Population genetic structure of the ground pangolin based on mitochondrial genomes
| dc.contributor.advisor | Grobler, J. P. | |
| dc.contributor.advisor | Kotzé, A. | |
| dc.contributor.advisor | Dalton, D. L. | |
| dc.contributor.author | Du Toit, Zelda | |
| dc.date.accessioned | 2015-09-03T11:07:53Z | |
| dc.date.available | 2015-09-03T11:07:53Z | |
| dc.date.issued | 2014-03 | |
| dc.description.abstract | English: Temminck’s ground pangolin, S. temminckii, is currently listed as Vulnerable on the IUCN Red Data List. However, their numbers are decreasing due to illegal hunting for bush meat and over-harvesting for traditional use in Africa. Pangolins are also exported to Asia as a delicacy and for use in traditional medicine. Currently, the greatest threat to ground pangolins in southern Africa is electrocution by electric fences on game farms. This project consisted of two parts. The first was to sequence the whole mtDNA genome of Temminck’s ground pangolin to identify gene regions and to determine the evolutionary relationship of the order Pholidota. Results generated using the primer walking method, indicated that the whole mtDNA of Temminck’s ground pangolin is 16,559 bp in length. The phylogenetic analysis shows that the order Pholidota form a sister grouping with the order Carnivora rather than with the order Xenarthra as would be expected. Data suggested a Laurasian origin approximately 87 mya and possible migration into Africa during the Paleocene era around 55 mya. The second part of the study was conducted in order to determine the phylogeography of Temminck’s ground pangolins in southern Africa. Twenty five samples were collected from four countries, namely Namibia, Zimbabwe, Mozambique and South Africa (Mpumalanga and the Northern Cape Provinces). The results obtained indicated a high level of genetic variation within populations and only a few individuals displayed private haplotypes, which resulted in an increase in haplotype diversity. Samples from Zimbabwe and Mozambique (Group 1) clustered together while samples from the Northern Cape and Mpumalanga Provinces of South Africa grouped with samples from Namibia (Group 2), suggesting either an ancestral or recent split between Groups 1 and 2. The BEAST analysis indicated that the two groups shared a recent common ancestor between 2.94 and 1.27 mya across the three gene regions. In addition, it was estimated that the Zimbabwe/Mozambique split occurred between 920 and 710 kya and the Kalahari/Namibia/Mpumalanga split between 1.16 mya and 790 kya. This pattern corresponds to the Mega Kalahari Sand Sea forming a barrier between individuals and populations around that time. This study is the first molecular analysis based on the mitochondrial DNA genome of Temminck’s ground pangolin in southern Africa and it provides an insight into the species’ population genetics across its range in southern Africa. However, additional research into the order Pholidota throughout Africa can assist in better understanding of genetic variation within African pangolin species and populations. Furthermore, such studies will also support the conservation of genetic variation within species and contribute to identifying evolutionary distinct populations to assist in developing effective conservation management plans for the different species of the order Pholidota. | en_ZA |
| dc.description.abstract | Afrikaans: Die huidige status van Temminck se grond itermagog, S. temminckii, is gelys as Kwesbaar op die Internasionale Unie vir die Bewaring van Natuurlewe (IUCN) se Rooi Data Lys. Nietemin, toon bevolkings ‘n klaarblyklike afname in getalle as gevolg van onwettige jagtery vir wildsvleis, sowel as groot stropings aanvraag vir tradisionêle gebruik in Afrika. Itermagoë word ook na Asië uitgevoer waar hulle beskou word as ‘n lekkerny en ook gebruik word in tradisionele medisyne. Die grootste gevaar vir itermagoë in Suider-Afrika is huidiglik doodskokking deur elektrisiteitsdrade op wildsplase. Hierdie projek het bestaan uit twee dele. Die eerste deel het behels om deur middle van volgordebepaling die volledige mitokondriale deoxyribonukleïensuur (mtDNS) genoom van Temminck se grond itermagog vas te stel, om die verskillende geen areas te identifiseer en evolusionêre verwantskappe van die orde Pholidota te bepaal. Resultate wat met behulp van die “primer walking” metode gegenereer is, het getoon dat die volledige mtDNS van Temminck se grond itermagog 16,559 bp lank is. Die filogenetiese analise het getoon dat die orde Pholidota ‘n sister groep vorm met die orde Carnivora eerder as groepeer met die orde Xenarthra soos verwag. Gevolglik toon die data ook ‘n Laurasiëse oorsprong, ongeveer 87 miljoen jaar gelede, sowel as moontlike migrasie na Afrika gedurende die Paleocene tydperk ongeveer 55 miljoen jaar gelede. Die tweede deel van die studie het gehandel oor die filo-geografie van Temminck se grond itermagog in Suider-Afrika. Vyf-en-twintig individue, afkomstig van vier lande, is bestudeer. Die lande het betaan uit Namibië, Mosambiek, Zimbabwe en Suid-Afrika (Mpumalanga- en Noord-Kaap Provinsies). Die resultate toon dat daar ‘n hoë vlak van genetiese divergensie tussen bevolkings is en net ‘n paar individue het unieke haplotiepes getoon wat gelei het tot verhoging in haplotiep diversiteit. Die resultate het verder getoon dat die individue van Zimbabwe en Mosambiek (Groep 1) saam groepeer terwyl individue van Noord-Kaap Provinsie en Mpumalanga Provinsie saam groepeer met individue van Namibië (Groep 2). Bogenoemde groeperings kan te wyte wees aan ‘n voorouer of moderne skeiding tussen die twee groepe. Die BEAST analise het getoon dat die twee groepe ‘n gemeenskaplike voorouer gedeel het tussen 2.94 en 1.27 miljoen jaar gelede oor die drie geen areas. Die resultate het verder getoon dat die Zimbabwe/Mosambiek skeiding tussen 920 en 710 duisend jaar gelede ontstaan het en die Kalahari/Mpumalanga/Namibië skeiding tussen 1.16 miljoen jaar gelede en 790 duisend jaar gelede oor die drie geen areas. Bogenoemde patroon is te wyte aan die Groot Kalahari Sand-See wat ‘n versperring tussen individue en bevolkings van daardie tyd gevorm het. Hierdie studie is die eerste molekulêre analise gebaseer op die mtDNS genoom van Temminck se grond itermagog in Suider-Afrika en dit veskaf ‘n beter insig tot die spesie se bevolkingsgenetika regoor hul verspreidings gebied in Suider-Afrika. Additionele navorsing van die orde Pholidota regoor Afrika is nietemin nodig ten einde ‘n beter begrip van die genetiese variasie in itermagog spesies en bevolkings te verkry. Die resultate dra ook by tot die bewaring van genetiese diversiteit in identifisering van unieke bevolkings, wat verder sal bydra tot die ontwikkeling van effektiewe bewaringsbestuursplanne vir al die spesies in die orde Pholidota. | af |
| dc.description.sponsorship | National Research Foundation (NRF) | |
| dc.identifier.uri | http://hdl.handle.net/11660/1149 | en_ZA |
| dc.language.iso | en | en_ZA |
| dc.publisher | University of the Free State | en_ZA |
| dc.rights.holder | University of the Free State | en_ZA |
| dc.subject | Mitochondrial DNA | en_ZA |
| dc.subject | Phylogeny | en_ZA |
| dc.subject | Phylogeography | en_ZA |
| dc.subject | Smutsia temminckii | en_ZA |
| dc.subject | Temminck’s ground pangolin | en_ZA |
| dc.subject | Pangolins | en_ZA |
| dc.subject | Pangolins -- Genetics | en_ZA |
| dc.subject | Animal population genetics | en_ZA |
| dc.subject | Dissertation (M.Sc. (Genetics))--University of the Free State, 2014 | en_ZA |
| dc.title | Population genetic structure of the ground pangolin based on mitochondrial genomes | en_ZA |
| dc.type | Dissertation | en_ZA |