A genetic analysis of the species and intraspecific lineages of Dactylopius Costa (Hemiptera: Dactylopiidae)
- Van Steenderen, Clarke Julian Mignon
- 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.
- Full Text:
- Date Issued: 2020
- 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.
- Full Text:
- Date Issued: 2020
Securing software development using developer access control
- Authors: Ongers, Grant
- Date: 2020
- Subjects: Computer software -- Development , Computers -- Access control , Computer security -- Software , Computer networks -- Security measures , Source code (Computer science) , Plug-ins (Computer programs) , Data encryption (Computer science) , Network Access Control , Data Loss Prevention , Google’s BeyondCorp , Confidentiality, Integrity and Availability (CIA) triad
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/149022 , vital:38796
- Description: This research is aimed at software development companies and highlights the unique information security concerns in the context of a non-malicious software developer’s work environment; and furthermore explores an application driven solution which focuses specifically on providing developer environments with access control for source code repositories. In order to achieve that, five goals were defined as discussed in section 1.3. The application designed to provide the developer environment with access control to source code repositories was modelled on lessons taken from the principles of Network Access Control (NAC), Data Loss Prevention (DLP), and Google’s BeyondCorp (GBC) for zero-trust end-user computing. The intention of this research is to provide software developers with maximum access to source code without compromising Confidentiality, as per the Confidentiality, Integrity and Availability (CIA) triad. Employing data gleaned from examining the characteristics of DLP, NAC, and Beyond- Corp—proof-of-concept code was developed to regulate access to the developer’s environment and source code. The system required sufficient flexibility to support the diversity of software development environments. In order to achieve this, a modular design was selected. The system comprised a client side agent and a plug-in-ready server component. The client side agent mounts and dismounts encrypted volumes containing source code. Furthermore, it provides the server with information of the client that is demanded by plug-ins. The server side service provided encryption keys to facilitate the mounting of the volumes and, through plug-ins, asked questions of the client agent to determine whether access should be granted. The solution was then tested with integration and system testing. There were plans to have it used by development teams who were then to be surveyed as to their view on the proof of concept but this proved impossible. The conclusion provides a basis by which organisations that develop software can better balance the two corners of the CIA triad most often in conflict: Confidentiality in terms of their source code against the Availability of the same to developers.
- Full Text:
- Date Issued: 2020
- Authors: Ongers, Grant
- Date: 2020
- Subjects: Computer software -- Development , Computers -- Access control , Computer security -- Software , Computer networks -- Security measures , Source code (Computer science) , Plug-ins (Computer programs) , Data encryption (Computer science) , Network Access Control , Data Loss Prevention , Google’s BeyondCorp , Confidentiality, Integrity and Availability (CIA) triad
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/149022 , vital:38796
- Description: This research is aimed at software development companies and highlights the unique information security concerns in the context of a non-malicious software developer’s work environment; and furthermore explores an application driven solution which focuses specifically on providing developer environments with access control for source code repositories. In order to achieve that, five goals were defined as discussed in section 1.3. The application designed to provide the developer environment with access control to source code repositories was modelled on lessons taken from the principles of Network Access Control (NAC), Data Loss Prevention (DLP), and Google’s BeyondCorp (GBC) for zero-trust end-user computing. The intention of this research is to provide software developers with maximum access to source code without compromising Confidentiality, as per the Confidentiality, Integrity and Availability (CIA) triad. Employing data gleaned from examining the characteristics of DLP, NAC, and Beyond- Corp—proof-of-concept code was developed to regulate access to the developer’s environment and source code. The system required sufficient flexibility to support the diversity of software development environments. In order to achieve this, a modular design was selected. The system comprised a client side agent and a plug-in-ready server component. The client side agent mounts and dismounts encrypted volumes containing source code. Furthermore, it provides the server with information of the client that is demanded by plug-ins. The server side service provided encryption keys to facilitate the mounting of the volumes and, through plug-ins, asked questions of the client agent to determine whether access should be granted. The solution was then tested with integration and system testing. There were plans to have it used by development teams who were then to be surveyed as to their view on the proof of concept but this proved impossible. The conclusion provides a basis by which organisations that develop software can better balance the two corners of the CIA triad most often in conflict: Confidentiality in terms of their source code against the Availability of the same to developers.
- Full Text:
- Date Issued: 2020
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