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Govender Ashrenee 2017.Pdf (1.676Mb) Testing the utility of DNA barcoding in South African Hemiptera: Using eThekwini species as a case study By Ashrenee Govender BSc. (Hons) Genetics Submitted in fulfillment of the academic requirements for the degree of Master of Science in the Discipline of Genetics School of Life Sciences College of Agriculture, Engineering, and Science University of KwaZulu-Natal Pietermaritzburg South Africa As the candidate’s supervisor(s) I, have approved this dissertation for submission. Supervisor: Dr S. Willows-Munro Supervisor: Prof M. Rouget Signature: Signature: Date: 16 January 2017 Date: 16 January 2017 Preface The research contained in this dissertation was completed by the candidate while based in the discipline of Genetics, School of Life Sciences of the College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa under the supervision of Dr S. Willows-Munro and Prof M. Rouget. These studies represent original work by the candidate and have not otherwise been submitted in any form to another University. Where use has been made of the work by other authors it has been duly acknowledged in the text. Supervisor: Dr S. Willows-Munro Supervisor: Prof M. Rouget Signature: Signature: Date: 16 January 2017 Date: 16 January 2017 ii College of Agriculture, Engineering, and Science Declaration of Plagiarism I, Ashrenee Govender, declare that: (i) the research reported in this dissertation, except where otherwise indicated or acknowledged, is my original work; (ii) this dissertation has not been submitted in full or in part for any degree or examination to any other university; (iii) this dissertation does not contain other persons’ data, pictures, graphs or other information, unless specifically acknowledged as being sourced from other persons; (iv) this dissertation does not contain other persons’ writing, unless specifically acknowledged as being sourced from other researchers. Where other written sources have been quoted, then: a) their words have been re-written but the general information attributed to them has been referenced; b) where their exact words have been used, their writing has been placed inside quotation marks, and referenced; (v) where I have used material for which publications followed, I have indicated in detail my role in the work; (vi) this dissertation is primarily a collection of material, prepared by myself, published as journal articles or presented as a poster and oral presentations at conferences. In some cases, additional material has been included; (vii) this dissertation does not contain text, graphics or tables copied and pasted from the Internet, unless specifically acknowledged, and the source being detailed in the dissertation and in the References sections. ___________________________________ Signature: Ashrenee Govender Date: 16 January 2016 Declaration Plagiarism 22/05/08 FHDR Approved iii Abstract The eThekwini municipal region and surrounding areas (Durban, Kwazulu-Natal, South Africa) are situated within the globally important Maputaland-Pondoland-Albany biodiversity hotspot. The biodiversity present in this region is under significant pressure from urbanization and climate change. This highlights the need to provide tools that can assist in the discovery and identification of species at an accelerated pace, to create biodiversity inventories which can be used for appropriate conservation planning. The creation of species inventories is a difficult task, more especially for hyper-diverse groups such as terrestrial arthropods. These groups can be morphologically cryptic or difficult to identify using traditional morphology-based taxonomy. Therefore, molecular-based methods of species identification have been proposed to assist in traditional taxonomy. DNA barcoding has been suggested as a mechanism which enables biologists to “label” or “tag” species, using nucleotide variations in short sequences known as DNA barcodes. This study investigates the utility of DNA barcoding and the use of the mitochondrial cytochrome oxidase c subunit 1 (COI) marker to identify species of Hemiptera efficiently and accurately. This study presents a preliminary DNA barcode reference library for Hemiptera collected from 18 different localities within and around the eThekwini municipal region. To test the success of DNA barcoding and the COI marker, matches between morphospecies and barcode clusters (BINs) were analyzed and the presence of the DNA barcode gap in the data was examined. The DNA barcode gap is the gap between the intraspecific and interspecific genetic distances, the lack of the DNA barcode gap suggests that taxa cannot be reliably sorted into species based on the genetic data. Analyses revealed that DNA barcoding using the COI marker is a successful method of identifying Hemiptera species in this study. Thereafter, a case study was selected within the Buffelsdraai Landfill Site Community Reforestation Project, to test whether DNA barcoding could be used to assess the potential of Hemiptera as an indicator of ecological restoration success. The Hemiptera species composition and assembly were assessed by analyzing multiple diversity indices, ordination, UPGMA cluster analysis and phylogenetic analysis. Hemiptera was seen to be sensitive to changes in an ecosystem which make this order an effective environmental and biological indicator. With the help of DNA barcoding, specific families of Hemiptera were identified as habitat-specific and good biological indicators for future studies of ecological restoration and reforestation. iv Acknowledgments I would like to express my heartfelt gratitude to the following people and organizations for their support: My supervisor, Dr Sandi Willows-Munro, for all your guidance, patience, constant support and for being my critical reader. I am truly grateful for all your help and encouragement throughout the years. Thank you for allowing me to grow and improve greatly as a scientist. My co-supervisor, Prof Mathieu Rouget, for all your valuable input, and guidance. Thank you for providing me with funding and for allowing me an opportunity of a life time to attend my first international conference in Morocco. I am truly grateful for all your support. The National Research Foundation (NRF), Durban Action Research Partnership (D’RAP), and Wildlands Conservation Trust for their financial support throughout the years. Thank you to the former and present members of the conservation genetics laboratory- Courtnee’, Sihle, Andrinajoro, Riel, Thina, Bright, Jimmy, Jade, Sophia, Isabella, Ian, Melanie and Martyn. Each one of you made the laboratory a better place, with a whole lot of laughter and fun times. My best friends – Nolyn, thank you for all the love, patience, support and for always believing in me. Courtnee’, thank you for all the craziness, laughter and motivation. Phylicia, even though you are so far away, thank you for always being there for me. Each one of you has played a vital role in my life and I truly love and appreciate you all. To my amazing parents, Anand and Kubashni, thank you for providing the greatest opportunity for me to pursue my dreams. You both, together with my sibling, Melashen, have given me so much of love and support not only through my studies but throughout the years of me growing up. Thank you for always being my pillars of strength and for always believing in me. I love all three of you with all my heart. v List of conferences and symposia 2015 1) SAEON GFW Drakensberg Global Change Monitoring Platform: Mini Symposium (October 2015) – Title: The Utility of DNA Barcoding in South African Hemiptera: Using eThekwini as a Case Study. 2) Symposium of Contemporary Conservation Practice (November 2015) - Title: The Utility of DNA Barcoding in South African Hemiptera: Using eThekwini as a Case Study – Prize won: (KZN Premier's Student Award) - 2nd Prize for the best student presentation. 3) Durban Action Research Partnership (D’RAP) Year-end Symposium (December 2015) - Title: The Utility of DNA Barcoding in South African Hemiptera: Using eThekwini as a Case Study – Prize won: 2nd Prize for the best student project presentation in the Community Reforestation Research Programme. 2016 4) Joint SAAB/SASSB Conference 2016 (January 2016) – Title: The Utility of DNA Barcoding in South African Hemiptera: Using eThekwini as a Case Study - Prize won: 2nd Prize for the best oral presentation by an MSc student. 5) UKZN SLS Research Day (May 2016) - Title: The Utility of DNA Barcoding in South African Hemiptera: Using eThekwini as a Case Study - Prize won: 1st Prize for the best oral presentation in the venue. 6) 3rd African Congress of Conservation Biology – Morocco (September 2016) - Title: The Utility of DNA Barcoding in South African Hemiptera: Using eThekwini as a Case Study. 7) Durban Action Research Partnership (D’RAP) Year-end Symposium (December 2016) - Title: The Utility of DNA Barcoding in South African Hemiptera: Using eThekwini as a Case Study. vi Table of Contents Preface …………………………………………………………………………………………….ii Declaration of Plagiarism ………………………………………………………………………...iii Abstract …………………………………………………………………………………………..iv Acknowledgments ………………………………..……………………………………………….v List of conferences and symposia ……………………………………………………………......vi List of Figures …………………………………………………………………………………... xii List of Tables ……………………………………………………………………………………xiv Chapter One: Literature review ……………………………………………….………………....1 1.1 Urbanization and biodiversity …………………………………………………………………1 1.1.1 Importance of species identification
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