Reconstructing Europeans' genetic evolution through computer simulations and heterochronous molecular data
Current research projects
Human genetic diversity in East Asia
FNS-funded project running since 2005: Early human settlements in East Asia: HLA molecular variation, population expansions and linguistic differentiations
Summary
This project aims at investigating current and new hypotheses on the human peopling history of East Asia through the analysis of highly variable genes in humans (HLA, mtDNA, Y-chromosome, and GM) and in relation to the evolution of human languages. It also proposes to explore the impact of different evolutionary forces on the HLA diversity observed in human populations (migration, demographic expansion and natural selection) by computer simulation. This project includes original methodological developments to tackle with the acute problems of using increasingly complex HLA data in population genetics and of disentangling the effects of multiple evolutionary forces acting on these genes
PI
Alicia Sanchez-Mazas & Estella S. Poloni
Principal collaborators
María Eugenia Riccio, Da Di, José Manuel Nunes, Mathias Currat, Laurent Sagart (CRLAO, Paris)
FNS-funded project: Genetic variability in East Africa: GM allotypes and mitochondrial control-region sequences in the Nyangatom and Dasenech from the Omo valley
Summary
This project aims to analyse several genetic polymorphisms (mtDNA HVSI, GM, HLA) in 30 years-old serum samples from two neighbouring populations of the Omo Valley in Southern Ethiopia in order to infer the level of genetic differentiation between these two linguistically different, but geographically very close populations. It also aims at investigating the molecular variability of the complete mtDNA molecule in a Mandenka population from Eastern Senegal. The main goal is to understand the genetic history of African populations in relation to current theories on modern humans origin and migrations’ history
PI
Estella S. Poloni, Yamama Naciri (CJB, Geneva) & Alicia Sanchez-Mazas
Impact of natural selection on human genetic diversity
FNS-funded project: Genetic variability in East Africa: GM allotypes and mitochondrial control-region sequences in the Nyangatom and Dasenech from the Omo valley
Summary
Projects aiming at estimating the impact of selective forces on the genetic diversity of human genes submitted to directional or balancing selection: lactase persistence (LAC*P), HLA, classical genes and others: how to disentangle the molecular signatures of human migrations and demographic history from those of natural selection in the genetic variation observed in present human populations? These projects include comparisons between neutrally evolving and selected polymorphisms, as well as the exploration of different evolutionary scenarios through computer simulations in relation to demographic and environmental factors
PI
Mathias Currat & Alicia Sanchez-Mazas
Principal collaborators
María Eugenia Riccio, Da Di, José Manuel Nunes, Mathias Currat, Laurent Sagart (CRLAO, Paris)
Most recent related publications
Sanchez-Mazas et al (2012) Philosoph Trans B
Gerbault et al. (2011) Philosoph Trans B
Currat et al. (2010) BMC Evol Biol
Gerbault et al. (2009) PLoS One
Genetic consequences of population past demography in Europe
FNS-funded project
Summary
Interdisciplinary projects aiming at reconstructing the prehistory of Humans in Europe using genetic data and realistic computer simulations. We particularly focus on the genetic consequences of the main population demographic events in Europe: i) the arrival of modern humans ~40,000 years ago, ii) possible retreat into southern refugee during glacial era ~ 20,000 years ago, followed by re-expansion toward the north and iii) the Neolithic transition ~10,000 years ago. Simulations of evolutionary scenarios, incorporating the influence of the environment are performed using a homemade program called SPLATCHE and developed in collaboration with L.Excoffier and N.Ray
PI
Mathias Currat
Principal collaborators
Nuno Silva, Laurent Excoffier (Bern), Nicolas Ray (Institute of Environmental Sciences, Geneva), Ron Pinhasi (Dublin, Irland), Joachim Burger (Mainz, Germany), Daniel Wegmann (Fribourg).
HLA-NET: A European network of the HLA diversity for histocompatibility, clinical transplantation, epidemiology and population genetics
EU-funded COST Action running since 2009
Summary
The main objectives of this Action are, through networking European research teams working on Human Leukocyte Antigen (HLA) molecular diversity in human populations, to standardize protocols and procedures for sampling, handling, storing and processing data and to develop a user-friendly bioinformatics platform accessible to scientists in different fields
PI
Alicia Sanchez-Mazas & José Manuel Nunes
Principal collaborators
Stéphane Buhler, Jean-Marie Tiercy (HUG) and more than 20 European laboratories
The HLA genetic structure of Switzerland through the analysis of more than 20,000 individuals from 15 regions
SER-funded Swiss COST project running since 2009
Summary
This project aims at analyzing the fine HLA genetic structure of the Swiss population through the statistical analysis of about 21,000 bone marrow donors recruited in 15 cantonal transfusion centers. Possible genetic variation across national linguistic boundaries and different geographic regions are investigated in order to define the HLA genetic profile and genetic structure of the Swiss population, to be used both in stem cell transplantation and epidemiological studies; to analyze the Swiss HLA genetic landscape in relation to that of other Europe countries; and to integrate the results into a broader reconstruction of European genetic history.
PI
Alicia Sanchez-Mazas
Principal collaborators
Stéphane Buhler, José Manuel Nunes, Jean-Marie Tiercy (HUG), Grazia Nicoloso (Bern)
Most recent related publications
AHPD: Analysis of HLA population data to reconstruct the history of modern humans and infer the role of natural selection
Project related to the International Histocompatibility and Immunogenetics Workshops
Summary
this project aims to improve our knowledge on the HLA molecular diversity of present human populations through international collaboration with tissue-typing laboratories in order to investigate their genetic history and to better understand the mechanisms underlying the evolution of this complex genetic system
PI
Alicia Sanchez-Mazas
Principal collaborators
María Eugenia Riccio, José Manuel Nunes, Mathias Currat, Da Di, Jean-Marie Tiercy and more than 15 International laboratories
Polymorphism of drug-metabolizing genes (NAT2 and others)
Summary
project aiming at exploring the evolution of human and ape diversity in NAT2, the best-known drug-metabolizing gene, as well as in other pharmacogenetic traits
PI
Estella S. Poloni, Audrey Sabbagh (Paris, France), Aparup Das (New Delhi, India), Pierre Darlu (Paris, France), Brigitte Crouau-Roy (Toulouse, France), Pascal Gagneux (La Jolla, California, USA)
Principal collaborators
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Most recent related publications
Sabbagh et al. (2008) BMC Genet
Global genetic diversity at Y chromosome and Nuclear STRs
Summary
Project aiming at describing the worldwide genetic structure of STRs (microsatellites) used in forensic studies (autosomes and Y chromosome).
PI
Estella S Poloni, Mathias Currat , Luisa Pereira (Porto, Portugal)
Most recent related publications
Alshamali et al. (2009) Hum Hered
Evolution of the grey mouse lemur (Microcebus murinus) in Northwestern Madagascar
Summary
Projects aiming at reconstructing the history and evolution of the grey mouse lemur (Microcebus murinus) as well as the effects of habitat loss and fragmentation on the genetic structure of this species.
Implication of mtDNA variation in the pathogenesis of lipoatrophy related to antiretroviral therapy
Summary
Project aiming at evidencing a possible role of mitochondrial genomic variants in the development of lipoatrophy after exposure to antiretroviral therapy among HIV-infected patients.
PI
Estella S Poloni, Millan Ortiz Serrano (University of Lausanne) , Amalio Telenti (University of Lausanne) Philip E. Tarr (University of Basel)
