Assessing the transition to agriculture in Western Anatolia and the Balkans using a spatially-explicit computer simulation approach
This project aims at investigating the origins of one of the most important economic and demographic event which occurred in Europe: the Neolithic transition.
- Did humans migrated (along with their domesticated animals) into new lands during the establishment of the Neolithic in western Anatolia and south-eastern Europe around 9,000 years ago ?
- Did Mesolithic hunter-gatherers adopt farming when they were in contact with migrant Neolithic populations ?
The focus is made on the Anatolia and the Balkans which constitutes a key staging area for the further spread of the Neolithic culture through Europe since 7.000 BC. Although detailed chronologies of Neolithisation exist for individual regions, the mode and tempo of the development of the Neolithic in the area remains problematic and a precise and comprehensive theory is still needed for the entire area between central Anatolia and central Europe.
Our project aims at investigating the processes by which the Neolithic culture diffused from Western Anatolia to the Balkans by using an inter-disciplinary model-based computer simulation approach. The computer simulation approach offers the advantage of merging information from different fields in the model, possibly prehistoric archaeology, landscape archaeology, zooarchaeology, palaeogeography, linguistics and genetics.
- To what extent the genetic pool of Europeans has been modified by the arrival of farming ?
- What was the degree of cultural transmission between hunter-gatherers and farming communities?
This inter-disciplinary research plan is strengthened by the integration of our lab within the "BEAN" Marie Curie international training network (ITN), financially supported by the European Union. In particular, close interactions with archaeologists and laboratories specialized in ancient DNA extraction are promoted by this international research network and allows us to develop realistic settlement scenarios for the Neolithic of Anatolia and to dispose of invaluable sources of genetics information.
Powerful computer clusters together with complex modelling/simulation procedures in link with genetic data and geographic information (GIS).
Most recent statistical methods for population genetics analyses and parameter estimation, such as the Approximate Bayesian Computation (ABC) approach.
Modern and ancient DNA samples
Combined analyse of DNA sequences from contemporary and ancient human populations generated using the last molecular technologies such as next generation sequencing (NGS).
International Inter-disciplinary network
This project belongs to the BEAN network, whose aim is to educate a new generation of researchers that will be able to combine the important aspects of various fields while developing specialized skills in their particular scientific discipline.
Selected publications related to the project
- 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.
- 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.
- 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 Seventh framework programme of the European Union and belonging to the BEAN ITN network (grant PITN-GA-2011-289966)
- Reconstructing Europeans' genetic evolution through computer simulations and heterochronous molecular data
- BEAN: Bridging the European and Anatolian Neolithic: Demography, Migration, and Ligestyle at the Advent of Civilization
- From the earliest modern humans to the onset of farming (45,000-4,500 BP)
- Dr Mathias Currat (PI)
- Nuno Silva (PhD)
- Nicolas Broccard (Master)
- Prof. Alicia Sanchez-Mazas
- Dr Estella Poloni
External collaborators and experts
- Prof. Joachim Burger (University of Mainz, Germany)
- Prof. Mark Thomas (University College London, England)
- Prof. Laurent Excoffier (University of Berne, Switzerland)
- Prof. Christina Papageorgopoulou (Democritus University of Thrace, Greece)
- Prof. Dan Bradley (Trinity College Dublin, Irland )
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
- 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.
- 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, 30(1):57-61.
- 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.
- Silva NM (15.01.2016) Assessing the Neolithic transition in southeast Europe using spatially-explicit simulations of ancient genetic data – BEAN closing meeting, Antalya, Turkey
- Currat M (15.01.2016) Investigating European prehistory through spatially-explicit simulations of genetic data – BEAN closing meeting, Antalya, Turkey
- Silva NM (14.07.2015) Simulation of spatial processes shaping genetic diversity across time - SMBE 2015, Vienna, Austria
- Currat M (13.03.2013) Investigating European genetic history through computer simulations - Department of Archeology research seminars, Durham, UK
- Currat M (16.01.2013) Investigating European genetic history through computer simulations - Genetic diversity and origins of Europeans conference, Geneva, Switzerland
- Silva NM (07.01.2013) Human Neutral Genetic Variation and Forensic STR Data - Molecular population genetics workshop, Geneva, Switzerland
- Currat M (06.07.2012) European population dynamics as seen from modern genetic data - 1st BEAN network workshop, Belgrade, Serbia
- 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 & Currat M (01-04.04.2014) - Comparing ancient and modern population genetic samples using a spatially-explicit simulation approach - Conference "Human evolution in the genomic era: Origins, populations and phenotypes", Leicester, UK
- Silva NM & Currat M (16-18.03.2014) - Comparing ancient and modern population genetic samples using a spatially-explicit simulation approach - Cell Symposium "Evolution of Modern Humans - From Bones to Genomes", Barcelona, Spain
- Silva NM & Rio J (07-09.11.2015) - Spatially-explicit computer simulations to investigate ancient population genetic diversity - CADMOS HPC course 2015, Leysin, Switzerland
- 04-08.07.2012 - BEAN LINUX workshop, Geneva, Switzerland