Genetic ancestry; Heterochronous data; Computer simulation; Europe; Genomics; Ancient DNA; Evolution; Paleogenomics; Population Genetics; Anthropology; Neandertal; Human
Broccard Nicolas, Silva Nuno Miguel, Currat Mathias (2021), Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe, in American Journal of Biological Anthropology
Currat Mathias, Arenas Miguel, Quilodràn Claudio S, Excoffier Laurent, Ray Nicolas (2019), SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal, in Bioinformatics
, 35(21), 4480-4483.
Quilodrán Claudio S., Nussberger Beatrice, Montoya-Burgos Juan I., Currat Mathias (2019), Hybridization and introgression during density-dependent range expansion: European wildcats as a case studyDENSITY-DEPENDENT DISPERSAL AND HYBRIDIZATION, in Evolution
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.
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.
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
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
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.
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
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.
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.
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
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.
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.
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.
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.