Epigenome and Paleogenome

Group leader

Biological phenomena can only be fully understood in the light of evolution. Comparative genomics contributes to this endeavor by helping to understand the links between genotype and phenotype through the analysis of the evolution of genomes. Recent phenotypic adaptations are particularly suited to identify the underlying genomic evolution because they minimize the complexity that is induced through neutral genetic drift. Our group conducts different projects concerning the recent evolution of genomes including modeling based on modern genomes and the direct witnesses of evolution, the genetic material from fossils. To do so, we use and develop palaeogenetic and palaeogenomic approaches, on one hand to document recent evolution and on the other hand to push back the methodological limits in order to study the most ancient samples originating from geographic regions that are unfavorable for DNA preservation. Our studies focus on a particular model of recent evolution, i.e., domestication as a special case of human-driven evolution.

We have developed an interdisciplinary research to follow up four principal research lines.
1.    Increasing the reliability of palaeogenetic analyses and pushing back their limits. We optimize and develop methods of molecular biology and genomics to increase their sensitivity while increasing in parallel the stringency of the contamination prevention and decontamination methods. In collaboration with chemists specialized in the analysis of the natural organic matter we study systematically the molecular composition of fossils in order to identify markers and/or critical parameters for DNA preservation.
2.    Phylogeography of animal domestication and of endangered and extinct species. We analyse different genetic markers, particularly mitochondrial DNA, to trace the evolution, from the Pleistocene to the present, of various species under human influence. We study the domestication of cattle, donkeys and cats, but also the evolution of populations of the Asiatic wild ass and the cheetah, both highly endangered species.
3.    Evolution of the cattle genome during domestication. We develop palaeogenomic approaches to identify the modifications of the bovine genome that have occurred during the domestication of the aurochs, the wild ancestor of the cattle.
4.    Palaeoepigenomics of the evolution of regulatory sequences. We develop the study of epigenomic modifications (DNA methylation) in ancient samples to measure the functional impact of sequence changes in evolutionary witnesses that could have induced modifications in gene expression.

The group is part of the Labex “Who am I?”

Sélection de publications

The paleogenetics of cat dispersal in the ancient world.
Ottoni, C., Van Neer, W., De Cupere, B., Daligault, J., Guimaraes, S., Peters, J., Spassov, N., Prendergast, M.E., Boivin, N., Morales-Muniz, A., Bălăşescu, A., Becker, C., Benecke, N., Boronenanț, A., Buitenhuis, H., Chahoud, J., Crowther, A., Llorente, L., Manaseryan, N., Monchot, H., Onar, V., Osypińska, M., Putelat, O., Studer, J., Wierer, U., Decorte, R., Grange, T., Geigl, E.-M. (2017) Nature Ecology & Evolution. 1: 0139
Abstract

Taming the Late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA.
Bennett, E.A., Champlot, S., Peters, J., Arbuckle, B.S., Guimaraes, S., Pruvost, M., Bar-David, S., Davis, S.J.M., Gautier, M., Kaczensky, P., Kuehn, R., Mashkour, M., Morales-Muñiz, M., Pucher, E., Tournepiche, J.-F., Uerpmann, H.-P., Bălăşescu, A., Germonpré, M., Y. Günden, C., Hemami, M.-R., Moullé, P.-E., Öztan, A., Uerpmann, M., Walzer, C., Grange, T.*, Geigl, E.-M.* (2017) Plos one 12(4): e0174216.
Abstract

Past climate changes, population dynamics and the origin of Bison in Europe.
Massilani, D., Guimaraes, S., Jean-Philip Brugal, J.-P., Bennett, E.A., Tokarska, M., Arbogast, R., Baryshnikov, G., Boeskorov, G., Castel, J.-C., Davydov, S., Madelaine, S., Putelat, O., Spasskaya, N., Uerpmann, H.-P., Grange, T.*, Geigl,E.-M.* (2016) BMC Biology 14:93-110.
Abstract

A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa.
Guimaraes S, Pruvost M, Daligault J, Stoetzel E, Bennett EA, Côté NM, Nicolas V, Lalis A, Denys C, Geigl EM*, Grange T.* (2017) Mol Ecol Resour. 17: 405-417.
Abstract

Library construction for ancient genomics: single strand or double strand?
Bennett, E.A., Massilani, D., Lizzo, G., Daligault, J., Geigl, E.-M., Grange, T. (2014) Biotechniques 56:289-300.
Abstract

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