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Tarrant J.Pdf It seems to me that if you wait until the frogs and toads have croaked their last to take some action, you’ve missed the point. Kermit the Frog dedication This thesis is dedicated to my son, Adam, and his generation, that they may know the splendour of our natural heritage as we have. ACKNOWLEDGEMENTS A project of this scope requires the input of numerous people, institutions and organisations. I am indebted to the following: My supervisors, Prof. Louis du Preez and Dr. Ché Weldon, who first inspired me six years ago with their enthusiasm for all things “frog”, and kindly invited me to continue my studies with the African Amphibian Conservation Research Group. Both have trusted me to be able to get on with this work whilst being based six hours away from campus. Thanks also to the secretaries of the “padda groep”, Carina de Beer and Leana Mostert who facilitated accommodation bookings for my trips to Potchefstroom as well as countless other admin- related necessities. To all my fellows in “die Padda Groep”; I have thoroughly enjoyed my trips to Potch, your trips to KZN and our adventures everywhere in-between in the paddawa; thanks for all you help and encouragement along the way. I am hugely indebted to Dr. Adrian Armstrong of Ezemvelo KZN Wildlife. Many aspects of this research would not have been possible without his help. He has been extremely generous with his time, not only for fieldwork throughout KwaZulu-Natal, but for many hours spent behind the computer screen working on predictive modelling for KwaZulu-Natal‟s threatened frog species. I have been lucky to travel to many parts of our beautiful country for fieldwork. Looking for rare and threatened species can be frustrating, tiring and thankless, but also highly rewarding when the right species finally turns up! Many people have assisted with fieldwork, most notably Adrian Armstrong, Ryan Bowman, Leon Meyer, Donnavan Kruger, James Harvey, Atherton de Villiers and my husband, Greg Tarrant. The following also assisted me in the field on various occasions: Gavin Baxter, Simon Berkeljon, Werner Conradie, Michael Cunningham, Sam Davidson-Phillips, Lizzie Gaisford, Gen James, John Measey, Les Minter, Dan Parker, Tyrone Ping and Andrew Turner. Analysis of skin swabs was conducted at the NRF Research Department, National Zoological Gardens, Pretoria. Many thanks to Dr. Desiré Dalton, Anri van Wyk and Prof. Anntoinette Kotze for facilitating this and conducting the necessary lab work. As this project covered sites across South Africa I am grateful to the following for a bed (and food) when needed: Grant and Claire Forrester (Cape Town, numerous occasions), Kate and Kerr Rogers (Cape Town 2009), Les and Jean Minter (both Polokwane and Barrydale 2008), Kirsten Wimberger and Steve Boyes (Hogsback, also for help in the field on numerous occasions), Adrian Armstrong (Hilton), my parents (Underberg) and in-laws (East London). iii For help with phylogenetic labwork and analysis I am indebted to Mathieu Badets, Leon Meyer and Donnavan Kruger and to the Microbiology Department at Potchefstroom for the use of their lab. Mathieu, in particular, dedicated much time to this. Audrey Ndaba, KwaZulu-Natal Museum (Pietermartizburg) and Gill Watson, Bayworld (Port Elizabeth), are thanked for their help in facilitating loans of museum specimens. Many people, including Adrian Armstrong, Mike Berjak, Werner Conradie, Michael Cunningham, Les Minter, Martin Pickersgill, Lynn Raw and Miguel Vences have provided advice and assistance with regard to various aspects of the project and this document. Dan Parker is thanked for his invaluable commentary on this manuscript, as well as for help with statistical analysis. When the time came for writing and peace I am grateful to Gavin Baxter for providing a tranquil haven (his home) for me to write in initially and then to Bridget Spangehl and all at “Speckled Frogs Daycare” for taking a rambunctious toddler off my hands! To all the schools, groups and societies who have invited me to talk to them about the plight of frogs – I can only hope that I have created some awareness and encouraged frog conservation on a personal level. To my husband and family who have encouraged me every step of the way (although who I am sure are pleased it is all over finally!). I will be forever grateful to Greg for his tremendous support over the years in allowing me to pursue my career in zoology. More recently, he has been an enormous help with our young son, Adam, allowing me to get out into the field and have some peaceful weekends to write. The Green Trust (WWF) has provided the majority of funding for this project. Thanks go to them, and specifically Thérèse Brinkcate, Cindy Mathys, Cynthia Smith and more recently, Augustine Morkel, for their ongoing support and interest in the project. The National Research Foundation also provided funding toward student bursaries. Research permits were provided by Ezemvelo KZN Wildlife (Permit Nos. 4485/2008, 4137/2008, OP 1180/2010 and 5080/2011); iSimangaliso Wetland Park Authority; SANParks (Table Mountain National Park, Agulhas National Park, Namaqua National Park), Cape Nature for the Western Cape Province (Permit No. AAA006-00022-0035) and Eastern Cape Parks & Tourism Agency (Permit No. RA 0109). Each are thanked for allowing access to a number of their reserves. Many private land-owners also granted access to their properties including ACSA, Mondi, Tongaat-Hulett and numerous farmers including Tom Turner of Kingussie Farm, Fort Nottingham and Ryan de Matthuis of Nonoti Sugar Estate. iv DECLARATION I declare that this thesis is my own work unless specifically acknowledges in the text. It has not been submitted before for any degree or examination in any other university. 2nd day of May 2012 v THESIS SUMMARY Amphibians are the most threatened Class of vertebrate on Earth, with 30% of all species IUCN Red Listed. This proportion is reflected in South Africa, where 29% of all species assessed in 2011 (SA-FRoG 2010; IUCN 2011; Measey 2011) fall into the threatened categories of Critically Endangered (7%), Endangered (12%) or Vulnerable (10%). This study is focussed on these species, with a particular emphasis on those that occur in the KwaZulu-Natal Province. The thesis is structured as follows: CHAPTER 1 gives a broad introduction to the global situation with regard to amphibian declines and the threats causing them as based on the literature. Additional information pertinent to successive chapters is given, including descriptions of KwaZulu-Natal‟s threatened frogs, detail on the disease chytridiomycosis and its causal agent, Batrachochytrium dendrobatidis (Bd), and the importance of the application of systematics for conservation. CHAPTER 2 provides baseline information on a national scale regarding the occurrence and prevalence of infection with Bd in South Africa‟s threatened frogs. This pathogen causes the disease chytridiomycosis and is responsible for amphibian declines globally. Samples were collected by means of skin swabs and analysed using quantitative PCR. Prevalence varied widely between threatened species (Avg. = 14.8%), with infection intensity being predominantly influenced by life history characteristics. The study also provides, for the first time, a distribution model for B. dendrobatidis occurrence in South Africa, indicating regions that are likely to harbour the pathogen. Such information is useful for application in disease prevention and control plans. CHAPTER 3 provides threat assessments for certain of the threatened species in KwaZulu-Natal, focussing on two sites per species, and makes recommendations on additional research requirements and appropriate conservation actions for these species. Particular emphasis is placed on Hyperolius pickersgilli, the province‟s only Critically Endangered species. vi CHAPTER 4 is focussed on the distribution of Hyperolius pickersgilli. Ecological niche modelling using Maxent was employed to predict the distribution of this species, and high probability areas were surveyed over two breeding seasons. Known historical sites were also re-visited and assessed for species presence. As a result of surveying, 5 new localities for the species were revealed, but half of the historical sites have been transformed to such an extent that the species no longer occurs there. In total, the species currently occurs at 17 localities, the majority of which are highly fragmented and threatened by human activity. The results of the survey were used to recalculate the area of occupancy (AOO) and extent of occurrence (EOO) for H. pickersgilli. Based on these findings, and the level of threat at the majority of sites and degree of fragmentation between them, the Critically Endangered status of this species remains warranted. CHAPTER 5 reviews the systematics of the Afrixalus spinifrons complex using morphological, call and molecular analysis. Although the first two methods have been used historically to delimit boundaries for taxa within this complex, genetic analysis has not been previously conducted. This study makes use of DNA sequencing from mitochondrial and nuclear gene markers to elucidate phylogenetic relationships within the complex. The results confirm that A. knysnae is part of the A. spinifrons clade, but is a separate species. Afrixalus spinifrons spinifrons and A. s. intermedius form distinct clusters, but are closely related confirming that the subspecies diagnosis as a representation of evolutionary divergence is accurate. The study does however differ from previous conclusions in that populations from the Eastern Cape group with A. s. intermedius from the KwaZulu-Natal midlands as opposed to A. s. spinifrons from the coast. Although these findings do not warrant designation of the subspecies to full species, they should be treated as evolutionary significant units for the purposes of conservation. vii OPSOMMING Met 30% van alle amfibieërspesies op die IUCN Rooilys word die Amfibia as die mees bedreigde Klas van die gewerwelde diere op aarde beskou. Hierdie syfers word weerspieël in Suid-Afrika, waar 29% van die spesies as bedreig geklasifiseer word.
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