Institut Jacques Monod

Grange Geigl Lab VA

Epigenome and Paleogenome

THIERRY GRANGE & EVA-MARIA GEIGL

« Nothing in biology makes sense except in the light of evolution” (Theodosius Dobzhansky, 1900-1975). Our overarching research theme is the study of the evolution of genomes in effort to deepen our understanding of the relationship between genotypes and phenotypes’ aiming at deepening our understanding of the evolutionary relationship between genotypes and phenotypes. Recent phenotypic adapatations are ideal to identify the underlying genomic evolution while minimizing the the confounding effects of genetic drift. Our laboratory is currently working on several research projects concerning the recent evolution of genomes through the analysis of ancient genomes from fossils, the direct witnesses of evolution. This paleogenomic approach adds a geological or historical time-scale to evolutionary studies anchoring and rendering more robust evolutionary modeling from present-day genomes. We use and develop paleogenetic and paleogenomic approaches to document evolutionary processes occurring over the last hundreds of thousands of years and to push methodological limits to enable the study of more ancient samples and fossils from geographic regions where the hot climate is particularly detrimental to DNA preservation.

We focus on two major research lines: 1) We study animal genomes throughout their domestication processes, as domestication represents a unique, accelerated and human-driven model of evolution of specific genomic regions. 2) We study the genomic evolution of human populations during the peopling of Europe since the last Ice Age.

Keywords : evolution, genomes, ancient DNA, paleogenomics, peopling, domestication

+33 (0)157278129      thierry.grange (at) ijm.fr / eva-maria.geigl (at) ijm.fr     @ThierryGrange5

Research

« Nothing in biology makes sense except in the light of evolution” (Theodosius Dobzhansky, 1900-1975). Our overarching research theme is the study of the evolution of genomes in effort to deepen our understanding of the relationship between genotypes and phenotypes’ aiming at deepening our understanding of the evolutionary relationship between genotypes and phenotypes. Recent phenotypic adapatations are ideal to identify the underlying genomic evolution while minimizing the the confounding effects of genetic drift. Our laboratory is currently working on several research projects concerning the recent evolution of genomes through the analysis of ancient genomes from fossils, the direct witnesses of evolution. This paleogenomic approach adds a geological or historical time-scale to evolutionary studies anchoring and rendering more robust evolutionary modeling from present-day genomes. We use and develop paleogenetic and paleogenomic approaches to document evolutionary processes occurring over the last hundreds of thousands of years and to push methodological limits to enable the study of more ancient samples and fossils from geographic regions where the hot climate is particularly detrimental to DNA preservation.

We focus on two major research lines: 1) We study animal genomes throughout their domestication processes, as domestication represents a unique, accelerated and human-driven model of evolution of specific genomic regions. 2) We study the genomic evolution of human populations during the peopling of Europe since the last Ice Age.

We have developed five interdisciplinary research themes:

  1. Paleogenomic study of the dynamics of bovine populations during the Pleistocene influenced by climate and humans. Through the analysis of mitochondrial and nuclear genomes in up to 150,000-year-old fossils, we retrace migrations, contractions, expansions, extinctions and replacements of aurochs and bison populations. We aim to discriminate between environmental and human-induced effects on the evolution of these large herbivore populations by comparing the two sister-species, Bos and Bison, as only Bos (the aurochs) was domesticated.
  2. Evolution of the bovine genome during domestication. We use paleogenomic approaches to reconstruct the genomic modifications that have occurred over the last ~9 000 years during the domestication of the aurochs, the wild ancestor of present-day cattle. We are characterizing in time and space the selection exerted by different ancient societies on particular genomic regions thus shaping the genomic make-up of present-day cattle breeds.
  3. Evolution of the cat genome during domestication. Using ancient genomes, we attempt to reconstruct the domestication history of the cat over the last ~10,000 years, which is very different from the one of cattle. The cat’s domestication largely followed the commensal pathway and selective breeding became a prominent domestication mechanism only very recently. Currently, we are also characterizing the genomic adaptation of the domestic cat alongside its interaction and hybridization with the European wildcat.
  4. Paleogenomics of the Neolithic of the Paris Basin. We analyze the genomes of individuals who lived in the Paris Basin between ~7,000 and 4,500 years ago to reconstruct the evolution of their corresponding populations, along with the gene flow, admixture and migrations that took place during this period. This study lends us broader insight into the evolution of the peopling of France as the Neolithic represents a key period for the development of societies leading to the present.
  5. Paleogenomics of the evolution of disease susceptibility and resistance on the territory of present-day France since the Neolithic. We are analyzing the co-evolution of humans and cattle and the influence of epidemics, including bovine zoonoses, on the genomes of the populations in the north and west of France from the Neolithic, 7,200 years ago, to the present.

Members

Group Leaders:

Thierry GRANGE
Téléphone : +33 (0)157278129
Email : thierry.grange (at) ijm.fr

Eva-Maria GEIGL
Téléphone : +33 (0)157278132
Email : eva-maria.geigl (at) ijm.fr

 

Members:

Fabien FAUCHEREAU Researcher
Lesley Caitlin MARTIN PhD Student
Manon STEPANOFF Master 2

Selected Publications

E. Andrew Bennett, Oğuzhan Parasayan, Sandrine Prat, Stéphane Péan, Laurent Crépin, Alexandr Yanevich, Thierry Grange*, Eva-Maria Geigl* Genome sequences of 36,000 to 37,000 year-old modern humans at Buran-Kaya III in Crimea. (2023) Nature Ecology and Evolution https://doi.org/10.1038/s41559-023-02211-9

Bennett, E.A., Weber, J., Bendhafer, W., Champlot, S., Peters, J., Schwartz, G., Grange, T., Geigl, E.-M. (2022) The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia. Science Advances 8, eabm0218. DOI : 10.1126/sciadv.abm0218

Guimaraes, S., Arbuckle, B., Peters, J., Adcock, S., Buitenhuis, H., Chavin, H., Manaseryan, N., Uerpmann, H.-P., Grange, T.*, Geigl, E.-M.* (2020) Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age. Science Advances, 6: eabb0030, DOI: 10.1126/sciadv.abb0030

Brunel, S., Bennett, E.A., Cardin, L., Garraud, D., Barrand Emam, H., Beylier, A., Boulestin, B., Chenal, F., Cieselski, E., Convertini, F., Dedet, B., Desenne, S., Dubouloz, J., Duday, H., Fabre, V., Gailledrat, E., Gandelin, M., Gleize, Y., Goepfert, S., Guilaine, J., Hachem, L., Ilett, M., Lambach, F., Mazière, F., Perrin, B., Plouin, S., Pinard, E., Praud, I., Richard, I., Riquier, V., Roure, R., Sendra, B., Thevenet, C., Thiol, S., Vauquelin, E., Vergnaud, L., Grange, T.*, Geigl, E.-M.*, Pruvost, M.* (2020) Ancient genomes from present-day France unveil 7,000 years of its demographic history. Proceedings of the National Academy of Sciences USA, 117(23):12791-12798, DOI:10.1073/pnas.1918034117.

Bennett, E.A., Crevecoeur, I., Viola, B., Derevianko, A.P., Shunkov, M.V., Grange, T., Maureille, B., Geigl, E.-M. (2019) Morphology of the Denisovan phalanx closer to modern humans than to Neandertals. Science Advances, 5:eaaw3950, DOI 10.1126/sciadv.aaw3950, DOI: 10.1126/sciadv.aaw3950

Grange, T., Brugal, J.-P., Flori, L., Gautier, M., Uzunidis, A., Geigl, E.-M. (2018) The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters. Diversity 10, 65; doi:10.3390/d10030065

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) The paleogenetics of cat dispersal in the ancient world. Nature Ecology & Evolution 1, 0139. DOI: https://doi.org/10.1038/s41559-017-0139.

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) Taming the Late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA. Plos one 12(4): e0174216. /doi.org/10.1371/journal.pone.0174216

Massilani, D., Guimaraes, S., 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) Past climate changes, population dynamics and the origin of Bison in Europe. BMC Biology 14:93-110. DOI 10.1186/s12915-016-0317-7

Guimaraes S, Pruvost M, Daligault J, Stoetzel E, Bennett EA, Côté NM, Nicolas V, Lalis A, Denys C, Geigl EM*, Grange T.* (2017) A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa. Mol Ecol Resour. 17: 405-417. doi: 10.1111/1755-0998.12565

Champlot S., Berthelot C., Pruvost M., Bennett E. A., Grange T. and Geigl E.M. (2010) An Efficient Multistrategy DNA Decontamination Procedure of PCR reagents for Hypersensitive PCR Applications. PLOS One, 5(9), e13042.

Pruvost, M., Schwarz, R., Bessa Correia, V., Champlot, S., Braguier, S., Morel, N., Fernandez-Jalvo, Y., Grange, T., Geigl, E.-M. (2007) Freshly excavated fossil bones are best for amplification of ancient DNA. Proc. Ntl. Acad. Sci. USA, 104, 739-744.

*shared senior authors

All the publications since 2017

Publications 

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Ottoni, C., Van Neer, W., De Cupere, B., Daligault, J., Guimaraes, S., Peters, J., Spassov, N., Prendergast, M. E., Boivin, N., Morales-Muñiz, A., Bălăşescu, A., Becker, C., Benecke, N., Boroneant, A., Buitenhuis, H., Chahoud, J., Crowther, A., Llorente, L., Manaseryan, N., … Geigl, E.-M. (2017). The palaeogenetics of cat dispersal in the ancient world. Nature Ecology & Evolution, 1(7), 1–7. https://doi.org/10.1038/s41559-017-0139
Guimaraes, S., Pruvost, M., Daligault, J., Stoetzel, E., Bennett, E. A., Côté, N. M.-L., Nicolas, V., Lalis, A., Denys, C., Geigl, E.-M., & Grange, T. (2017). A cost-effective high-throughput metabarcoding approach powerful enough to genotype 44 000 year-old rodent remains from Northern Africa. Molecular Ecology Resources, 17(3), 405–417. https://doi.org/10.1111/1755-0998.12565

 

Preprint 

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Bennett, E. A., Crevecoeur, I., Viola, B., Derevianko, A. P., Shunkov, M. V., Grange, T., Maureille, B., & Geigl, E.-M. (2019). Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals. Science Advances, 5(9), eaaw3950. https://doi.org/10.1126/sciadv.aaw3950

 

Book chapter

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Geigl, E.-M., & Grange, T. (2023, October 23). Homo sapiens : comment deux crânes réécrivent l’histoire de son apparition en Europe – Nouvelle recherche. The Conversation. http://theconversation.com/homo-sapiens-comment-deux-cranes-reecrivent-lhistoire-de-son-apparition-en-europe-nouvelle-recherche-216195
Nature, R. C. by S. (2023, October 4). Crimea’s place in Europe 36,000 years ago: a tale of ancient genomes. Research Communities by Springer Nature. https://ecoevocommunity.nature.com/posts/crimea-s-place-in-europe-36-000-years-ago-a-tale-of-ancient-genomes
Avant les chevaux, des hybrides d’ânes produits pour faire la guerre | CNRS. (2022, January 14). https://www.cnrs.fr/fr/avant-les-chevaux-des-hybrides-danes-produits-pour-faire-la-guerre
Carpentier, C. (2021, January 21). Contribution de la paléogénétique à l’archéologie [Billet]. Rencontres scientifiques et techniques de l’Inrap. https://sstinrap.hypotheses.org/5382
Geigl, E.-M. (2020). La pré- et protohistoire de l’Europe révélée par la paléogénomique. Histoire de la recherche contemporaine. La revue du Comité pour l’histoire du CNRS, Tome IX-n°2, 139–141. https://doi.org/10.4000/hrc.4808
Geigl, E.-M. (2020, September 13). Qui a habité en France ces 9 000 dernières années ? The Conversation. http://theconversation.com/qui-a-habite-en-france-ces-9-000-dernieres-annees-139769
Geigl, E.-M. (2020, January 13). Une petite phalange réécrit l’histoire évolutive des humains. The Conversation. http://theconversation.com/une-petite-phalange-reecrit-lhistoire-evolutive-des-humains-123156
Geigl, E.-M. (2018). La paléogénétique en tant qu’approche archéométrique au cours des 30 dernières années. ArcheoSciences. Revue d’archéométrie, 42, 135–144. https://doi.org/10.4000/archeosciences.5575
Grange, T., & Geigl, E.-M. (2018). Grâce à la domestication, le chat a gagné le monde / Thierry Grange. Grâce à la domestication, le chat a gagné le monde / Thierry Grange. https://www.mediatheque.mc/Default/doc/SYRACUSE/1271673/grace-a-la-domestication-le-chat-a-gagne-le-monde-thierry-grange
How cats conquered the Ancient world: a 9,000-years DNA tale. (2017). TheScienceBreaker. https://doi.org/10.25250/thescbr.brk062
Geigl 01 57 27 81 32, E.-M. (2016, October 26). 50 000 ans d’histoire du bison européen retracée grâce à l’ADN ancien | CNRS Biologie. https://www.insb.cnrs.fr/fr/cnrsinfo/50-000-ans-dhistoire-du-bison-europeen-retracee-grace-ladn-ancien
Actualités des fouilles et de la recherche | Archéologia n° 606. (n.d.). Retrieved February 19, 2024, from https://www.faton.fr/archeologia/numero-606/domestication-animale/actualites-fouilles-recherche.55371.php#article_55371
Démographie. Le peuplement de la France à la Protohistoire grâce à la paléogénomique | Archéologia n° 589. (n.d.). Retrieved February 19, 2024, from https://www.faton.fr/archeologia/numero-589/l-archeologie-sous-marine/demographie-peuplement-france-a-protohistoire-grace-a-paleogenomique.51504.php#
Why haven’t cats evolved since domestication, unlike other animals? (n.d.). New Scientist. Retrieved June 2, 2023, from https://www.newscientist.com/lastword/mg25233611-200-why-havent-cats-evolved-since-domestication-unlike-other-animals/

Theses

Thèses de l’équipe depuis 2010:

  • Jeanne Mattei :« Paléogénomique de la domestication des chats » soutenue le 20 décembre 2023
  • Oguzhan Parasayan : “Genomic evolution of of ancient French populations” soutenue le 20 décembre 2022
  • Wejden Bendhafer : « Paléogénomique de l’évolution des Bovina et l’impact sur la domestication des bovins». Soutenance de thèse le 20/12/2021.
  • Caitlin Martin : « The evolution of and selection upon the human genome since the invention of agriculture: a historical perspective on diseases”; en cours depuis Octobre 2020
  • Samantha Brunel : « Analyse paléogénétique du peuplement de la France ». Soutenance de thèse le 14/11/2018.
  • Olivier Gorgé : «Diagénèse de l’ADN bactérien et analyses métagénomiques de pathologies bactériennes du passé ». Soutenance de thèse le 13/12/2016.
  • Diyendo Massilani : « Paléogénomique des Bovina et de leur domestication ». Soutenance de thèse le 6/7/ 2016.
  • Nathalie Côté : « Apports de la paléogénétique à l’étude des helminthes garstro-interstinaux anciens». Soutenance de thèse le 16/12/2015 .
  • Sophie Champlot : « Colonisation et domestication de l’Europe et du pourtour méditerranéen », Ecole Doctorale « Gènes, Génomes et Cellules », soutenue le 13/7/2010.

Collaborations

Collaborations scientifiques avec plus de 60 chercheurs nationaux et internationaux de 20 pays, surtout des archéologues, archéozoologues, paléoanthropologues

GRANTS – FUNDING

Financements de l’équipe depuis 2010 :

2021-2024           Projet européen WIDESPREAD-05-2020 – Twinning: « Mapping The Neolithic Expansion In The Mediterranean: A Scientific Collective To Promote Archaeogenomics And Evolutionary Biology Research In Turkey” (H2020-WIDESPREAD-2020-5; CSA 952317; NEOMATRIX

2018-2021           “Paléogénomique de la domestication des bovins pour enrichir les stratégies durables de sélection (PATH2BOS) », ANR, coordinateur : Thierry Grange

2016-2021           “ Etude Génétique de la population Française (FROGH)“, ANR, coordinateur : Christian Dina, Institut du Thorax, UMR 1087/ UMR 6291, Nantes. Equipe « Epigénome & Paléogénome » :  « Paléogénomique de la population médiévale de l’Ouest de la France ».

2015-2019           “Genetic characterization of Ancestral French populations using ancient DNA (ANCESTRA)” ANR JCJC – ANR-15-CE27-0001; Coordinatrice: Mélanie Pruvost, Institut Jacques Monod, Paris.

2014-2016           “The origins of Equid domestication”, National Science Foundation (NSF) Prime Award N° BCS-1311551; Coordinateur: Benjamin Arbuckle, University of Chapel Hill, North Carolina, USA. « Epigénome & Paléogénome » :  “Paleogenetics of the domestication of horses in Anatolia and the Caucasus”

2010-2014           “Influence de l’installation des hommes modernes au Maroc sur l’évolution de la biodiversité des petits vertébrés terrestres (MOHMIE)“ ; Agence Nationale de Recherche (ANR) n° 2009 PEXT 004 05; Coordinatrice : C. Denys, Muséum National d’Histoire Naturelle. « Epigénome & Paléogénome » :  “Paléogénétique des rongeurs au cours des derniers 120,000 ans”

News

23 octobre 2023 – New article published in Nature Ecology and Evolution : Genome sequences of 36-37,000 year-old modern humans at Buran-Kaya III in Crimea

10 mars 2023 – Seminar at the Collège deFrance “L’évolution des populations humaines et animales : une histoire de migrations et métissages“. 

This seminar correspond to a part of the course “L’histoire de l’humanité vue sous l’angle de la paléogénomique” given by Lluis Quinatana-Murci.

A new study by the Grange/Geigl team published in Science Advances on 14 January 2022!

  • Before the introduction of the domestic horse in Mesopotamia, valuable equids were being harnessed to ceremonial or military four wheeled wagons and used as royal gifts, but their true nature remained unknown.
  • According to a palaeogenetic study, these prestigious animals were the result of a cross between a domestic donkey and a wild ass from Syria, now extinct.
  • This makes them the oldest example of an animal hybrid produced by humans.

> CNRS Press release

 

Fête de la science 2021 – Conférence “La génétique du peuplement de l’Europe depuis l’âge des glaces”

 

Communications de notre recherche par le CNRS :

https://archives.cnrs.fr/insb/article/2016/e-m-geigl

https://inee.cnrs.fr/fr/cnrsinfo/ladn-ancien-au-secours-despeces-en-voie-de-disparition-retracer-leur-evolution-pour-mieux

https://lejournal.cnrs.fr/articles/comment-le-chat-a-conquis-le-monde

https://www.cnrs.fr/fr/un-nouveau-morceau-de-phalange-rapproche-plus-les-denisoviens-des-humains-modernes-que-des

https://www.cnrs.fr/fr/7-000-ans-dhistoire-demographique-en-france

https://insb.cnrs.fr/fr/cnrsinfo/ladn-ancien-montre-que-les-chevaux-domestiques-ont-ete-introduits-au-sud-du-caucase-et-en

https://www.cnrs.fr/fr/avant-les-chevaux-des-hybrides-danes-produits-pour-faire-la-guerre

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