Biodiversity patterns and conservation of the coastal forests of Eastern Africa

The earth is in the midst of a sixth major extinction crisis with biodiversity highly threatened by climate change at global scales. Biodiversity is crucial to humans due to the ecosystem functioning and services it provides, and therefore the conservation of biodiversity is paramount to human prosperity in in the future. This PhD thesis uses amphibians to examine biodiversity patterns across the Coastal Forests of Eastern Africa (CFEA), a global biodiversity hotspot. The CFEA comprises of a network of tiny fragmented forest patches thought to be the remnants of a once widespread tropical forest that spanned across tropical Africa from West to East prior to major tectonic activity in the Miocene. The gradual aridification of the African continent since then, combined with significant climate and sea level oscillations during the Pliocene and Pleistocene contributed to the natural fragmentation of the CFEA, but human impacts have severely accelerated the pace of forest loss. The work in this thesis integrates field work, taxonomy, morphology, molecular techniques and spatial data to measure biodiversity across the CFEA, explain its distribution and provide a conceptual framework in which this data can be usefully applied for future conservation efforts. A broad scale DNA barcoding project forms the basis of all work in the thesis, assimilating museum specimens and archived spatial records with newly collected data from recent fieldwork to create the most thorough inventory of the CFEA amphibians currently known. Chapter 1 focuses on the use of Next Generation Sequencing (NGS) data for five widespread species clades to estimate phylogeny and population structure, genetic distances between populations, and explain these patterns using long-term environmental data. Chapter 2 maps the spatial distribution of evolutionary history measured from phylogenetic branch lengths for multiple intraspecific lineages within species, highlighting places which appear to be refugia and examining their environmental correlates and conservation. Chapter 3 uses close to the full assemblage of Tanzania and Kenya (55 species) to categorize the types of endemism present, distinguishing areas that are ‘museums’ supporting ancient diversity (paleo-endemism) from ‘cradles’ that support recently evolved diversity (neo-endemism). Chapter 4 combines morphological, genetic and spatial data to describe a new endemic species of treefrog, Hyperolius ruvuensis, from a highly threatened reserve in coastal Tanzania. A synthesis chapter summarises the work in the thesis and outlines new directions for CFEA conservation.