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Reconstructing Europeans' genetic evolution through computer simulations and heterochronous molecular data

English title Reconstructing Europeans' genetic evolution through computer simulations and heterochronous molecular data
Applicant Currat Mathias
Number 156853
Funding scheme Project funding (Div. I-III)
Research institution Unité d'anthropologie Département de génétique et évolution Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Genetics
Start/End 01.01.2015 - 31.12.2018
Approved amount 408'588.00
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All Disciplines (2)

Discipline
Genetics
Anthropology, Primatology

Keywords (12)

Genetic ancestry; Heterochronous data; Computer simulation; Europe; Genomics; Ancient DNA; Evolution; Paleogenomics; Population Genetics; Anthropology; Neandertal; Human

Lay Summary (French)

Lead
Quand et comment s’est formé le patrimoine génétique des populations européennes actuelles ? Malgré l’accumulation de nombreuses données génétiques, et plus récemment génomiques, l’histoire génétique du continent européen reste toujours mal connue, notamment parce que les données sur les populations passées sont fragmentaires et hétérochroniques. Ce projet contribue à ce domaine de recherche en développant de nouvelles méthodes d’analyse des données existantes, par simulations informatiques et intégration de différentes sources d’information (génétique, génomique, environnement, archéologie).
Lay summary

Contenu et objectifs du travail de recherche

Le développement rapide des techniques de laboratoire a permis de produire de bases de données génétiques et génomiques provenant de populations humaines vivant actuellement autour du globe. De plus, il est désormais possible d’extraire de l’ADN fossile à partir d’ossements préhistoriques. Or, malgré l’accumulation de ces données, l’histoire génétique du continent européen reste mal connue.

Ce projet vise à développer et à utiliser une approche par simulation informatique de modèles complexes afin d’étudier l’évolution des populations européennes depuis l’arrivée des premiers Homo sapiens sur ce continent et leurs interactions avec Neandertal. Il vise notamment à étudier l’impact des fluctuations climatiques et l’influence de la transition Néolithique et d’événements démographiques ultérieurs sur la structure et la diversité génétique des populations européennes. L’originalité de l’approche proposée tient dans la possibilité d’analyser conjointement des données moléculaires contemporaines et anciennes (hétérochronie) dans un cadre réaliste qui tient compte notamment des migrations et des interactions entre populations.

Contexte scientifique et social du projet de recherche

Outre son intérêt historique, ce projet relève de la recherche en biologie évolutive puisqu’il va permettre de mieux comprendre des mécanismes biologiques complexes, intégrant la génétique/génomique et la démographie des populations. Les méthodes développées et les résultats obtenus pourront ensuite être étendus et appliqués à d’autres problématiques et à d’autres organismes.

Direct link to Lay Summary Last update: 10.10.2014

Responsible applicant and co-applicants

Employees

Publications

Publication
Cryptic Biological Invasions: a General Model of Hybridization
Quilodrán Claudio S., Austerlitz Frédéric, Currat Mathias, Montoya-Burgos Juan I. (2018), Cryptic Biological Invasions: a General Model of Hybridization, in Scientific Reports, (1), 2414-2414.
Effect of hybridization with genome exclusion on extinction risk
Quilodrán Claudio S., Currat Mathias, Montoya-Burgos Juan I. (2018), Effect of hybridization with genome exclusion on extinction risk, in Conservation Biology, 32(5), 1139-1149.
Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations
Silva Nuno Miguel, Rio Jeremy, Kreutzer Susanne, Papageorgopoulou Christina, Currat Mathias (2018), Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations, in Evolutionary Applications, 1-14.
Range expansion as an explanation for introgression in European wildcats
Nussberger B., Currat M., Quilodran C.S., Ponta N., Keller L.F. (2018), Range expansion as an explanation for introgression in European wildcats, in Biological Conservation, 49-56.
Investigating population continuity with ancient DNA under a spatially explicit simulation framework
Silva Nuno Miguel, Rio Jeremy, Currat Mathias (2017), Investigating population continuity with ancient DNA under a spatially explicit simulation framework, in BMC Genetics, (1), 114-114.
Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe
Unterländer Martina, Palstra Friso, Lazaridis Iosif, Pilipenko Aleksandr, Hofmanová Zuzana, Groß Melanie, Sell Christian, Blöcher Jens, Kirsanow Karola, Rohland Nadin, Rieger Benjamin, Kaiser Elke, Schier Wolfram, Pozdniakov Dimitri, Khokhlov Aleksandr, Georges Myriam, Wilde Sandra, Powell Adam, Heyer Evelyne, Currat Mathias, Reich David, Samashev Zainolla, Parzinger Hermann, Molodin Vyacheslav I., et al. (2017), Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe, in Nature Communications, 14615-14615.
Early Neolithic genomes from the eastern Fertile Crescent
Broushaki Farnaz, Thomas Mark G., Link Vivian, Lopez Saioa, van Dorp Lucy, Kirsanow Karola, Hofmanova Zuzana, Diekmann Yoan, Cassidy Lara M., Diez-del-Molino David, Kousathanas Athanasios, Sell Christian, Robson Harry K., Martiniano Rui, Bloecher Jens, Scheu Amelie, Kreutzer Susanne, Bollongino Ruth, Bobo Dean, Davoudi Hossein, Munoz Olivia, Currat Mathias, Abdi Kamyar, Biglari Fereidoun, Craig Oliver E., Bradley Daniel G., Shennan Stephen, Veeramah Krishna R., Mashkour Marjan, Wegmann Daniel, Hellenthal Garrett, Burger Joachim (2016), Early Neolithic genomes from the eastern Fertile Crescent, in SCIENCE, (6298), 499-503.
Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia
Alves Isabel, Arenas Miguel, Currat Mathias, Sramkova Hanulova Anna, Sousa Vitor C., Ray Nicolas, Excoffier Laurent (2016), Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia, in Molecular Biology and Evolution, (4), 946-958.
Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages under Selection
Currat Mathias, Gerbault Pascale, Di Da, Nunes José M., Sanchez-Mazas Alicia (2016), Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages under Selection, in Evolutionary Bioinformatics, EBO.S33488-EBO.S33488.
Early farmers from across Europe directly descended from Neolithic Aegeans
Hofmanová Zuzana, Kreutzer Susanne, Hellenthal Garrett, Sell Christian, Diekmann Yoan, Díez-del-Molino David, van Dorp Lucy, López Saioa, Kousathanas Athanasios, Link Vivian, Kirsanow Karola, Cassidy Lara M., Martiniano Rui, Strobel Melanie, Scheu Amelie, Kotsakis Kostas, Halstead Paul, Triantaphyllou Sevi, Kyparissi-Apostolika Nina, Urem-Kotsou Dushka, Ziota Christina, Adaktylou Fotini, Gopalan Shyamalika, Bobo Dean M., Winkelbach Laura, Blöcher Jens, Unterländer Martina, Leuenberger Christoph, Çilingiroğlu Çiler, Horejs Barbara, Gerritsen Fokke, Shennan Stephen J., Bradley Daniel G., Currat Mathias, Veeramah Krishna R., Wegmann Daniel, Thomas Mark G., Papageorgopoulou Christina, Burger Joachim (2016), Early farmers from across Europe directly descended from Neolithic Aegeans, in Proceedings of the National Academy of Sciences, (25), 6886-6891.
Upper Palaeolithic genomes reveal deep roots of modern Eurasians
Jones Eppie R., Gonzalez-Fortes Gloria, Connell Sarah, Siska Veronika, Eriksson Anders, Martiniano Rui, McLaughlin Russell L., Gallego Llorente Marcos, Cassidy Lara M., Gamba Cristina, Meshveliani Tengiz, Bar-Yosef Ofer, Müller Werner, Belfer-Cohen Anna, Matskevich Zinovi, Jakeli Nino, Higham Thomas F. G., Currat Mathias, Lordkipanidze David, Hofreiter Michael, Manica Andrea, Pinhasi Ron, Bradley Daniel G. (2015), Upper Palaeolithic genomes reveal deep roots of modern Eurasians, in Nature Communications, (1), 8912-8912.
Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia
Di Da, Sanchez-Mazas Alicia, Currat Mathias (2015), Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia, in BMC Evolutionary Biology, (1), 240-240.

Collaboration

Group / person Country
Types of collaboration
Prof. Joachim Burger, Institut für Anthropologie, University of Mainz Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr Nicolas Ray, Institute for Environmental Sciences, University of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Christina Papageorgopoulou, Democritus University of Thrace Greece (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Daniel Wegmann, Department of Biology, University of Fribourg Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Ancient DNA: A Time-machine to study Evolution Poster Estimation of partial population continuity and genetic contribution using spatially explicit simulations 29.08.2018 Leukerbad, Switzerland Rio Jérémy;
International conference on Ecological Sciences Poster Estimation of genomic contributions in a partial population replacement context using spatio-temporally explicit simulations 22.08.2018 Rennes, France Rio Jérémy;
Evolution Montpellier 2018 || Joint Congress on Evolutionary Biology Poster Estimation of partial population continuity and genetic contribution using spatially explicit simulations 19.08.2018 Montpellier, France Rio Jérémy;
Evolution Montpellier 2018 || Joint Congress on Evolutionary Biology Poster Investigation of the Neolithic transition along the Danube route using ancient DNA and spatially explicit simulations 19.08.2018 Montpellier, France Currat Mathias;
Evolution Montpellier 2018 || Joint Congress on Evolutionary Biology Poster The many population genetic and demographic routes to islands of genomic divergence 19.08.2018 Montpellier, France Quilodrán Venegas Claudio Sebastián;
Biology'18 Poster Estimating ancient genetic contribution with aDNA under a spatial simulation framework 15.02.2018 Neuchâtel, Switzerland Rio Jérémy;
Conference Human Evolution: Fossils, Ancient and Modern Genomes Poster Estimating ancient genetic contribution with aDNA under a spatial simulation framework 20.11.2017 Wellcome Genome Campus, Hinxton, Great Britain and Northern Ireland Rio Jérémy;
6th annual meeting of IGE3 (Institute for Genetics Genomics Geneva) Talk given at a conference Building a spatiotemporal European population continuity network using paleogenomic data and computer simulations 07.11.2017 Genève, Switzerland Rio Jérémy;
Mini-workshop on mathematical modeling of human migration and range expansion Talk given at a conference A spatially-explicit modelling framework to simulate genetic diversity in interacting populations 18.10.2017 Tokyo, Japan Currat Mathias;
2017 annual SMBE meeting (Society for Molecular Biology and Evolution) Talk given at a conference Investigating population continuity with ancient DNA under a spatially explicit simulation framework 02.07.2017 Austin, Texas, United States of America Rio Jérémy;
Biology'16 Poster Simulation of ancient DNA data using a spatially-explicit modeling framework 11.02.2016 Lausanne, Switzerland Monteiro Da Silva Nuno Miguel;
BEAN closing meeting Talk given at a conference Assessing the Neolithic transition in southeast Europe using spatially-explicit simulations of ancient genetic data 15.01.2016 Kemer-Antalya , Turkey Monteiro Da Silva Nuno Miguel;
BEAN closing meeting Talk given at a conference Investigating European prehistory through spatially-explicit simulations of genetic data 15.01.2016 Kemer-Antalya , Turkey Currat Mathias;
CADMOS HPC Course Poster Spatially-explicit computer simulations to investigate ancient population genetic diversity 07.09.2015 Leysin, Switzerland Monteiro Da Silva Nuno Miguel; Rio Jérémy;
2015 annual SMBE meeting (Society for Molecular Biology and Evolution) Talk given at a conference Simulation of spatial processes shaping genetic diversity across time 12.07.2015 Vienna, Austria Monteiro Da Silva Nuno Miguel;
Seminar at Department of Biology, University of Fribourg Individual talk Spatial explicit simulation of human ancient DNA 06.03.2015 Fribourg, Switzerland Monteiro Da Silva Nuno Miguel;


Self-organised

Title Date Place
Mini-symposium on population genomics, ancient DNA and the evolution of European populations 12.11.2018 Zermatt, Switzerland

Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Dr Mathias Currat – Simulating genetic patterns in European human evolution Scientia International 2016
Media relations: radio, television La révolution génomique à l'honneur RTS 1 Western Switzerland 2016

Awards

Title Year
IGE3 Salary Award 2017

Associated projects

Number Title Start Funding scheme
182577 Paleogenomic investigation of the Evolution of European populations using computational simulations 01.01.2019 Project funding (Div. I-III)

Abstract

The analysis of the genome of Europeans presents a great potential for reconstructing the genetic history of this continent, which is still poorly understood. Despite the rapid accumulation of genetic and genomic data, no consensus has been reached so far about how the current European genetic pool has been shaped by demographic events since the arrival of the first modern humans (Homo sapiens) and the disappearance of Neanderthals, around 45,000 years ago. This is probably due to the complexity of the underlying evolutionary processes, but also to the variety of biostatistical and computational methods used independently on data available for different portions of the genome. The retrieval of ancient DNA (aDNA) from old European human remains, while very promising, has led to more questions than answers. In particular, the results based on such data suggest an abrupt genetic transition between prehistoric populations and extant Europeans of the same geographic area. This finding challenges most results based on modern DNA, which support the view that European genetic diversity has been shaped in great part by demographic events taking place during ancient prehistoric times (e.g. Paleolithic, Mesolithic and Neolithic). Because the development of analytical tools does not follow the pace of genetic and genomic data production, current results have been obtained with methods suffering from severe limitations; in particular, some methods do not explicitly account for ancient molecular data while others do not consider movements of populations through space. The present project aims at providing new insights on the evolution of Europeans by compiling and analysing heterochronous molecular data in a joint fashion through an integrative approach using a newly developed spatially-explicit computer simulation method called SERIAL SPLATCHE, bringing together information on demography, migration, archaeology and environment. This approach is expected to overcome the major limitations and unrealistic assumptions of currently existing methods, by explicitly considering together population structure and migration as well as the specific characteristics of aDNA. It will lead to the development of a new more efficient and unbiased test for detecting population discontinuity through time. Our innovative method will be applied to a very large amount of molecular data available for European populations (ancient and modern) in order to reconstruct the evolution of this continent. The strategy consists in using genetic data on specific portions of the genome, currently available for numerous population samples, to infer the most likely scenario for the settlement history of Europe, and then to validate this scenario by using less numerous, but genome-wide, data. In addition to delivering a substantial amount of results from the systematic analysis of all available genetic and genomic European data, which has never been done so far, this project is expected i) to reconcile the conclusions of today's studies on modern and ancient DNA; ii) to determine to what extent post-Neolithic demographic processes have impacted on the genetic diversity of Europeans; iii) and to clarify the processes by which modern humans hybridized with other archaic species, namely Neanderthal.We believe that our project is timely and holds the promise of solving current interrogations and long-standing debates on Europeans’ genetic evolution. Moreover, it will constitute a fundamental theoretical framework for analysing the evolution of neutral genetic diversity, which will be extremely valuable as a reference model for future genome scan researches aiming at detecting and studying the evolution of disease-related genes and genes under selection. The methods developed in the context of this project are also expected to be very useful in conservation biology and in ecology, both for retrospective and prospective investigations.
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