Population and conservation genetics

Lounés Chikhi

Genetic and genomic data are influenced by the demographic history of populations. This history is the result of events that include population collapses, expansions, or admixture processes. It also involves the connection and disconnection of populations (i.e. varying population structure). Such changes in population structure and connectivity can be caused by many factors, including climate change over short or long periods or human activities in both the most recent and ancient past.

The research group, led by Lounés Chikhi, is interested in the genetic consequences of such events. We are thus interested in the methods used to improve our understanding the recent evolutionary history of species and on the development of new methods or approaches to that aim.

They also, and crucially, want to understand the limits of genetic or genomic data as inferential tools. We thus ask: how much of what we write and publish should be considered as story-telling, and how much can be considered as solid. This is a question that may be much more open than we, as a community, may wish to admit.

Applications of the research is varied. Researchers have been working on humans (e.g. the Neolithic transition in Europe), and on many endangered species (e.g. orang-utans, lemurs, dolphins, African primates). They are also collaborating on projects involving domesticated species (e.g. cattle, sheep).

Work currently done at the Population and Conservation Genetics (PCG) group involves fieldwork in Madagascar, Guiné-Bissau and Portugal, and the genetic typing of endangered species or populations (lemurs, endemic and invasive rodents, red colobus, bottlenose dolphins), data analysis and simulation. We also work on more analytical work, even though this is mainly done through a collaboration with colleagues from Toulouse (see below).

Researchers are also moving towards the use of genomic data (RAD-seq and full genome sequencing). Who isn’t ? They collaborate with the laboratory Evolution & Diversité Biologique, in Toulouse, where Lounès Chikhi is a Senior researcher (Directeur de Recherche) and with colleagues from several institutions outside and inside Portugal. This includes the UK (Cardiff University, Bristol University), France (IMT - Institut de Mathématiques de Toulouse, INSA - Institut National des Sciences Appliquées de Toulouse, INRA - Institut National de Recherche Agronomique), Madagascar (Univ. Mahajanga, Antananarivo, Antsirana), or Malaysia (Danau Girang Field Station).

 

Research Projects 

Demographic and Genetic Responses

Demographic and Genetic Responses

Habitat loss and habitat fragmentation are among the major causes of biodiversity loss affecting tropical forests across the world.

Conservation et génétique

Conservation et génétique

Project funded by the Institut Français de la Biodiversité (in collaboration with Prof. Brigitte Crouau-Roy).

 

Publications

  • Scerri EML, Thomas MG, Manica A, Gunz P, Stock J, Stringer C, Grove M, Groucutt HS, Timmermann A, Rightmire GP, d’Errico F, Tryon C, Drake N, Brooks AS, Dennell R, Durbin R, Henn B, Lee-Thorp J, deMenocal P, Petraglia ÇD, Thompson JC, Scally Q, Chikhi L (2018), Did our species evolve in subdivided populations across Africa, and why does it matter? Trends in Ecology & Evolution, 33(8): 582-594.
  • Chikhi L, Rodriguez WV, Grusea S, Santos P, Boitard S, Mazet O (2018). The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice. Heredity, 120, 13-24.
  • Salmona, J, Heller, R, Quéméré E, Chikhi, L (2017) Climate change and human colonization triggered habitat loss and fragmentation in Madagascar. Molecular Ecology, 26(19), 5203-5222.
  • Schwitzer C, Mittermeier RA, Johnson SE, Donati G, Irwin M, Peacock H, Ratsimbazafy J, Razafindramanana J, Louis Jr. EE, Chikhi L, Colquhoun IC, Tinsman J, Dolch R, LaFleur M, Nash S, Patel E, Randrianambinina B, Rasolofoharivelo T, Wright PC. (2014)  Averting lemur extinctions amidst Madagascar’s political crisis. Science  343 : 842-43
  • Rasteiro, R., Bouttier P-A., Sousa, V., Chikhi, L. (2012)  Investigating sex-biased migration during the Neolithic transition in Europe. Proc. Roy Soc. B  279 : 2409-2416
  • Quéméré, E., Amelot, X., Pierson, J.,Crouau-Roy, B., Chikhi, L. (2012)  Genetic data suggest a natural pre-human origin of open habitats in northern Madagascar and question the deforestation narrative in this region . Proc. Natl. Acad. Sci, USA  109 : 13028-33
  • Chikhi, L., Sousa, V., Luisi, P., Goossens, B., Beaumont, M.A. (2010)  The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics  186 : 983-995
  • Chikhi, L. (2009)  Genetic data and story-telling: from Archeogenetics to Astrologenetics? An update to “Clinal variation in the nuclear DNA of Europeans” By Chikhi, L., Destro-Bisol, G., Pascali, V., Baravelli V., Dobosz, M., Barbujani, G. Published in 1998 in Human Biology, Human Biology  81, (5-6) : 639-643

 

News

Lounés Chikhi, Principal  Investigator

PhD in Population Genetics, Université Pierre et Marie Curie, France

ORCID

Phone: +351 214 464 671

E-mail: [email protected]