Source of introduced populations of Hemidactylus mabouia (Moreau de Jonnès, 1818) into the Eastern Cape Province and the potential spread to other South African regions
- Authors: Jeme, Alungile
- Date: 2023-03-29
- Subjects: Introduced vertebrates , Hemidactylus , Tropical house gecko , Species Distribution Model , Biogeography South Africa Eastern Cape , Biological invasions
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422334 , vital:71933
- Description: Human movements globally have resulted in dispersal and introduction of terrestrial and marine organisms into areas outside of their native range. Species that have been introduced to new habitats can either be alien (not causing any harm to the new environment) or invasive alien species (destroying or competing with the indigenous species for resources). Investigating the source of these introductions is important as it provides baseline information about their biology and evolution. It also allows for better prevention measures for future invasions and for effective conservation strategies. In this study, I investigate the source of the introduced populations of tropical house geckos Hemidactylus mabouia in the Eastern Cape Province using two mitochondrial gene regions, ribosomal 16S and NADH dehydrogenase subunit 4 (ND4). We also look at the potential spread of these species using species distribution models (SDMs). The phylogeny showed that the introduced populations into the Eastern Cape were genetically similar to both H. mabouia lineages found in Central & Southern Africa. The phylogeny produced two clades from which the majority of the introduced samples were grouped in a clade with samples from Angola, DRC, and Mozambique, and only a few nested within the second clade with the South African native population. Haplotype networks from both genes also showed two clades, matching those found in the phylogeny. The introduced samples were associated with samples from Angola and those from South Africa (native) as these localities had a number of shared haplotypes. SDMs showed less evidence that these individuals could naturally move west down the coast as the probability of occurrence was below 0.4 from the Eastern Cape to the Western Cape. Our conclusion was that the introductions may be due to multiple avenues like species moving down the east coast or human translocation including trade routes. From this we can conclude that geckos are largely translocated through human movement as they are known for their opportunistic behaviours as they are commensal with humans. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
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- Date Issued: 2023-03-29
Integrative systematic structuring of the widespread psammophiid snakes (Psammophiidae): a multi-evidence species delineation approach
- Authors: Keates, Chad
- Date: 2021-10-29
- Subjects: Psammophis South Africa , Herpetology , Herpetology Africa , Molecular biology , Psammophis Classification , Psammophis Genetics , Psammophis Morphology , Psammophis Phylogeny , Morphology Mathematics , Psammophylax
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/295077 , vital:57288 , DOI 10.21504/10962/295079
- Description: Species form the foundations upon which we build our understanding of the natural world. Although a focus of much scientific attention, our understanding of species is stunted by the intrinsic ‘fuzziness’ of boundaries within nature. Due to the complexity of the evolutionary process, coupled with an ever-changing abiotic landscape, species are hard to delineate, even at the best of times. Whilst various species concepts and sophisticated delimitation methods have helped scientists tease apart species, many species complexes persist. This is because taxonomy is a discrete ordering system imposed upon the continuous and intercalated structure of life. To improve our understanding of a wide-ranging family of snakes, I investigated the taxonomy and evolutionary structuring within Psammophiidae using both molecular and morphological approaches, employing phylogenetic, phylogeographic, and morphometric analyses on the group. The systematic complexity of the family (as evidenced by past research) coupled with the group’s widespread distribution and ecological importance, made the taxon an ideal candidate for a broad-sweeping multi-level systematic analysis using multiple species delimitation methods. Additionally, in this thesis I attempted to build on the ground-breaking work of Christopher Kelly by addressing several knowledge gaps identified within the family, and in so doing, produce the most thorough evolutionary and taxonomic study of Psammophiidae possible. Given the taxonomic uncertainty associated with the family, Chapter Two used a representative sampling from every available species (near complete taxon sampling approach) in the family. The chapter used both standard and time-calibrated phylogenetic modelling and distance/threshold-based species delimitation, to elucidate the finer-level structuring within the family. Geometric morphometrics was used to determine whether there were diagnosable differences in head structure between the different genera. The final phylogenetic tree incorporated 320 samples, representing the most comprehensive phylogenetic reconstruction of the family to date. By using a near-complete taxon sampling approach, I was able to resolve previously unsupported relationships within the family whilst also identifying several novel instances of an under- and over-appreciation of species diversity within the family. Geometric morphometrics also identified clear distinctions between genera based on head shape (head width and ‘beakedness’). This chapter showcased the importance of complete taxon sampling and robust methodology for species delimitation and the deleterious effect of species concepts when implemented in isolation. In Chapter Three, I narrowed the scope of the study to focus on the genus level. Psammophylax (Fitzinger 1843) is an abundant, yet poorly studied genus of grass snakes, endemic to Africa. The generalist nature of the genus and wide-spanning distributions of the constituent species has given rise to several subspecies and a poor understanding of the taxonomic structuring within the genus. The overlapping distributions (sympatry) of many of Psammophylax species, coupled with the potential for cryptic speciation via mechanisms such as convergent evolution, made the group the ideal candidate for a broad-sweeping systematic study (as evidenced in Chapter Two). By applying the suite of analyses used in Chapter Two to the generic level, we aimed to determine the effectiveness of a multi-evidence species delineation approach when tackling systematic problems at lower taxonomic levels. A genetic phylogeny of six of the seven species was estimated using multiple phylogenetic and distance/ threshold-based species delimitation methods. To support the molecular analyses, we conducted morphological analyses on the body (traditional morphology) and head (geometric morphometrics) separately. Phylogenetic analyses recovered a similar topology to past studies, but with better resolution and node support. I found substantial genetic structuring within the genus, supported by significantly different head shapes between Ps. a. acutus and other Psammophylax species. Psammophylax a. acutus was recovered as sister to its congeners, and sequence divergence values and morphometrics supported its recognition as a new genus. Increased sampling in East Africa (Tanzania, Kenya, and Ethiopia) revealed that Psammophylax multisquamis is polyphyletic, necessitating the description of a new, morphologically cryptic, species from northern Tanzania. The distribution of Ps. multisquamis sensu stricto is likely restricted to Kenya and Ethiopia. Within this chapter, taxon-specific phylogenetic analyses yielded stronger intrageneric support as compared to Chapter Two, allowing for more defensible conclusions about taxonomical amendments. Geometric morphometrics proved similarly useful (as compared to Chapter Two) in teasing apart genera within the family but lacked the robustness to delineate species within Psammophylax with confidence, highlighting the apparent convergence of form within the genus. In Chapter Four, I investigated the evolutionary structuring within the Southern African endemic Psammophylax rhombeatus. The structural and environmental heterogeneity within the region has given rise to many morphological forms distributed throughout the country, with previous studies neglecting the associated molecular significance of these forms. Irrespective of their small sample sizes, both Chapter Two and Three identified substantial phylogenetic structuring within the species, making Ps. rhombeatus the ideal candidate for a multi-faceted systematic review, using a combination of phylogenetics, geometric morphometrics and, for the first time in this species, phylogeographic analyses. By investigating a single species, in detail, I was able to assess the effectiveness of the methodologies implemented in previous chapters on systematic sorting using the multi-evidence species delineation approach. Phylogenetic and haplotype analysis retrieved four well-supported clades: southeast South Africa (SESA), southwest South Africa (SWSA), north-eastern South Africa (NESA) and western South Africa (WSA). Although not variable enough to warrant taxonomic re-evaluation, the clades represented important genetic hotspots, with relatively high intraspecific genetic divergence values separating them, irrespective of the small geographic distances separating populations. This is likely a product of the taxon’s habitat-generalist lifestyle, enabling them to bypass vicariant barriers that might otherwise cause speciation in less versatile species. The clades are also geographically distinct, with little overlap, indicating previous vicariance, a finding that is supported by the split of Ps. rhombeatus from Ps. ocellatus in the mid-Pliocene, followed by the diversification of Ps. rhombeatus into four clades throughout the Pleistocene. The genetic structuring observed in Ps. rhombeatus may be a product of population expansion following ancient refugial isolation (potentially Last Glacial Maximum [LGM]). The molecular distinctiveness of the clades was not replicated in the morphological component of this chapter, with neither dorsal nor lateral geometric morphometric analyses of head shape showing any discernible distinctiveness based on geography. Whilst head shape has not been shown to be an effective delineator of evolutionary units at the species level (within this taxon), body colour, scalation, and snout-vent length has been linked to morphotypes within the species based on the work of Broadley (1966). These morphological groupings are loosely attributable to the molecular clades identified in the phylogenetic analyses, highlighting the complex interplay of genetic and morphological characteristics in the process of speciation, and their representation in systematic accounts. This thesis represents the most thorough evolutionary and systematic study of the family currently possible. In addition to identifying and describing both a new genus and species, this thesis also highlighted several instances of an over- and under-appreciation of species diversity within Psammophiidae. By applying a multi-evidence species delineation approach to this thesis, I show the intricacy of the evolutionary process (at various taxonomic levels) and showcase the ease to which species boundaries can be confounded when species concepts are implemented in isolation. These findings also highlighted the importance of sample size, sample range, species delimitation method on the outcome of taxonomic analyses, and their interpretation. Lastly, this thesis addressed the knowledge gaps left by Christopher Kelly’s PhD work and investigated the findings of recent papers that attempted to do the same. Whilst this study answers the questions of old, the taxon-intensive focus revealed several new knowledge gaps within the family, highlighting how much we know about snake systematics, and furthermore, how much we still need to learn about evolutionary structuring. , Thesis (PhD) -- Faculty of Science, Environmental Science, 2021
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- Date Issued: 2021-10-29
An evolutionary study of legless skinks’ (Acontias Cuvier, 1817) head and vertebrae morphology
- Authors: Evlambiou, Anthony Andreas
- Date: 2021-10
- Subjects: Skinks South Africa , Acontias South Africa , Typhlosaurus South Africa , Acontias Morphology , Acontias Phylogeny , Acontias Evolution , Vertebrae , Skull Growth , Evolutionary developmental biology
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/190690 , vital:45018
- Description: Environmental factors and/or processes can produce differences in general shape between individuals or particular parts of individuals. Examples of these biological processes may include ontogenetic development, adaptation to local geographic factors, or long-term evolutionary diversification. An organism is not likely to be able to optimise a single structure for multiple purposes and so trade-offs are likely to occur. An example of such a structure is the cranium, as it can be used for multiple activities such as defensive and sexual behaviour, locomotion, prey capture, and ingestion. Morphological characteristics have historically been used in the description of species. Genetic analyses have gained popularity as species delineation techniques and have been particularly useful in identifying cryptic species, especially among morphological conserved species like legless skinks of the subfamily Acontinae (e.g. Acontias Cuvier, 1817 and Typhlosaurus Weigmann, 1834). However, completely doing away with morphological techniques during species descriptions is not the best option. Therefore, novel methods to identify species, especially those with similar body plans, are needed. In this dissertation, we explore the links between head shape and vertebral number to environmental pressures to determine whether the evolutionary process is driven by environmental pressures (soil or biome) or is retained through ancestry. A novel species/clade delineation linked to vertebral number is also investigated. Head shape was expected to have a close link to the environment and the number of vertebrae was expected to have a closer link to ancestry. The first chapter investigates the drivers behind Acontias head shape evolution using geometric morphometric techniques. We found that environmental pressures did affect the evolution of head shape especially in the “soil” and “biome” categories but further investigation is advised. The second chapter explores the viability of using vertebral counts as a novel method for species and/or clade delineation in Acontias and to determine whether vertebral number can be linked to the environment. Delineating species based on vertebral count is likely not an option, however, delineating clades proved to show promising results. A link between vertebral count and environment was found in Acontias with larger bodied species occurring in different environments to smaller body species. In conclusion, the genus Acontias is difficult to delineate morphologically. Genetic sequence analyses can indicate differences and delineate the species. Even though there were differences in morphology based on environmental factors, it is not sufficient to delineate this subfamily alone. Further research is advised and this dissertation provides a good basis to work with. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2021
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- Date Issued: 2021-10
Phylogeography and reproductive isolation of the brown mussel, Perna perna, on the South African coastline
- Authors: Barker, Cassandra
- Date: 2021-10
- Subjects: Mexilhao mussel South Africa , Phylogeography South Africa , Mexilhao mussel Reproduction , Mexilhao mussel Genetics , Intertidal organisms South Africa , Mexilhao mussel Climatic factors South Africa , Cytochrome oxidase , Mitochondrial DNA , Haplotype network
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10962/190041 , vital:44958
- Description: Maintenance of a species’ abundance and adaptive potential is partially dependent on its genetic diversity. Distinct genetic lineages within a species can differ significantly in their resistance and resilience to environmental pressure. An assessment of such differences is key to grasp the adaptive potential of a species. Physical environmental conditions are significant determinants of the distribution of species and their genetic lineages. Under climate change scenarios, the assessment of the temporal stability of the spatial distribution of genetic structure has important consequences for conservation as it offers key insights into the adaptive potential and evolutionary capacity of a species. This thesis investigated the phylogeography and reproductive isolation of Perna perna, the brown mussel. This species is an ecologically and economically important intertidal mussel on South Africa’s coastline. It was determined in 2007 that there were two distinct genetic lineages of P. perna present on South Africa’s coastline, the Eastern and Western lineage. This thesis compared mitochondrial DNA between samples collected in 2007 and samples collected in 2019 to determine differences in genetic structure of P. perna over time. This thesis further investigated the reproductive timing of the two lineages to determine if this contributes to the maintenance of the genetic structure of this species. The results show that there is a shift in the distribution of the Eastern lineage since 2007, an increase in the range of the overlap region, and there was a change in genetic diversity in the form of private haplotypes between 2007 and 2019. The lineages have unsynchronised spawning and reproductive patterns are more closely linked to changes in temperature. While the lineages have shown slight distributional changes over time, the influence of environmental conditions and the predicted changes in sea surface temperatures could see a change in future populations’ fitness and dispersal. Thus, changes in sea surface temperature could affect reproductive timing and the future genetic stability of the species. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2021
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- Date Issued: 2021-10
A genetic analysis of the species and intraspecific lineages of Dactylopius Costa (Hemiptera: Dactylopiidae)
- Authors: Van Steenderen, Clarke Julian Mignon
- Date: 2020
- Subjects: Dactylopius
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/151491 , vital:39135
- Description: The Cactaceae family comprises 15 genera and nearly 2000 species. With one exception, these are all native to the Americas. Numerous cactaceous species are invasive in other parts of the world, resulting in considerable damage to ecosystem functioning and agricultural practices. The most successful biological control agents used to combat invasive Cactaceae belong to the Dactylopius genus (Hemiptera: Dactylopiidae), comprising eleven species. The Dactylopiidae are exclusively cactophagous and are usually host-specific. Some intraspecific lineages of dactylopiids, often referred to as `biotypes', also display host-specificity, and are used to control particular species of invasive Cactaceae. To date, two lineages within Dactylopius opuntiae (`ficus' and `stricta'), and two within D. tomentosus (`cholla' and `imbricata') have been released in South Africa to control Opuntia ficus-indica and O. stricta, and Cylindropuntia fulgida and C. imbricata, respectively. The `californica var. parkeri' lineage is currently under consideration for release in South Africa for the control of C. pallida. Australia has already released these five lineages, and approved the release of an additional three in 2017; namely D. tomentosus `bigelovii', `cylindropuntia sp.', and `acanthocarpa x echinocarpa'. Many of the Dactylopius species are so morphologically similar, and in the case of lineages, identical, that numerous misidentifications have been made in the past. These errors have had serious implications, such as failed attempts at the biological control of cactus weeds. This thesis aimed to generate a multi-locus genetic database to enable the identification of the species and lineages in the Dactylopiidae family, and to test its accuracy. Seven species were included in the analysis, including two lineages within D. opuntiae and six within D. tomentosus. Genetic characterisation was achieved through the DNA sequencing of three gene regions; namely mitochondrial 12S rRNA and cytochrome c oxidase I (COI), nuclear 18S rRNA, and fragment analysis using two inter-simple sequence repeats (ISSRs). Nucleotide sequences were very effective for species-level identification, where the 12S, 18S, and COI regions showed 100%, 94.59%, and 100% identification accuracy rates, respectively. Additionally, the 12S and COI markers distinguished between half of the D. tomentosus lineages (`californica', `cholla', and `imbricata'), with identification accuracies of 100%. The `echinocarpa x acanthocarpa', `bigelovii', and `cylindropuntia sp.' lineages formed one clade. None of the DNA genetic markers showed a separation between the `ficus' and `stricta' lineages within D. opuntiae. Fragment analysis through the use of ISSRs provided higher-resolution results, and addressed this gap by showing a well-supported separation between the two lineages, and between wild populations collected in the Eastern Cape Province in South Africa. The identification accuracy of the `ficus' and `stricta' lineages was 81.82%. This is the first time that a method has been developed that can distinguish between these lineages. An additional component of this thesis was the creation of three user-friendly R-based programs to assist with: 1. ISSR data processing. 2. The identification of query Dactylopius nucleotide sequences relative to the gene databases created here. 3. A graphical user interface (GUI) version of the R package `SPIDER', which is useful for the assessment of the accuracy of genetic barcode data. A successful biological control programme relies on the correct identification of the agent in question, and so it is imperative that cactus biological control practitioners are able to distinguish between Dactylopius species and lineages in order to release the most effective ones onto target Cactaceae. The laboratory protocols reported, and data processing tools created here, have largely addressed this need and offer valuable practical applications. These include: 1. The flagging of potential new species, cryptic species, and lineages of dactylopiid species released as new biocontrol agents. 2. Validating the identifications made by taxonomists based on morphology. 3. Confirming to which species, and, where applicable, to which lineage, a field-collected sample belongs. 4. Identifying hybrids resulting from lineage crosses. Ensuring that the correct Dactylopius species are utilised for biological control will improve the control of invasive Cactaceae and protect biodiversity and agricultural productivity.
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- Date Issued: 2020