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Chege M, Sewalt B, Lesilau F, de Snoo G, Patterson BD, Kariuki L, Otiende M, Omondi P, de Iongh H, Vrieling K, Bertola LD. Genetic diversity of lion populations in Kenya: Evaluating past management practices and recommendations for future conservation actions. Evol Appl 2024; 17:e13676. [PMID: 38505216 PMCID: PMC10950092 DOI: 10.1111/eva.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
The decline of lions (Panthera leo) in Kenya has raised conservation concerns about their overall population health and long-term survival. This study aimed to assess the genetic structure, differentiation and diversity of lion populations in the country, while considering the influence of past management practices. Using a lion-specific Single Nucleotide Polymorphism (SNP) panel, we genotyped 171 individuals from 12 populations representative of areas with permanent lion presence. Our results revealed a distinct genetic pattern with pronounced population structure, confirmed a north-south split and found no indication of inbreeding in any of the tested populations. Differentiation seems to be primarily driven by geographical barriers, human presence and climatic factors, but management practices may have also affected the observed patterns. Notably, the Tsavo population displayed evidence of admixture, perhaps attributable to its geographic location as a suture zone, vast size or past translocations, while the fenced populations of Lake Nakuru National Park and Solio Ranch exhibited reduced genetic diversity due to restricted natural dispersal. The Amboseli population had a high number of monomorphic loci likely reflecting a historical population decline. This illustrates that patterns of genetic diversity should be seen in the context of population histories and that future management decisions should take these insights into account. To address the conservation implications of our findings, we recommend prioritizing the maintenance of suitable habitats to facilitate population connectivity. Initiation of genetic restoration efforts and separately managing populations with unique evolutionary histories is crucial for preserving genetic diversity and promoting long-term population viability.
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Affiliation(s)
- Mumbi Chege
- Wildlife Research and Training InstituteNaivashaKenya
- Institute of Environmental Sciences CMLLeiden UniversityLeidenThe Netherlands
| | - Bobbie Sewalt
- Institute of Biology IBLLeiden UniversityLeidenThe Netherlands
| | - Francis Lesilau
- Institute of Environmental Sciences CMLLeiden UniversityLeidenThe Netherlands
| | - Geert de Snoo
- Institute of Environmental Sciences CMLLeiden UniversityLeidenThe Netherlands
- Netherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Bruce D. Patterson
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoUnited States
| | | | - Moses Otiende
- Wildlife Research and Training InstituteNaivashaKenya
| | | | - Hans de Iongh
- Institute of Environmental Sciences CMLLeiden UniversityLeidenThe Netherlands
- Department of Evolutionary EcologyUniversity of AntwerpAntwerpBelgium
- Department BiologyUniversity of AntwerpAntwerpBelgium
| | - K. Vrieling
- Institute of Biology IBLLeiden UniversityLeidenThe Netherlands
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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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Wielstra B, Burke T, Butlin RK, Schaap O, Shaffer HB, Vrieling K, Arntzen JW. Efficient screening for ‘genetic pollution’ in an anthropogenic crested newt hybrid zone. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0582-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Doorduin L, van den Hof K, Vrieling K, Joshi J. The lack of genetic bottleneck in invasive Tansy ragwort populations suggests multiple source populations. Basic Appl Ecol 2010. [DOI: 10.1016/j.baae.2009.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Caño L, Escarré J, Vrieling K, Sans FX. Palatability to a generalist herbivore, defence and growth of invasive and native Senecio species: testing the evolution of increased competitive ability hypothesis. Oecologia 2008; 159:95-106. [DOI: 10.1007/s00442-008-1182-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Accepted: 09/25/2008] [Indexed: 10/21/2022]
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Joshi J, Vrieling K. The enemy release and EICA hypothesis revisited: incorporating the fundamental difference between specialist and generalist herbivores. Ecol Lett 2005. [DOI: 10.1111/j.1461-0248.2005.00769.x] [Citation(s) in RCA: 320] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Heritabilities of nectar production in the wild species Echium vulgare were estimated as realised heritability under controlled and field conditions. The nectar production of offspring from high- and low-nectar-producing parents was significantly different in both controlled and field conditions, indicating that nectar production is in part genetically determined. The present study is the first one to report a genetic component of variation of nectar production in a wild plant species in the field. Heritability estimated under controlled conditions was 0.13 and therewith less than the heritability estimated under field conditions, which amounted to 0.26. Offspring of high-nectar-producing plants produced comparable amounts of nectar in the growth chamber (1.28 microl) and in the field (1.22 microl). In contrast, the nectar production of offspring of low-nectar-producing plants was significantly higher in the growth chamber (0.95 microl) than in the field (0.55 microl), indicating a genotype by environment interaction. The level of heritability of nectar production was dependent on the environment. Under less favourable conditions, like those in the field, heritability of nectar production increased. Nectar production was not correlated with any of the vegetative or reproductive traits measured, and hence no costs of nectar production could be detected. Results obtained stress the importance of field measurements in determining heritabilities.
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Affiliation(s)
- K A Leiss
- Institute of Biology, University of Leiden, Kaiserstraat 63, 2311 GP Leiden, The Netherlands.
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Vrieling K, Saumitou‐Laprade P, Meelis E, Epplen JT. Multilocus DNA fingerprints in the plant
Cynoglossum officinale
L. and their use in the estimation of selfing. Mol Ecol 2003. [DOI: 10.1046/j.1365-294x.1997.00219.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- K. Vrieling
- Laboratoire de Génétique et Évolution des Populations Végétales, URA CNRS 1185, Université de Lille, Bâtiment SN2, F‐59655 Villeneuve d'Ascq Cedex, France,
- Institute of Evolutionary and Ecological Sciences, Van der Klaauw Laboratory, PO Box 9516, 2300 RA Leiden, the Netherlands,
| | - P. Saumitou‐Laprade
- Laboratoire de Génétique et Évolution des Populations Végétales, URA CNRS 1185, Université de Lille, Bâtiment SN2, F‐59655 Villeneuve d'Ascq Cedex, France,
| | - E. Meelis
- Institute of Evolutionary and Ecological Sciences, Van der Klaauw Laboratory, PO Box 9516, 2300 RA Leiden, the Netherlands,
| | - J. T. Epplen
- Molecular Human Genetics, Ruhr‐Universität, W‐44780 Bochum, Germany
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Korbecka G, Vrieling K, Squirrell J, Hale ML, Wolff K. Characterization of six microsatellite loci in Echium vulgare (Boraginaceae). ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1471-8286.2003.00421.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Vrieling K, Saumitou‐ Laprade P, Cuguen J, Van Dijk H, De Jong T, Klinkhamer P. Direct and indirect estimates of the selfing rate in small and large individuals of the bumblebee pollinated
Cynoglossum officinale
L (
Boraginaceae
). Ecol Lett 2002; 2:331-337. [DOI: 10.1046/j.1461-0248.1999.00093.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- K. Vrieling
- Laboratoire de Génétique et Évolution des Populations Végétales. UPRESA CURS 901C. Université de Lille. Bâtiment SN2. F‐59655 Villeneuve d’Ascq CEDEX France. And, Institute of Evolutionary and Ecological Sciences, Van der Klaauw Laboratory, PO Box 9516, 2300 RA Leiden, The Netherlands.,
| | - P. Saumitou‐ Laprade
- Laboratoire de Génétique et Évolution des Populations Végétales. UPRESA CURS 901C. Université de Lille. Bâtiment SN2. F‐59655 Villeneuve d’Ascq CEDEX France.,
| | - J. Cuguen
- Laboratoire de Génétique et Évolution des Populations Végétales. UPRESA CURS 901C. Université de Lille. Bâtiment SN2. F‐59655 Villeneuve d’Ascq CEDEX France.,
| | - H. Van Dijk
- Laboratoire de Génétique et Évolution des Populations Végétales. UPRESA CURS 901C. Université de Lille. Bâtiment SN2. F‐59655 Villeneuve d’Ascq CEDEX France.,
| | - T.J. De Jong
- Institute of Evolutionary and Ecological Sciences, Van der Klaauw Laboratory, PO Box 9516, 2300 RA Leiden, The Netherlands.,
| | - P.G.L. Klinkhamer
- Institute of Evolutionary and Ecological Sciences, Van der Klaauw Laboratory, PO Box 9516, 2300 RA Leiden, The Netherlands
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Vrieling K, van Wijk CAM. Cost assessment of the production of pyrrolizidine alkaloids in ragwort (Senecio jacobaea L.). Oecologia 1994; 97:541-546. [DOI: 10.1007/bf00325894] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/1993] [Accepted: 02/08/1994] [Indexed: 11/25/2022]
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