Doctoral Degrees (Botany and Zoology)
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Browsing Doctoral Degrees (Botany and Zoology) by browse.metadata.advisor "Cherry, Michael"
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- ItemEvaluating the effects of biogeography and fragmentation on the taxonomic, functional, and genetic diversity of forest-utilising bats in a South African biodiversity hotspot(Stellenbosch : Stellenbosch University, 2020-12) Moir, Monika Ilka; Rambau, Ramugondo Victor; Cherry, Michael ; Richards, Leigh Rosanne; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Bats are a highly diverse mammalian order and are some of the most economically important non-domesticated vertebrates, providing many ecosystem services that contribute to the global economy. Yet, they remain a largely understudied taxon, particularly in the Eastern Cape province of South Africa, in which basic surveys of bat assemblages utilising indigenous forests are lacking. Indigenous forests constitute South Africa’s smallest and most fragmented biome yet support disproportionally high biodiversity. They have been fragmented throughout most of their evolutionary history due to global palaeoclimatic shifts; the responses of bats to forest fragmentation and historical climatic shifts in this habitat have been poorly studied. This study addresses these gaps with the broad aims of compiling a species inventory from 17 forests across the Eastern Cape and KwaZulu-Natal provinces; assessing the effects of fragmentation and biogeography on taxonomic and functional diversity of bat assemblages; and determining how genetic diversity and population genetic structure are informed by forest habitat associations and fragmentation. A multi-faceted approach of sampling methods, including capture and acoustic recording, and species identification techniques (morphology, acoustics, and DNA barcoding) were used to assemble an inventory of 25 species, with range extensions noted for six species. The first reference call library of hand released bats for forests in this region is presented, which may be used for species identification in further acoustic surveys. A minimum acoustic monitoring period of 6 to 7 nights per forest is recommended for future surveys. Forest biogeography was an important determinant of the functional diversity of insectivorous bat assemblages. Forest edge effects were found to demonstrate a positive relationship with functional evenness, thus motivating for maintenance and conservation of forest edges, particularly in temperate regions. Larger forearm length and low wing loading were identified as morphological traits exhibiting greater sensitivity to fragmentation, flagging species exhibiting these traits as potentially vulnerable to habitat fragmentation. The effect of historical climate-induced fluctuations of forest extent on population genetic structuring and demographic histories for six species was investigated using two mitochondrial markers, cytochrome b and D-loop. Population genetic trends were not informed by forest habitat associations, but rather by species-specific traits of dispersal ability, philopatry, and roost utilisation. Low genetic diversity and high population structure identify two species, Rhinolophus swinnyi and Laephotis botswanae, for conservation priority. Demographic responses to the Last Glacial Maximum (LGM) were not detected, with all six species displaying population expansions over this time. It appears that volant insectivores in eastern South Africa were less affected by the harsh conditions of the LGM than elsewhere. The dusky pipistrelle (Pipistrellus hesperidus) was used as a model organism to investigate the gene flow, genetic diversity, and migration of a forest-utilising species across the region with the use of eight microsatellite markers. The effects of urbanisation and agricultural development on gene flow were also examined. Findings of low population structure, low migration rates, and two genetic discontinuities were presented. This species does not depict dependence on forested habitats to maintain genetic connectivity on the landscape. The data also suggest that agricultural development and urbanisation have not yet had an impact on gene flow, thus providing a baseline with which to monitor the effects of future anthropic development on this species. Overall, this study has provided novel insights into the taxonomic, functional, and genetic diversity of forest-utilising bats in relation to biogeographical history and fragmentation within eastern South Africa
- ItemLandscape and Paleoclimatic influences on the genetic population structure of four forest-dependent passerines in the Eastern Cape of South Africa(Stellenbosch : Stellenbosch University, 2021-12) Mulvaney, Jake Matthew; Cherry, Michael; Matthee, Conrad; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Anthropogenic activity has placed increasing pressure on the restricted, fragmented forest biome of South Africa. Recent assessments of forest-dependent avifauna strongly indicate the vulnerability of this taxon to deforestation, and ongoing forest exploitation. Half of the forest- dependent bird species in South Africa have reportedly experienced range declines over the past quarter century, most notably within forests of the Eastern Cape province that are incorporated in the Maputaland-Pondoland-Albany Biodiversity Hotspot. These apparent declines have motivated a need to understand the population dynamics, and forest connectivity patterns of forest-dependent avifauna within the country, to better inform conservation efforts seeking to preserve the genetic integrity of these vulnerable bird species. This study investigated the population genetic structures of four range-declining forest- dependent Oscine passerines across the Eastern Cape and southern KwaZulu-Natal provinces of South Africa: Batis capensis (range decline: 1.30%), Cossypha dichroa (range decline: 19.53%), Phylloscopus ruficapilla (range decline 20.69%), and Pogonocichla stellata (range decline 23.02%). These four bird species are small-bodied (<50g) insectivores, that preferentially inhabit the temperate Afromontane forests, and represent a globally important functional group vulnerable to forest fragmentation. The landscape genetics study conducted on these four species revealed that reported range declines did not correspond closely to the genetic responses of these bird species to anthropogenic activity. Batis capensis showed substantial geneflow disruption, and declining effective populations, whereas P. ruficapilla and P. stellata populations appeared comparatively stable, although P. stellata did exhibit geneflow disruption. Only the South African endemic C. dichroa displayed simultaneous decline in distribution and effective population size, alongside geneflow disruptions, highlighting a vulnerability to forest loss and degradation. Landscape resistance modelling revealed the importance of both forest and coastal/mesic thicket for maintaining geneflow within these species. A phylogeographic study investigated the regional species-climate relationships of B. capensis, P. ruficapilla and P. stellata. The effective populations of these species were found not to have been constrained during the last glacial maximum – a climate event speculated to have resulted in drastically restricted forest distributions across South Africa. Furthermore, lowland scarp forests were affirmed as climate refugia for B. capensis and P. stellata, while the Afromontane forests of the Amatole Mountains and central Transkei appear to have harboured regional source populations of P. ruficapilla. Finally, comprehensive mist-netting of regional forests during sampling collection for the genetic studies afforded an opportunity to compare the effectiveness of point counts and mist- netting survey techniques at representing aspects of regional forest bird community structure. These comparisons found that point counts alone were sufficient to reliably assess these bird communities, with mist-netting contributing negligibly towards species detection. Combined survey efforts under-represented forest-edge foragers, woodland and grassland habitat generalists (collectively comprising ~63.6% total diversity), large birds, Palaearctic migrants, and carnivores (raptors), highlighting the potential shortcomings of these survey techniques in determining bird community composition. Overall, this study provided novel insights into forest connectivity; and past forest dynamics of forest-dependent insectivorous passerines within previously poorly investigated forests of the southern Maputaland-Pondoland-Albany Biodiversity Hotspot, and provides recommendations for future field surveys of these forests.
- ItemShared marking site use in African wild dogs (Lycaon pictus)(Stellenbosch : Stellenbosch University, 2024-03) Claase, Megan Jane; Cherry, Michael ; Jordan, Neil R.; McNutt, John W.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: African wild dogs (Lycaon pictus) have recently been shown to use latrines, or shared marking sites (SMSs), which are long lasting communal areas where multiple packs visit to deposit scent marks. The aim of this study is to understand how wild dogs use these locations, and what this behaviour means for communication and territoriality in this species. Chapter one explores seasonal variation in visitation rates across the study period, and aims to determine habitat selection of SMS locations in the landscape. Results indicate a seasonal difference in how often wild dogs visit SMS, with visits significantly decreasing during the annual denning season. Despite this dip in visitation during denning when their ranges are substantially contracted, wild dogs visit SMSs year-round. This supports the theory that SMSs play a key role in territorial advertisement and inter-pack communication in this species. SMSs are more likely to be found closer to roads, while grassland and permanent water areas are not selected for, patterns consistent with our existing knowledge of wild dog movement ecology. The second chapter aims to identify and explore the intrinsic and extrinsic characteristics driving individual scent marking patterns in both the inter- and intra-pack contexts. Dominant wild dogs scent mark more than subdominants, while patterns observed between the sexes appear to be context dependant. Dominant females overmark more than dominant males in the inter-pack context, while the opposite is seen in the intra-pack context. These results are consistent with a resource defence function of wild dog latrines, but suggest that the resource defended may differ between the sexes. Females may be more invested in the physical territory, while males may be more invested in advertising a bonded pair, likely a critical component of communicating with neighbouring packs. The final chapter explores how resident packs may tailor their territorial behaviour in response to rival identity, specifically determining if they exhibit a “dear enemy” or “nasty neighbour” response. Using behavioural data captured from camera traps as a natural experiment, results show that wild dogs generally exhibit a dear enemy response at the group level, but that this response is moderated by pack size, with larger packs exhibiting a nasty neighbour response. Data show individual, wild dogs from larger packs overmark larger groups more than they overmark small groups, while individuals from small packs avoid overmarking large groups. These patterns may be driven by variation in the size of intruding groups representing different threat, and serve to highlight key variables which may be overlooked in scent presentation experiments. Overall, this study provides detailed insights into SMSs use in wild dogs which offer insights into territoriality and communication in this endangered species. This information may be used to assist in their conservation such efforts to manipulate their ranging behaviour artificially using scent.