Testing NGS applications: Population genomics of lions and the African buffalo

Category: 
Pilot project
Acronym: 
GBS_Big_Mammals
Coordinator: 
Nathalie Smitz (RMCA)
JEMU partner: 
JEMU team
Project summary: 
As it is the case for many other large African mammals, lions (Panthera leo) and the African buffalo suffer from environmental disturbances. As a result, their number has sharply declined during the last decades. The lion is now listed as "Vulnerable" according to the IUCN Red List as listed in Appendix II of the CITES. The genetic erosion of populations accentuates the problems related to their conservation. Indeed, populations are becoming increasingly small and fragmented. Gene flow is therefore restricted and the genetic diversity of the species gradually runs out. This is especially the case when populations are confined to protected areas without gene flow among them. Such genetic drift can affect the reproductive capacity of the species and can increase the frequency of genetic diseases (i.e., inbreeding depression). The purpose of this project, combining phylogeographical, population genetics and conservation genetics approaches, is to assess more accurately the impact of the isolation of populations on their genetic diversity, and the risks related to inbreeding on their long-term survival. Such data are essential to establish effective local conservation strategies and thus to preserve these species. To meet these goals, we will analyze the genetic diversity of different populations from Africa and we will estimate putative gene flow among them. This approach will lead to a better understanding of the impact of recent population fragmentations and ultimately to an accurate estimation of long-term survival chances of the studied populations. This study will be based on a large set of SNP (Single Nucleotide Polymorphism) markers, obtained from GBS runs.
Collaborations: 
Johan Michaux, Conservation Genetics Unit, University of Liège, Belgium; Daniel Cornélis, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, France/Zimbabwe; P. Chardonnet, Fondation Internationale pour la Gestion de la Faune, France; Pim Van Hooft, Resource Ecology Group, University of Wageningen, The Netherlands; Rasmus Heller, Bioinformatics, University of Copenhagen, Denmark; Virginie Winant, AGORA-MOLCOL project, Royal Museum for Central Africa, Belgium.
Lab work progress: 
Completed: library prepared and NGS run performed
Data analysis: 
Completed
Starting date: 
2014
Project status: 
Completed

Peer reviewed papers:

  • Smitz N, Jouvenet O, Ambwene Ligate F, Crosmary W-G, Ikanda D, Chardonnet P, et al. (2018) A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania. PLoS ONE 13(11): e0205395. https://doi.org/10.1371/journal.pone.0205395
  • Smitz N, Van Hooft P, Heller R, Cornélis D, Chardonnet P, Kraus R, Greyling B, Crooijmans R, Groenen M, Michaux J, (2016) Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing. Mammalian Biology, 81 , 595 - 603.
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith