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Anthropoloy, genetics and peopling history
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Our Research

The AGP laboratory conducts research on the diversity and biological evolution of human populations, with the main objective of reconstructing the history of world settlement since the origin of Homo sapiens.

We perform biostatistical and bioinformatics analysis (including computer simulations) of molecular data for different regions of the genome such as the HLA region, mitochondrial DNA and the Y chromosome, but also classical systems and nuclear SNPs and STRs. This genetic diversity is studied in human populations from all continents and linked to information from other disciplines including prehistoric archaeology, paleoanthropology, historical linguistics and epidemiology.

We also study the diversity of quantitative human traits (e.g. pigmentations or body measurements) both in the modern scientific context, and in that of the history of anthropology (e.g. evolution of the concept of race).

Our laboratory offers various subjects for monographs, masters and doctoral theses in relation to the fields of research described above, and on request from the laboratory's research directors.

Current research projects

We currently have three funded research projects running.

Molecular diversity and evolution of HLA genes in Africa (HLA-AFRICA)

This project aims at investigating the molecular diversity and evolution of the MHC (HLA) genes involved in adaptive immunity in a large set of human populations in Africa. It will answer the question of whether genetic adaptations to pathogenic environments, which are thought to drive the evolution of MHC genes, have significantly modelled the genetic structure of populations in this continent, which will enlighten our knowledge on the evolutionary mechanisms that marked the history of our species. Read more

Paleogenomic investigation of the Evolution of European populations using computational simulations

Research on human evolution has been significantly boosted by the emergence of paleogenomics: the retrieval of genome wide molecular information from skeletal and dental remains. These data have provided a direct testimony of genetic diversity in the past. Their analysis has led to significant advances on hotly debated questions by providing a better understanding of the main events that shaped the diversity of today's populations. Read more

Human genomic population structure and phenotype-genotype variation in ADME genes along a latitudinal transect from Africa to Europe

This project besides its potential to elucidate the evolutionary paths taken by functionally important genomic components, we believe that the project, by performing a joint assessment of the role of genetic polymorphisms in several clinically important drug-metabolizing genes, will provide a standard for future studies. Read more

Past research projects

Browse a selection of research projects we've completed over the years.

This project aims at investigating the role of both human peopling history and environmental factors on the molecular diversity and evolution of the major histocompatibility complex (MHC) in humans - the HLA system.

This project aims at investigating current and new hypotheses on the peopling history of East Asia by modern humans. Did the first Homo sapiens arrive in East Asia from East Africa and the Near East through a unique, southern coastal route, or did they also follow another route north to the Himalayas to occupy Northeast Asia? When and from where did the speakers of the Austroasiatic linguistic family expand to achieve their current geographic distribution between India and Southeast Asia?

Current global climate changes will impact rainfall regimes resulting in a reduction of river flow, especially in small tributaries and headwaters. As a consequence, freshwater organisms will have to respond by downstream population displacements leading to new interactions among populations and species.

This research project aims at modelizing the impact of entropic modifications on the genetic integrity of freshwater organisms. The fishes of the family Cyprinidae will be used as model organisms as they represent most of the fish biodiversity in European continental waters and because they are particularly subjected to interspecific hybridization.

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)

Most recent related publications:

  • Di & Sanchez-Mazas (2011) Am J Phys Anthropol
  • Riccio et al. (In press) Hum Biol
  • Sanchez-Mazas et al., eds. (2008)

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

Most recent related publications:

  • Poloni et al. (2009) Ann Hum Genet;
  • Sanchez-Mazas & Poloni (2008) ELS

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

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).

Web site: Bean project

Most recent related publications:

  • Currat & Silva (2013) Human Heredity
  • Arenas et al (2013) Mol Biol Evol
  • Pinhasi et al (2012) Trends in Genetics
  • Arenas et al, (2012) Mol Biol Evol
  • Currat (2012) Topoi book
  • Currat & Excoffier (2011) PNAS
  • François et al. (2010) Mol Biol Evol
  • Currat et al. (2008) Evolution

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

Web site: HLA-net

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)

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

Web site: AHPD

Most recent related publications:

  • Buhler et al. (2011) PLoS One
  • Nunes et al. (2010) Tissue Antigens
  • Fadhlaoui-Zid et al. (2010) Tissue Antigens
  • Harbo et al. (2010) Tissue Antigens

Summary: Databases and computer tools for the study of HLA and other genetic markers.

PI: José Manuel Nunes & Alicia Sanchez-Mazas

Principal collaborators: Christelle Vangenot

Web site: Generate and AHPD

Most recent related publications:

  • Buhler et al. (2011) PLoS One
  • Nunes et al. (In press) Hum Biol
  • Nunes et al. (2010) Tissue Antigens

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)

Most recent related publications:

  • Sabbagh et al. (2008) BMC Genet

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

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.

PI: Mathias Currat, Ute Radespiel (Hannover, Germany), Lounès Chikhi (Toulouse, France)

Most recent related publications:

  • Schneider et al. (2010) BMC Evol Biol

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)

Most recent related publications:

  • Otiz et al. (2009) J Infect Dis
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