on adaptive polymorphism and habitat preference evolution, as well as the use of population genetics tools for population biology inferences in host parasite systems. His current research is on hosts and parasites co-structure and the use of molecular markers in ecological inference, in particular in epidemiological systems. He’s also working on the theoretical and applied population genetics of clonal organisms. He current research is mostly on trypanosomiasis and leishmaniasis. He is the author of more than 150 scientific articles and of one text book on the population genetics of parasites and their vectors.


  • Fstat, Genepop, Genetix, Easypop, MEGA, R, RStudio, and Excel.
    R packages: hierfstat