A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania

• Published in: PloS one 2018-11, Vol.13 (11), p.e0205395-e0205395
• Main Authors: Smitz, Nathalie, Jouvenet, Olivia, Ambwene Ligate, Fredrick, Crosmary, William-George, Ikanda, Dennis, Chardonnet, Philippe, Fusari, Alessandro, Meganck, Kenny, Gillet, François, Melletti, Mario, Michaux, Johan R
• Format: Article
• Language: English
• Subjects: Alleles; Analysis of Variance; Animal populations; Animals; Anthropogenic factors; Biodiversity; Biological evolution; Biology and Life Sciences; Computational Biology; Cytochrome; Cytochrome b; Cytochromes; Earth Sciences; Ecology and Environmental Sciences; Endangered & extinct species; Environmental effects; Environmental protection; Evolutionary genetics; Gene flow; Genes, Mitochondrial; Genetic diversity; Genetic drift; Genetic structure; Genetic Variation; Genetics; Genetics, Population; Genome-Wide Association Study; Genomes; Geographical distribution; Geography; Habitat loss; High-Throughput Nucleotide Sequencing; Inbreeding; Inbreeding depression; Land degradation; Land use; Life sciences; Lions - classification; Lions - genetics; Livestock; Microsatellite Repeats; Microsatellites; Mitochondria; Museums; Panthera leo; People and Places; Polymorphism, Single Nucleotide; Population decline; Population Dynamics; Population genetics; Pressure effects; Prey; Sciences du vivant; Single-nucleotide polymorphism; Subpopulations; Tanzania; Threatened species; Tourism; Wildcats; Wildlife conservation; Zoologie; Zoology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0205395

The African lion (Panthera leo), listed as a vulnerable species on the IUCN Red List of Threatened Species (Appendix II of CITES), is mainly impacted by indiscriminate killing and prey base depletion. Additionally, habitat loss by land degradation and conversion has led to the isolation of some subpopulations, potentially decreasing gene flow and increasing inbreeding depression risks. Genetic drift resulting from weakened connectivity between strongholds can affect the genetic health of the species. In the present study, we investigated the evolutionary history of the species at different spatiotemporal scales. Therefore, the mitochondrial cytochrome b gene (N = 128), 11 microsatellites (N = 103) and 9,103 SNPs (N = 66) were investigated in the present study, including a large sampling from Tanzania, which hosts the largest lion population among all African lion range countries. Our results add support that the species is structured into two lineages at the continental scale (West-Central vs East-Southern), underlining the importance of reviewing the taxonomic status of the African lion. Moreover, SNPs led to the identification of three lion clusters in Tanzania, whose geographical distributions are in the northern, southern and western regions. Furthermore, Tanzanian lion populations were shown to display good levels of genetic diversity with limited signs of inbreeding. However, their population sizes seem to have gradually decreased in recent decades. The highlighted Tanzanian African lion population genetic differentiation appears to have resulted from the combined effects of anthropogenic pressure and environmental/climatic factors, as further discussed.