My main research interest relates to the evolution of genetic diversity and differentiation between natural populations, at various hierarchical levels where diversity is expressed (from genes to phenotypic traits). The main emphasis of my research activities is the understanding of evolutionary forces that contribute to the distribution of diversity and differentiation. While focusing at the beginning on the past history of tree populations, my current interest addresses future evolution in the context of environmental changes.  I am therefore using microevolutionary approaches by linking genetics, genomics and ecology, along six major research areas.

1. Experimental and theoretical approaches

My research combines theoretical and experimental approaches. An important goal is to gather population data at various spatial and geographic scales to describe and dissect population differentiation, and to depict general distribution patterns. These data are then compared to theoretical predictions obtained by analytical derivations or simulations, where various different evolutionary scenarios are tested.

2. Study species

I am working on long lived temperate tree species, as European white oaks, mainly Quercus petraea (sessile oak) and Quercus robur (pedunculate oak)) and other related Fagaceae species. Extensive diversity assessments were conducted at various spatial scales at the molecular and phenotypic level. We have recently concentrated our monitoring efforts along geographic gradients that mimic spatially temporal variation expected under climate change. These data sets are further completed by genomic and genetic resources (genetic maps, EST libraries, QTLs  …) and made available to the scientific community via an electronic portal.

3. Monolocus vs multilocus differentiation

A major difference between phenotypic and molecular differentiation is related to the different architecture of traits. Phenotypic traits are multilocus traits and markers are most generally single locus traits. These differences result in different expectations for differentiation, as linkage disequilibrium may largely inflate differentiation for phenotypic traits (Qst) in comparison to single locus markers or genes (Fst). I am exploring the mechanistic and evolutionary causes of the decoupling of diversity between traits and genes.

4. Adaptive vs neutral differentiation

During recent years we conducted several gene expression studies in European oaks to identify genes controlling traits of important ecological and adaptive significance (bud burst and tolerance to anoxia). We are currently assessing diversity in these genes in natural populations of white oak species that exhibit contrasting adaptive responses, in comparison to earlier differentiation obtained with neutral markers, with the aim to identify molecular footprints of natural selection.

5. Genomic distribution of genetic differentiation

Locating genomic regions responding to natural selection is being investigated by scanning the dense genetic maps for differentiation. These investigations are being conducted by two complementary ways: mapping QTLs of adaptive traits and scanning Fst values of markers along linkage groups of genetic maps of Q. petraea and Q. robur.

6. Population and species differentiation

We are monitoring differentiation between populations within different oak species, but also among two closely related white oak species (Q. petraea  Q. robur Q.pubescens and Q.pyrenaica). Differentiation is seen as a common footprint of multilocus selection  responsible for species divergence is this oak complex




2014-2020 Project TREEPEACE supported by the European Union (ERC Advanced Grant FP7 -339728) «From the Holocene to the Anthropocene: the pace of microevolution in trees » Principal Investigator: Antoine Kremer

There are widespread concerns that trees, due to their long life-span, are not able to cope with the rapid ongoing climate change. While many studies have so far investigated potential impacts of climate change on forests, much less attention has been given to the potential evolutionary responses of tree populations. However there is a large body of evidence stemming from experimental evolutionary genetics showing that adaptive differentiation has extensively occurred during past environmental changes. TREEPEACE challenges these views and explores the pace at which evolutionary change has taken place during past gradual and under current rapid environmental change.  It builds on the reconstruction of evolutionary trajectories during the Holocene and Anthropocene to infer evolutionary rates, taking temperate oaks as a case study. The project assembles insights and contributions from paleobotany, ecology, ecophysiology, genetics, genomics and evolution in a generic framework for the assessment and prediction of rates of evolution at different hierarchical levels (genome to phenome). Beyond the assessments of past and current evolutionary change, the project provides an integrative simulation framework that will allow the monitoring and prediction of adaptive responses of trees under various evolutionary scenarios.

2014-2018  Project ANR MECC « Mechanisms of adaptation to Climate Change : how will phenotypic plasticity, microevolution and migration affect forest tree phenology » » supported by ANR. . Coordinated by  Ophélie Ronce.  5 research units.

Even if greenhouse gas emissions decrease in the next decades, rapid change in temperature and rainfall will occur, with long-term implications for the viability of ecosystems and their services. A major scientific challenge is thus to predict the adaptation of natural populations to this changing world in terms of migration, plasticity, and genetic change. In this project, we aim at studying the interplay of the three above mechanisms to describe and forecast adaptation of forest trees to climate change. More specifically, we want to (1) evaluate the adaptive value of phenotypic plasticity in current and future climates at different spatial and temporal scales, (2) understand how microevolution in interaction with phenotypic plasticity and gene flow shape phenotypic variation, as well as predict how these three mechanisms of adaptation would act on phenotypic variation in the future, (3) use our increased understanding of phenotypic variation in time and space and its dynamics to better predict current and future species distribution under several scenarios of climate change.

2011-2020 Cluster of Excellence COTE supported by the  Commissariat Général à l’Investissement. « Continental to coastal ecosystems : evolution, adaptability and governance ». Coordinated by  Antoine Kremer (UMR BIOGECO) and Hélène Budzinski (UMR EPOC). 10 labs belonging to  University of  Bordeaux 1, Bordeaux 2 , Bordeaux 4, INRAE, CNRS, IFREMER and  CEMAGREF. COTE aims to identify the drivers of ecosystem evolution, to decipher their responses to global changes, and to provide predictive tools and methods for their regulation. It brings together complementary disciplines, ranging from environmental physics and chemistry, ecology and evolutionary sciences to economics and social sciences. The LabEx will investigate how interactions of neighboring natural versus cultivated and coastal versus terrestrial ecosystems may drive specific changes in functions and services of ecosystems. The LabEx is composed of 10 laboratories belonging to major national research institutions involved in environmental sciences of terrestrial and aquatic ecosystems, and gathers about 200 scientists.