Reconstructing Europeans' genetic evolution through computer simulations and heterochronous molecular data
When and how was constituted the genetic pool of European populations? Despite the accumulation of many genetic and genomic data, the genetic history of the European continent is still poorly understood, partly because data on past populations are fragmented and heterochronic. This project contributes to this area of research by developing new methods of data analysis, by computer simulations and integration of different information sources (genetics, genomics, environment, archeology).
- What were the interactions between early modern humans (Homo sapiens) who arrived on the European continent and their Neanderthal contemporaries?
- What has been the impact of climate changes on the distribution and genetic diversity of hunter-gatherers living in Europe?
The rapid development of laboratory techniques has produced huge genetic databases for human populations currently living around the globe and even full genomes. In addition, it is now possible to extract DNA from fossil bones from prehistoric era if the conditions of preservation of those remains are good enough. However, despite the accumulation of these data, the genetic history of the European continent is still poorly understood. The development of methods of analysis does not follow the pace of data production. In particular, there are very few methods to jointly analyze contemporary and ancient DNA (heterochrony), and none in a realistic framework that takes into account the geographical distribution of populations and migration, both of which have played a very important role in determining the genetic structure of human populations. This project aims to develop and use new approaches by computer simulations of complex models that incorporate these different features.
This project has an interest in evolutionary biology as it will provide a better understanding of complex biological mechanisms, including genetics / genomics and population demography. The study of how specific genetic variant may spread in populations over time could be applicable to disease-causing genes in a second time.
In addition, the project also has a historical significance as it aims at better understanding the evolution of European populations since the arrival of Homo sapiens on this continent and their relationships with related species such as Neanderthals.
Finally, it is relevant to evolution in general, as well as ecology and conservation genetics, since the methods developed can be extended and applied to other issues and other organizations (e.g. the for research on invasive species) either retrospectively or prospectively.
- To what extent the Neolithic transition has involved the arrival of farmers from the Middle East and therefore the integration of their genes ?
- What are the events subsequent to the Neolithic that have significantly influenced the genetic structure of European populations ?
This interdisciplinary research plan includes national and international collaborations, including the universities of Freiburg and Mainz (Germany).
Project main innovations
Computer simulation of complex and realistic evolutionary processes
Integration of different information sources (genetics, genomics, environment, demography, archeology) into the models.
Combined analysis of genetic and genomic data from ancient and contemporary human populations.
Use of the most modern statistical methods for analysis and estimation of parameters, such as "Approximate Bayesian Computation" (ABC).
Selected publications in relation to the project
- Excoffier L, Quilodran CS & Currat M. (2014) Models of hybridization during range expansions and their application to recent human evolution. in 'Cultural Developments in the Eurasian Paleolithic and the Origin of Anatomically Modern Humans' edited by Derevianko AP & Shunkov M. Dept. of the Institute of Archaeology and Ethnography SB RAS. Pp. 122-137.
- Currat M, Silva NM. (2013) Investigating European genetic history through computer simulations. Human Heredity, vol. 76, no. 3-4, 142-153.
- Arenas M, Francois O, Currat M, Ray N, Excoffier L. (2013) Influence of Admixture and Paleolithic Range Contractions on Current European Diversity Gradients. Molecular Biology and Evolution, vol. 30, no. 1, p. 57-61.
- Currat M. (2012) Consequences of population expansions on European genetic diversity, in "Population Dynamics in Prehistory and Early History: New Approaches Using Stable Isotopes and Genetics", eds. J. Burger, E. Kaiser & W. Schier. (Topoi / Berlin Studies of the Ancient World 5.) Berlin: Walter de Gruyter & Co, 3-15.
- Pinhasi R, Thomas M G, Hofreiter M, Currat M and Burger J. (2012) The genetic history of Europeans. Trends in Genetics, 28 (10), 496-505.
- Currat M, Excoffier L. (2011) Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression. Proceedings of the National Academy of Sciences USA, 13;108(37):15129-34.
- Excoffier L, Currat M. (2011) Models of hybridization during range expansions and their application to recent human evolution, in Characteristic features of the Middle to Upper Paleolithic Transition in Eurasia, eds A.P. Derevianko, M.V. Shunkov, Russian Academy of Sciences, 90-99.
- Ray N *,Currat M *, Foll M, Excoffier L. (2010) SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics, Vol 26(3): 2993-2994 *equal contribution
- Currat M, Poloni ES, Sanchez-Mazas A. (2010) Human genetic differentiation across the Strait of Gibraltar. BMC Evolutionary Biology 10:237.
- Francois O, Currat M, Ray N, Han E, Excoffier L and Novembre J. (2010) Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture. Molecular Biology and Evolution 27(6):1257-1268.
- Gerbault P, Moret C, Currat M, Sanchez-Mazas A. (2009) Impact of Selection and Demography on the Diffusion of Lactase Persistence. PLoS One 4(7):e6369.
- Currat M and Excoffier L. (2005) The effect of the Neolithic expansion on European molecular diversity. Proceedings of the Royal Society London B. 272, 679-688.
- Currat M and Excoffier L. (2004) Modern Humans did not admix with Neanderthals during their range expansion. PLoS Biology, Vol. 2, No. 12, e41.
A research project funded by the Swiss National Science Foundation (SNF grants 31003A_156853, Applicant Dr Mathias Currat)
- Assessing the transition to agriculture in Western Anatolia and the Balkans using a spatially-explicit computer simulation approach
- BEAN: Bridging the European and Anatolian Neolithic: Demography, Migration, and Ligestyle at the Advent of Civilization
External collaborators and experts
- Prof. Joachim Burger (University of Mainz, Germany)
- Prof. Daniel Wegmann (University of Fribourg, Switzerland)
- Dr Nicolas Ray (University of Geneva, Switzerland)
Computer programs related to the project
- SPLATCHE 2 - SPatiaL And Temporal Coalescent in a Heterogeneous Environment.
- SELECTOR - Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection.
Outcome of the project
- Unterländer M, Palstra F, Lazaridis I, Pilipenko A, Hofmanová Z, Groß M, Sell C, Blöcher J, Kirsanow K, Rohland N, Rieger B, Kaiser E, Schier W, Pozdniakov D, Khokhlov A, Georges M, Wilde S, Powell A, Heyer E, Currat M, Reich D, Samashev Z, Parzinger H, Molodin V I, Burger J. (2017) Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nature Communication vol. 8, p. 14615.
- Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davoudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah KR, Mashkour M, Wegmann D, Hellenthal G, Burger J. (2016) Early Neolithic genomes from the eastern Fertile Crescent. Science Vol. 353, Issue 6298, pp. 499-503.
- Hofmanová Z, Kreutzer S, Hellenthal G, Sell C, Diekmann Y, Diez-del-Molino D, Dorp L, López S, Kousathanas A, Link V, Kirsanow K, Cassidy LM, Martiniano R, Strobel M, Scheu A, Kotsakis K, Halstead P, Triantaphyllou S, Kyparissi-Apostolika N, Urem-Kotsou D, Ziota C, Adaktylou F, Gopalan S, Bobo DM, Winkelbach L, Blöcher J, Unterländer M, Leuenberger C, çilingiroglu C, Horejs B, Gerritsen F, Shennan SJ, Bradley DG, Currat M, Veeramah KR, Wegmann D, Thomas MG, Papageorgopoulou C and Burger J. (2016) Early farmers from across Europe directly descended from Neolithic Aegeans. Proceedings of the National Academy of Sciences USA, published ahead of print June 6, 2016.
- Alves I, Arenas M, Currat M, Hanulova AS, Sousa VC, Ray N and Excoffier L. (2016) Long distance dispersal shaped patterns of human genetic diversity in Eurasia. Molecular Biology and Evolution, vol. 33, no. 4, p. msv332.
- Currat M, Gerbault P, Di D, Nunes JM and Sanchez-Mazas A. (2015) Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection. Evolutionary Bioinformatics 2015:Suppl. 2 27-39.
- Jones E, Gonzalez-Fortes G, Connell S, Siska V, Eriksson A, Martiniano R, McLaughlin R, Gallego Llorente M, Cassidy L, Gamba C, Meshveliani T, Bar-Yosef O, Muller W, Belfer-Cohen A, Matskevich Z, Jakeli N, Higham T, Currat M, Lordkipanidze D, Hofreiter M, Manica A, and Pinhasi R & Bradley D. (2015) Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature communication, 6:8912.
- Di D, Sanchez-Mazas A, Currat M. (2015) Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia. BMC Evolutionary Biology 2015, 15:240
- Simulating genetic patterns in European human evolution (2016) Scientia
- Silva NM, Currat M (14.07.2015) Simulation of spatial processes shaping genetic diversity across time - SMBE 2015, Vienna, Austria
- Currat M, Gerbault P, Di D, Nunes JM and Sanchez-Mazas A. (10-13.05.2016) - SELECTOR: Forward-in-Time, Spatially Explicit Modeling Software to Simulate HLA Lineages - "EFI" Conference, Kos, Greece
- Silva NM & Currat M (11-12.02.2016) - Simulation of ancient DNA data using a spatially-explicit modeling framework - Conference "Biology16", Lausanne, Switzerland
- Silva NM, Rio J, Currat M (07-09.11.2015) Spatially-explicit computer simulations to investigate ancient population genetic diversity - CADMOS HPC course 2015, Leysin, Switzerland