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Tensen L, Jansen van Vuuren B, Groom R, Bertola LD, de Iongh H, Rasmussen G, Du Plessis C, Davies-Mostert H, van der Merwe D, Fabiano E, Lages F, Rocha F, Monterroso P, Godinho R. Spatial genetic patterns in African wild dogs reveal signs of effective dispersal across southern Africa. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.992389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Across much of Africa, decades of civil war, land reforms, and persecution by humans have decimated wildlife populations. African wild dogs (Lycaon pictus) have declined dramatically during the past decades, but have shown recent natural recolonisation of some areas. In Angola, they were rediscovered after almost five decades when no surveys were being conducted, and they have recolonised areas in southern Zimbabwe and northern South Africa. Wild dogs were also reintroduced to Mozambique, where only few individuals remained. Against this backdrop, understanding genetic structure and effective dispersal between fragmented populations is essential to ensure the best conservation approaches for the long-term survival of the species. Our study investigated population genetic diversity, differentiation and gene flow of wild dogs across southern Africa, to include areas where they have recently been rediscovered, reestablished or reintroduced. Our results point to four weakly differentiated genetic clusters, representing the lowveld of Zimbabwe/Limpopo, Kruger NP, Angola/KAZA-TFCA, and the managed metapopulation, counterbalanced by moderate levels of effective dispersal on a southern African scale. Our results suggest that if the human footprint and impact can be significantly minimized, natural dispersal of wild dogs could lead to the demographic recovery of the species in southern Africa.
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Bertola LD, Vermaat M, Lesilau F, Chege M, Tumenta PN, Sogbohossou EA, Schaap OD, Bauer H, Patterson BD, White PA, de Iongh HH, Laros JFJ, Vrieling K. 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; 23:321. [PMID: 35459090 PMCID: PMC9027350 DOI: 10.1186/s12864-022-08510-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/29/2022] [Indexed: 11/23/2022] Open
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08510-y.
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Affiliation(s)
- L D Bertola
- City University of New York, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA. .,Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands. .,Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.
| | - M Vermaat
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - F Lesilau
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Kenya Wildlife Service, Nairobi, Kenya
| | - M Chege
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Kenya Wildlife Service, Nairobi, Kenya
| | - P N Tumenta
- Centre for Environment and Developmental Studies, Cameroon (CEDC), Yaounde, Cameroon.,Regional Training Centre Specialized in Agriculture, Forest and Wood, University of Dschang, BP 138, Yaounde, Cameroon
| | - E A Sogbohossou
- Laboratoire d'Ecologie Appliquée, Université d'Abomey-Calavi, 03 BP 294, Cotonou, Benin
| | - O D Schaap
- Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
| | - H Bauer
- Wildlife Conservation Research Unit, Zoology, University of Oxford Recanati-Kaplan Centre, Tubney, OX13 5QL, UK
| | - B D Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | - P A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA
| | - H H de Iongh
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Department of Biology, Evolutionary Ecology Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - J F J Laros
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - K Vrieling
- Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
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Bertola LD, Jongbloed H, van der Gaag KJ, de Knijff P, Yamaguchi N, Hooghiemstra H, Bauer H, Henschel P, White PA, Driscoll CA, Tende T, Ottosson U, Saidu Y, Vrieling K, de Iongh HH. Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo). Sci Rep 2016; 6:30807. [PMID: 27488946 PMCID: PMC4973251 DOI: 10.1038/srep30807] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.
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Affiliation(s)
- L D Bertola
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H Jongbloed
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - K J van der Gaag
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - P de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - N Yamaguchi
- Qatar University, Department of Biological and Environmental Sciences, College of Arts and Sciences, PO Box 2713, Doha, Qatar
| | - H Hooghiemstra
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - H Bauer
- WildCRU, Recanati-Kaplan Centre, University of Oxford. Tubney House, Abingdon Road, OX13 5QL, UK
| | - P Henschel
- Panthera, 8 West 40th Street, 18th Floor, New York, NY 10018, USA
| | - P A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - C A Driscoll
- Wildlife Institute of India, Dehradun 248001, Uttarakhand, India
| | - T Tende
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - U Ottosson
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - Y Saidu
- Nigeria National Park Service, PMB 0258 Garki-Abuja, Nigeria
| | - K Vrieling
- Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H H de Iongh
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,University of Antwerp, Department Biology, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
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