Genetic diversity, genetic structure, and scale of dispersal in Kruger National Park Lions (Panthera leo); implications for management and conservation.

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dc.contributor.advisorHoal, Eileenen_ZA
dc.contributor.advisorMatthee, Conrad A.en_ZA
dc.contributor.advisorvan Coeverden de Groot, Peteren_ZA
dc.contributor.authorHofmeyr, Jenniferen_ZA
dc.contributor.otherStellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences. Molecular Biology and Human Genetics.en_ZA
dc.date.accessioned2022-02-25T05:00:30Zen_ZA
dc.date.accessioned2022-04-29T12:51:38Zen_ZA
dc.date.available2023-03-18T03:00:10Zen_ZA
dc.date.issued2022-04en_ZA
dc.descriptionThesis (MSc)--Stellenbosch University, 2022.en_ZA
dc.description.abstractENGLISH ABSTRACT: The African lion is currently classified as vulnerable in the IUCN Red List of Threatened species (Bauer et al. 2016). The KNP lion population is by far the largest free-ranging South African lion population and therefore it is of great importance for lion conservation and management to describe the processes that maintain their genetic diversity patterns. General diversity is important to maintain the ability of a population to respond to changing climate ensuring their survival. With this work, I contribute new quantitative genetic data allowing novel demographic inferences for the Kruger National Park (KNP) lion (Panthera leo) population which can be used in their ongoing management. Analysis was done on 158 lion samples using 11 dinucleotide microsatellite markers for the full data set and then for comparison between geographic regions within the park (north and south), sexes, and temporal sampling (one year with large sample size). Results were compared to two other studies, (Miller et al. 2014; van Hooft et al. 2018) conducted using samples from KNP and lion studies done on other large lion populations in Tanzania, Zimbabwe, and Namibia (Spong et al. 2002; Morandin et al. 2014; Lyke et al. 2013; Tensen et al. 2018). The KNP lion population showed moderate variability and weak to moderate genetic structure with low to moderate levels of gene flow across the park, with an FST of 0.055 (P≤0.05), inbreeding coefficient (FIS) of 0.488 (P≤0.05) (heterozygote deficiency), and overall inbreeding coefficient of individual relative to the total population (FIT) of 0.516 (P≤0.05). The mean expected heterozygosity (He) (0.619) and mean observed heterozygosity (Ho) (0.409), for the KNP lion population show moderate to low diversity levels with a fixation index of 0.299. Spatially explicit analysis was done using TESS version 2.3 (Durand et al. 2009), resulting in two genetic groups I complete the first comprehensive study of scale of dispersal within KNP lions via spatial autocorrelation and compare the full dataset, large sampling year (2010 set), and males to females. The results indicate that individuals 100 to 150km apart are not closely related. For the 2010 samples, a higher positive autocorrelation coefficient (r) was found for individuals within 100km. The full data set for males show no strong spatial autocorrelation but when sampling in 2010 only a positive spatial autocorrelation was detected between individuals at 100km. Female autocorrelation is strong <50km at zero autocorrelation persisted beyond +/- 90km in all analyses with the 2010 set indicating stronger positive autocorrelation in the <50km class. Recommendations include maintaining connectivity and corridors with neighbouring countries, ensuring habitat expansion efforts are continued and allowing for dispersal. Non-invasive sampling and genotyping could facilitate extensive near-simultaneous sampling of KNP leading to more precise and accurate genetic structuring and dispersal estimates of KNP lions. The advent of these non-invasive technologies means one can relatively easily characterise the recolonisation dynamic of other Great Limpopo Transfrontier Park (GLTP) areas.en_ZA
dc.description.abstractAFRIKAANS OPSOMMING: Die Afrika-leeu word tans as kwesbaar in die IUCN Rooilys van Bedreigde spesies geklassifiseer (Bauer et al. 2016). Die KNP-leeubevolking is verreweg die grootste vrylopende Suid-Afrikaanse leeubevolking en daarom is dit van groot belang vir leeubewaring en -bestuur om die prosesse te beskryf wat hul genetiese diversiteitspatrone handhaaf. Algemene diversiteit is belangrik vir ‗die vermoe van ‗n bevolking om op veranderende klimaat te reageer en hul voortbestaan te verseker. Met hierdie werk dra ek nuwe kwantitatiewe genetiese data by wat nuwe demografiese afleidings vir die Krugerwildtuin (KNP) leeubevolking (Panthera leo) moontlik maak wat in hul deurlopende bestuur gebruik kan word. Ontleding is op 158 leeumonsters gedoen deur 11 dinukleotiedmikrosatellietmerkers vir die volledige datastel te gebruik en dan vir vergelyking tussen geografiese streke binne die park (noord en suid), geslagte en tydelike steekproefneming (een jaar met groot steekproefgrootte). Resultate is vergelyk met twee ander studies, (Miller et al. 2014; van Hooft et al. 2018) wat uitgevoer is met behulp van monsters van KNP en leeustudies wat op ander groot leeubevolkings in Tanzanië, Zimbabwe en Namibië gedoen is (Spong et al. 2002; Morandin et al. 2014; Lyke et al. 2013; Tensen et al. 2018). Die KNP-leeupopulasie het ‗n matige genetiese variasie en swak tot matige genetiese struktuur getoon met lae tot matige vlakke van geenvloei oor die park, met 'n FST van 0.055 (P≤0.05), intelingskoëffisiënt (FIS) van 0.488 (P≤0.05) (heterosigotiese tekort), en algehele intelingkoëffisiënt van individu relatief tot die totale populasie (FIT) van 0.516 (P≤0.05). Die gemiddelde verwagte heterosigositeit (He) (0.619), en gemiddelde waargenome heterosigositeit (Ho) (0.409), vir die KNPleeupopulasie toon matige diversiteitsvlakke met 'n fiksasie-indeks van 0.299. Ruimtelike eksplisiete analise is gedoen met behulp van TESS weergawe 2.3 (Durand et al. 2009), wat tot twee genetiese groepe gelei het. Ek voltooi die eerste omvattende studie van skaal van verspreiding binne KNP-leeus via ruimtelike outokorrelasie en vergelyk die volledige datastel, groot steekproefjaar (2010-stel) en mannetjies met wyfies. Die resultate dui daarop dat individue 100-150 km uitmekaar nie nou verwant is nie. Vir die 2010-monsters is 'n hoër positiewe outokorrelasiekoëffisiënt (r) gevind vir individue binne 100 km. Die volledige datastel vir mannetjies toon geen sterk ruimtelike outokorrelasie nie, maar met steekproefneming in 2010 is 'n positiewe ruimtelike outokorrelasie tussen individue op 100km bespeur. Verspreidingsresultate dui daarop dat wyfies met afstande meer as +/- 90km tussen individue nie nou verwant is nie. Die 2010-wyfies datastel skets 'n soortgelyke prentjie maar met 'n sterker positiewe outokorrelasiekoëffisiënt. Daar is afgelei dat leeubeweging en geenvloei in KNP ruimtelik gekorreleer is en dat daar 'n sterk tydelike en geslagseffek is. Aanbevelings sluit in die handhawing van konnektiwiteit met buurlande, om te verseker dat habitatuitbreidingspogings voortgesit word en om verspreiding toe te laat. Nie-indringende steekproefneming en genotipering kan uitgebreide, byna gelyktydige steekproefneming van KNP fasiliteer wat lei tot meer presiese en akkurate genetiese strukturering en verspreidingsberamings van KNP-leeus. Die koms van hierdie nie-indringende tegnologieë beteken dat 'n mens die herkoloniseringsdinamiek van ander Groter Limpopo Oorgrenspark -areas relatief maklik kan karakteriseer.af_ZA
dc.description.versionMastersen_ZA
dc.embargo.terms2023-02-24
dc.format.extentxi, 87 pages : illustrationsen_ZA
dc.identifier.urihttp://hdl.handle.net/10019.1/125044
dc.language.isoen_ZAen_ZA
dc.subjectAfrican lions, Panthera leo, Microsatellites, Dispersal, Spatial autocorrelation, Population demographics, Kruger National Park, Conservation geneticsen_ZA
dc.subject.lcshLion -- Kruger National Park (South Africa)en_ZA
dc.subject.lcshEndangered speciesen_ZA
dc.subject.lcshAnimal diversity conservationen_ZA
dc.subject.lcshUCTDen_ZA
dc.titleGenetic diversity, genetic structure, and scale of dispersal in Kruger National Park Lions (Panthera leo); implications for management and conservation.en_ZA
dc.typeThesisen_ZA
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