Genética de Populações e da Conservação

Interesse da Investigação

Genetic data are increasingly used in areas such as anthropology, conservation biology, ecology and evolutionary biology. These data are used to address issues related to the demographic history of populations and species. This includes the detection, quantification, and dating of population collapses, expansions, or admixture processes, using neutral markers and the identification of markers under selection. Our group is interested in developing new and using/testing existing methods to uncover such events for a wide range of species. The aim is to understand the recent evolutionary history of these species and the limits of genetic data as inferential tools. Applications go from human evolution (e.g. the Neolithic transition in Europe) to conservation genetics of wild (e.g. orang-utans, lemurs) and domesticated species (e.g. cattle, sheep).
Most of the work currently done here involves data analysis and simulation, but a number of ongoing projects also involve the genetic typing of different species. In particular, data are obtained in collaboration with the group Lounes Chikhi belongs to in Toulouse (as a CNRS researcher in the Unité Mixte de Recherche Evolution et Diversité Biologique, lead by Prof. Brigitte Crouau-Roy) or with different colleagues, including several in Portugal, in the U.K., in France, Madagascar, or Malaysia (see collaborations below).

SPAms and LEA Software

Membros do Grupo

Projecto de Investigação

Demographic and Genetic Responses to Habitat Fragmentation and Habitat Loss in Large Forest Mammals

Habitat loss and habitat fragmentation are among the major causes of biodiversity loss affecting tropical forests across the world. For instance, the state of Sabah (Malaysia) in north-eastern Borneo has undergone intensive deforestation in the last 100-150 years. With only a third to a half of the original forest remaining, many of Sabah’s native species are currently under serious threat. Despite the existence of a few continuous forest reserves most forest mammals survive in small, isolated habitat patches. The Bornean Asian forest elephant (Elephas maximus borneensis) and the Bornean orang-utan (Pongo pygmaeus) are among the most endangered species living in Sabah, and are affected by the increasing conversion of forest into palm-oil plantations. In this project we aim to use genetic data to understand the effect of forest fragmentation on these species. We shall use genetic data obtained from non invasive (faecal) samples to analyse the patterns of genetic diversity within and between populations sampled in fragmented and non-fragmented environments. This study is the result of an ongoing collaboration with the laboratory of Pr. Bruford and Dr. B. Goossens at Cardiff University, and the Danau Girang Field Centre (DGFC), Institute of Tropical Biology and Conservation, Universiti Malaysia Sabah. Dr. B. Goossens is currently located in Malaysia, and is the Director of the DGFC .

Funding

Fundação para a Ciência e a Tecnologia (FCT) Project Grant (Portugal)

Colaboradores

Cardiff University
Mike Bruford
Benoit Goossens

UMR CNRS 5174 Evolution et Diversité Biologique
Brigitte Crouau-Roy

Institute for tropical biology and conservation, Universiti Malaysia Sabah
Benoit Goossens
Mohd Fairus Jalil

Projecto de Investigação

Conservation, phylogéographie et génétique de lémuriens dans des habitats fragmentés de Madagascar et de l’archipel des Comores

This project is funded by the Institut Français de la Biodiversité and managed in France within the UMR CNRS 5174 Evolution et Diversité Biologique (in collaboration with Prof. Brigitte Crouau-Roy).
Madagascar is well known for its extremely diverse and mostly endemic fauna and flora. However, the island has suffered from drastic environmental changes in last millennia, leading to the extinction of many species. It is believed that more than 90% of the original forest cover has disappeared and previously connected forest habitats are now fragmented. Lemurs are forest-dwelling animals and are thus particularly affected by these changes. Three of the eight families of Malagasy lemurs present at the time of human arrival have disappeared and two additional families have lost their largest-bodied members. The exact causes of these extinctions and of the corresponding environmental changes are not fully clear. In particular, the relative importance of natural and anthropogenic factors is likely to have varied from one region to another and from a group of species to another. Even considering human impact only, the debate continues over the nature of these changes (hunting / direct vs. indirect human deforestation) and whether they occurred during the early stages of the human colonization or in the 20th century. Habitat destruction and fragmentation are clearly among the most serious threats facing lemurs and most species in Madagascar. Additionally, a number of studies have shown the negative impact of forest fragmentation on species richness. However, the consequences of these disturbances on the genetic structure of fragmented populations have not been studied for many species and are still poorly understood. Population genetics studies will be crucial for the effective conservation of many species, now restricted to isolated forest fragments, in order to develop conservation priorities and to define or create corridors between isolated forest fragments. In this project we aim to decipher the patterns of genetic diversity in lemur species with a special focus on the Eulemur species (B. Crouau-Roy and P. Barazer) and on Propithecus tattersalli and the related Propithecus species.

Funding

Institut Français de la Biodiversité, France

Colaboradores

Paul Sabatier University, Toulouse - Brigitte Crouau-Roy, Christophe Thébaud
Université de Mahajanga - Prof. Clément Rabarivola
Fanamby (Non-Governmental Organisation)

Other Collaborators across other ongoing projects:

IGC - Pedro Fernandes, Isabel Gordo
FCUL - Manuela Coelho
Cardiff University - Mike Bruford,
Benoit Goossens
Paul Sabatier University, Toulouse - Brigitte Crouau-Roy, Christophe Thébaud
Reading University - Mark Beaumont
University of Veterinary Medicine, Hannover - Ute Radespiel
Ferrara University - Guido Barbujani

Publicações

(Selected) Updated December (2008).

Radespiel, U, Rakotondravony, R, Chikhi, L (2008). Natural and anthropogenic determinants of genetic structure in the largest remaining metapopulation of the endangered golden-brown mouse lemur, Microcebus ravelobensis American Journal of Primatology 70 :1-11

Chikhi, L. (2008). News and Commentary: How accurate can genetic data be? Heredity 101 :471-472

Barbujani G., Chikhi, L. (2007). Human genetic diversity and its history In Handbook of Statistical Genetics, eds D. Balding, M. Bishop, and C. Cannings, 3rd edition

Goossens, B.*., Chikhi, L.*., Ancrenaz, M., Lackman-Ancrenaz, I., Andau, M., Bruford, M.W. *Shared first authorship. (2006). Genetic signature of anthropogenic population collapse in orang-utans PLoS, Biology, 4(2) :285-291

Chikhi, L. Beaumont, M.. (2005). Modelling Human Genetic History Encyclopaedia of Genetics, Genomics, Proteomics & Bioinformatics.

Chikhi, L., Bruford, M.W. (2005). Mammalian population genetics and genomics Mammalian Genomics (ed. Ruvinsky A, Marshall Graves J). CABI Publisher 21 :539-583

Goossens, B., Chikhi, L., Jalil, M.F., Ancrenaz, M., Lackman-Ancrenaz, I., Mohamed, M., Andau, P., Bruford, M.W. (2005). Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan populations from Sabah, Malaysia. Mol. Ecol. 14 :441-456

Chikhi, L., Nichols, R.A., Barbujani G., Beaumont M.A. (2002). Y genetic data support the Demic diffusion model. Proc. Natl. Acad. Sci, USA 98 :11007-11013

Goldstein, D.B., Chikhi, L. (2002). Human migrations and population structure : what we know and why it matters Annual Review of Genomics and Human Genetics 3 :129-152

Chikhi, L., Destro-Bisol, G., Bertorelle, G., Pascali, V., Barbujani, G. (1998). Clines of nuclear DNA suggest a largely Neolithic ancestry of the European gene pool Proc. Natl. Acad. Sci, USA 95 :9053-9058