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Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa
Thesis (PhD (Zoology))--Univeristy of Pretoria, 2019
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University of Pretoria
2026
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| _version_ | 1867613577433579520 |
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| access_status_str | Open Access |
| author2 | Bloomer, Paulette |
| author_browse | Bloomer, Paulette |
| author_facet | Bloomer, Paulette |
| collection | Thesis |
| dc_rights_str_mv | © 2025 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Thesis (PhD (Zoology))--Univeristy of Pretoria, 2019 |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/110468 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:38:21.763Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/110468 Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa Bloomer, Paulette u02527154@up.ac.za Bennett, Nigel C. Chimimba, Christian T. Maswanganye, K.A UCTD Sustainable Development Goals (SDGs) Phylogeography Hyrax Namaqua Rock Mouse Species Distirbution Modelling Molecular biology Thesis (PhD (Zoology))--Univeristy of Pretoria, 2019 Understanding the processes and patterns of gene flow and diversity within species requires detailedknowledge of how different life history traits enable organisms to adapt to their environments. Another valuable insight stems from the inference of past population distributions as reflected by contemporary phylogeographic patterns. The present study uses a multilocus approach to elucidate the evolutionary mechanisms underlying species distributions and diversity of three small mammals from southern Africa. The study explores the evolutionary history within two species of Hyracoidea, namely the rock hyrax (Procavia capensis) and the yellow-spotted hyrax (Heterohyrax brucei) and the diversification of the Grassland-Savanna clade of a murine rodent, the Namaqua rock mouse (Micaelamys namaquensis). All three species are rock-dwelling and distributed throughout southern Africa. Procavia capensis has a wide distribution spanning most of the African continent, whilst H. brucei is intermittently distributed from the northern parts of South Africa extending into the centre of east and central Africa. Micaelamys namaquensis is a widely distributed species able to adapt to different habitats, although rocky areas are preferred. Individuals of P. capensis, H. brucei and M. namaquesnsis were analysed using mitochondrial DNA (cytochrome b) and nuclear (introns & microsatellites) regions. The cyt b gene was used to study the matrilineal relationships, with a subset of individuals used to amplify the nuclear introns (AP5 and / or PRKC1) in each species. The intron and microsatellite data were used to identify patterns of genetic diversity and gene flow exhibited. Analyses of cyt b in P. capensis revealed two distinct groupings, the southern and northern lineages, with more than 30 unique haplotypes found within each group. In Heterohyrax two deeply divergent lineages were revealed; their taxonomic and conservation status should be evaluated. Although constrained by small sample size, unique haplotypes were discovered, with potential restrictions on gene flow between disjunct locations. The cyt b data of the Namaqua rock mouse displayed high levels of genetic diversity, with 52 maternal haplotypes. This revealed that the grasslands of southern Africa are complex, with signals of admixture between haplogroups. Grasslands are also characterised by a high species turnover and are extremely variable, with increased expansions and declines in response to changing environment. The microsatellite data were used to elucidate the extent of gene flow found between the different areas and to further investigate if this process is sex-biased. For the hyrax species I found minimal unidirectional gene flow between lineages, whilst the Namaqua rock mouse exhibited bi-directional gene flow. I identified areas within hyrax that could have served as refugia during unfavourable times, in turn acting as sources for reestablishment of contact when climate conditions improved. Hyrax distribution seems to be driven by food availability. By contrast the Namaqua rock mouse seems to be able to subsist and recover quickly from bottlenecks. With the dwindling habitat due to several anthropogenic factors (e.g. habitat fragmentation, climate change), improved management of biological diversity, especially in threatened environments, together with knowledge of drivers of species distributions and population dynamics within different landscapes are crucial. Zoology and Entomology PhD (Zoology) Unrestricted Faculty of Natural and Agricultural Sciences SDG-15: Life on land SDG-13: Climate action 2026-06-08T09:42:20Z 2026-06-08T09:42:20Z 2019-04 2018 Thesis * A2019 http://hdl.handle.net/2263/110468 N/A en © 2025 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf University of Pretoria |
| spellingShingle | UCTD Sustainable Development Goals (SDGs) Phylogeography Hyrax Namaqua Rock Mouse Species Distirbution Modelling Molecular biology Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa |
| title | Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa |
| title_full | Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa |
| title_fullStr | Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa |
| title_full_unstemmed | Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa |
| title_short | Phylogeographic patterns of diversification in three saxicolous small mammals Micaelamys namaquensis Smith, 1834 (Rodentia: Muridae), Procavia capensis Pallas, 1766 and Heterohyrax brucei Gray, 1868 (Hyracoidea: Procaviidae) of South Africa |
| title_sort | phylogeographic patterns of diversification in three saxicolous small mammals micaelamys namaquensis smith 1834 rodentia muridae procavia capensis pallas 1766 and heterohyrax brucei gray 1868 hyracoidea procaviidae of south africa |
| topic | UCTD Sustainable Development Goals (SDGs) Phylogeography Hyrax Namaqua Rock Mouse Species Distirbution Modelling Molecular biology |
| url | http://hdl.handle.net/2263/110468 |