Paleogenomic investigation of the Evolution of European populations using computational simulations

Their analysis has led to significant advances on hotly debated questions by providing a better understanding of the main events that shaped the diversity of today's populations. Although paleogenomics has contributed to tracing the main lines of human evolution on the European continent, these studies have also opened the door to many new interrogations.

The present project aims to investigate the evolutionary consequences of the successive population turnovers and admixture events that occurred in Europe during Prehistory using original computational simulation approaches.In our previous project, we developed a new computational method to jointly simulate modern and ancient genetic and genomic data under complex evolutionary models.

This interdisciplinary mathematical modeling approach uses a spatially explicit framework, bringing together information on demography, migration, archaeology and environment. We were able to obtain meaningful results on the evolution of European populations by applying this original method to samples distributed in a time series. In the present project, we plan to pursue our research on the evolution of Europeans by investigating new questions that have arisen from our previous project and from other recent paleogenomic studies regarding three major events involving genomic mixing between different populations.

First, we seek to better characterize in space and time the hybridization process between Neanderthals and Homo sapiens entering Europe ~45,000 years ago. Second, we aim to detail the mode of dispersal of farmers and their sex-specific interactions with hunter-gatherers along the Danube Route during the Neolithic transition, which started ~ 8,000 years ago. Third, we seek to understand if the arrival of the pastoral populations from the Eurasian steppe linked to the “Yamnaya” complex of the early Bronze Age, which occurred ~ 5,000 years ago, was facilitated by the spread of pathogens.

Our goal is to study the evolutionary consequences of these three main events that have certainly left imprints in the genomes of present-day Europeans in relation with the health of populations and their adaptation to their environment. To reach our objectives, we propose to extend two original and integrative bioinformatic methods to explore the persistence of genomic patterns under realistic evolutionary scenarios involving population (or species) admixture. Indeed, computational simulation is a powerful tool to test complex hypotheses, especially when it is integrated to a Bayesian estimation procedure. It will allow us to combine population movements, admixture events, demographic variation through time and the effects of natural selection in the models.

Our project thus holds the promise of better comprehension of the fascinating topic of European prehistory.More generally, we aim to understand the dynamics of admixture across time and space when different layers of populations succeed one another.

Our approach lies at the crossroads between population genomics and population dynamics and aims at filling the gap between these two fields of research.

We believe that our methodological developments will be useful in many research contexts, not only in human population genetics and genomics but also in ecology and conservation, for retrospective and prospective investigations of the dynamics of interbreeding between species. We aim to propose new methodological perspectives for the analysis of paleogenomic data.