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Anthropology Unit

Anthropology Unit | University of Geneva

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

Project scope

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.

Des cartes montrant la simulation de la propagation du néolithique en l'Europe et le remplacement progressif des chasseurs-cueilleurs.
Computer simulations are used to study the effects of different waves of migration in Europe, including the emergence of modern humans.
Crânes de NNéandertaliens de La Chapelle-aux-Saints (France) et de Teshik-Tash (Ouzbékistan)
Ancient DNA extracted from fossilized bones (eg Neanderthals) are analyzed to extract information about the population history of Europe.

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

Swiss FNS logo

A research project funded by the Swiss National Science Foundation (SNF grants 31003A_156853, Applicant Dr Mathias Currat)

Related projects

Internal collaborators

External collaborators and experts

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

Publications
Scientific dissemination
Oral communications
  • Silva NM, Currat M (14.07.2015) Simulation of spatial processes shaping genetic diversity across time - SMBE 2015, Vienna, Austria
Posters
  • 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
University of Geneva
Dpt. of Genetic & Evolution
Anthropology Unit
Quai Ernest-Ansermet 30
1205 Genève
Switzerland
Ph +41 22 379 69 67
Fax +41 22 379 31 94