Conservation assessment of threatened frogs in KwaZulu–Natal and a national assessment of chytrid infection in threatened South African species
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. 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.