Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

L D Bertola; M Vermaat; F Lesilau; M Chege; P N Tumenta; E A Sogbohossou; O D Schaap; H Bauer; B D Patterson; P A White; H H de Iongh; J F J Laros; K Vrieling

doi:10.1186/s12864-022-08510-y

Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

BMC Genomics. 2022 Apr 22;23(1):321. doi: 10.1186/s12864-022-08510-y.

Authors

L D Bertola^{1

2

3}, M Vermaat^{4

5}, F Lesilau^{6

7}, M Chege^{6

7}, P N Tumenta^{8

9}, E A Sogbohossou¹⁰, O D Schaap¹¹, H Bauer¹², B D Patterson¹³, P A White¹⁴, H H de Iongh^{6

15}, J F J Laros^{4

5}, K Vrieling¹¹

Affiliations

¹ City University of New York, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA. laura.bertola@gmail.com.
² Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands. laura.bertola@gmail.com.
³ Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands. laura.bertola@gmail.com.
⁴ Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
⁵ Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
⁶ Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.
⁷ Kenya Wildlife Service, Nairobi, Kenya.
⁸ Centre for Environment and Developmental Studies, Cameroon (CEDC), Yaounde, Cameroon.
⁹ Regional Training Centre Specialized in Agriculture, Forest and Wood, University of Dschang, BP 138, Yaounde, Cameroon.
¹⁰ Laboratoire d'Ecologie Appliquée, Université d'Abomey-Calavi, 03 BP 294, Cotonou, Benin.
¹¹ Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.
¹² Wildlife Conservation Research Unit, Zoology, University of Oxford Recanati-Kaplan Centre, Tubney, OX13 5QL, UK.
¹³ Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA.
¹⁴ Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA.
¹⁵ Department of Biology, Evolutionary Ecology Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium.

Abstract

Background: Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting.

Results: In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail.

Conclusions: The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Keywords: Africa; Biodiversity; Conservation; Evolutionary history; Genomic variation; Genomics; Genotyping; Lion; Single Nucleotide Polymorphism (SNP); Wildlife.

MeSH terms

Animals
Genetic Variation
Humans
Lions* / genetics
Panthera* / genetics
Phylogeny
Polymorphism, Single Nucleotide
Whole Genome Sequencing

Grants and funding

820.01.002/Nederlandse Organisatie voor Wetenschappelijk Onderzoek