Phylogeographic structure of the honey badger (Mellivora capensis)

Rhodes, James I. (James Ian) (Stellenbosch : Stellenbosch University, 2006-04)

Thesis (MSc)--University of Stellenbosch, 2006.

Thesis

ENGLISH ABSTRACT: The aim of this study was to investigate the phylogeographic structuring of the honey badger, Mellivora capensis, a highly mobile medium sized carnivore with an extensive distribution throughout sub-Saharan Africa extending into the Middle East and India. Particular focus was placed on providing preliminary data potentially useful for the development of translocation policies for this species in southern Africa. Where possible, genetic results were also compared with current trinomial designations to determine whether subspecies status given to geographical groupings was supported by the genetic data. Mitochondrial control region sequence data was obtained for most a selection of specimen’s available while nuclear microsatellite variation was determined for a subset of individuals where there were sufficient sample sizes available. Phylogeographic structuring of the maternal mitochondrial lineage was initially obscured by the coamplification of a closely related numt. To overcome co-amplification, the numt was identified and mtDNA specific primers were designed. Mitochondrial DNA results are based on the most variable 230 bp of the control region (sequenced for 78 individuals) while five polymorphic nuclear microsatellite markers were scored (for 55 individuals). Analysis, employing both nuclear and mitochondrial data, showed that although a pattern of isolation by distance can be detected, there was evidence for the presence of phylogeographic structuring between eastern and southern Africa. This could be interpreted as due to vicariance, probably associated by rifting and climatic occilations during the Pleistocene. Analyses support the identification of distinct management units for eastern and southern African populations although some evidence exists for secondary introgression between these two regions. Following this, we recommend that translocations between these broad geographic areas should be avoided. Within these geographic areas, because of a general pattern of isolation by distance, we recommend that individuals for translocations come from geographically proximate populations. In some instances, phylogeographic structuring is concordant with subspecies designations but additional sampling will be needed to make any firm taxonomic conclusions.

AFRIKAANSE OPSOMMING: Die doelwit van hierdie studie was om die filogeografiese struktuur van die ratel, Mellivora capensis, ‘n hoogs bewegende medium groot karnivoor met ‘n wydverspreide distribusie deur sub-Sahara Afrika wat strek tot in die Midde Ooste en India, te bepaal. Spesifieke fokus is geplaas op die voorsiening van preliminêre data potensieel bruikbaar vir dir ontwikkeling van verplasing strategieë vir hierdie spesie in suidelike Afrika. Genetiese resultate is, waar moontlik, vergelyk met huidige drieledige kategorieë om te bepaal of subspesies ondersteun word deur die genetiese data. Mitochondriale ‘control region’ DNS volgorde data was verkry vir die meeste van die monsters beskikbaar en kern mikrosatelliet variasie was bepaal vir ‘n gedeelte van individue waar voldoende monster groottes beskikbaar was. Filogeografiese strukturering van die materne mitochondriale merker was oorspronklik versteek deur die ko-amplifikasie van ‘n naby verwante ‘numt’. Om die ko-amplifikasie te oorkom is die ‘numt’ geïdentifiseer en mtDNS spesifieke voorvoerders is ontwerp. Mitochondriale DNS resultate is gebaseer op die mees veranderlike 230 bp van die ‘control region’ (waar die DNS volgorde vir 78 individue bepaal is) en vyf polimorfiese kern mikrosatelliet merkers (in 55 individue). Analises, wat gebruik maak van kern en mitochondriale data, toon wel ‘n patroon van isolasie deur afstand, maar ook ‘n duidelike sigbare filogeograpfiese strukturering tussen oostelike en suidelike Afrika. Hierdie is geïnterpreteer as vikariansie, heel waarskynlik ge-assosieer deur berg verskuiwings en klimaatsveranderinge deur die Pleistocene. Analises ondersteun die identifikasie van definitiewe verkillende bestuurseenhede vir oostelike en suidelike Afrika maar sekere bewyse bestaan dat sekondêre introgressie tussen streke bestaan. Dit word aanbeveel dat translokasies tussen hierdie geografiese areas voorkom moet word. Binne geografiese areas, as gevolg van ‘n algemene patroon van isolasie deur afstand, is dit aanbeveel dat individue vir verplasing van nabygeleë populasies moet wees. In sommige gevalle het filogeografiese strukturering ooreen gestem met subspesies kategorieë, maar verdere materiaal is nodig voor definitiewe taksonomiese besluite geneem kan word.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/21732
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