Biodiversity Patterns and Conservation of the Coastal Forests of Eastern Africa

Biodiversity patterns and conservation of the coastal forests of Eastern Africa Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturewissenschaftlichen Fakültat der Universität Basel von Christopher David Barratt aus Großbritannien Basel, 2017 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. em. Peter Nagel (Fakultätsverantwotlicher), PD Dr. Simon P. Loader (Dissertationsleiter), Prof. Neil D. Burgess (Korreferent) Basel, 18th April 2017 Prof. Dr. Martin Spiess The Dean of Faculty Biodiversity patterns in space and time Biological diversity is distributed unevenly across the earth. Well known current biodiversity gradients such as the latitudinal (e.g. Fig. 1), altitudinal diversity gradients and the mid-domain effect have contributed significantly to our understanding of diversity patterns. However, how biodiversity has changed over time is also an important factor that can explain past and current patterns (Mannion et al., 2014). In the past decades, significant progress in our understanding of biodiversity at spatial and temporal scales have been made (Rosenzweig, 1995; Gaston & Blackburn, 2007), and how this relates to global change and conservation (Kerr et al., 2007). Endemism, and the persistence of biodiversity over time is hypothesized to be strongly influenced by long-term climatic stability and topography (Sandel et al., 2011; Harrison & Noss, 2017). Over millions of years, refugia are suspected to play a crucial role in maintaining biodiversity during times of geological and climate change (Mayr & O'Hara, 1986, Moreau, 1933, Dynesius & Jansson, 2000). The persistence of diversity over time in refugia is known to lead to areas that support unique biodiversity that has become locally extinct elsewhere. This is especially true in areas with complex topography where a species may only need to move a small distance in response to climate change compared to the large distance that a species in a flat landsape would need to move to adapt to the same climate change conditions. Recent studies using the concept of climate change velocity as a measure of long-term climate stability have shown that areas subjected to high levels of climate change are associated with a marked absence of small ranged birds, mammals and amphibians (Sandel et al., 2011), with areas that are comparatively stable identified as essential refugia for narrow-ranged species that are sensitive to habitat change. Fig. 1. Global patterns of amphibian species richness, from the Global Amphibian Assessment. Conservation of biodiversity Biodiversity is essential as it forms the foundation for all natural resources that humans need to survive and persist. Although it is an extremely broad and sometimes ambiguously used term, ‘biodiversity’ may be simply summarised as the variety of life (the variation of species, functional traits and genes). The multile facets of biodiversity provide the foundation for ecosystem functions that control the movement of energy (e.g. primary production, nutrient cycling, decomposition), and the ecosystem services they provide to humanity (e.g. direct 2 benefits such as water, food, medicine, fuel, climate regulation, disease control) (Blackburn, 2008). Soon after the 1992 Earth Summit in Rio de Janeiro, interest in understanding biodiversity loss and how it may affect ecosystem functioning and services increased dramatically. This led to a proliferation of research in these fields and the establishment of several major global initiatives such as the Global Biodiversity Assessment launched by the United Nations Environment Programme, and the biodiversity science research agenda produced by Diversitas, (now the Future Earth project within the International Council for Science). In the quarter of a century since the Rio Earth Summit, there is now unequivocal evidence that biodiversity loss is intricately linked to ecosystem functioning (Cottingham et al., 2001; Balvanera et al., 2006; Cardinale et al., 2007) and is a major driver of global change (Tilman et al., 2014). Moreover, evolutionarily diverse communities have been shown to increase ecosystem stability over time and their functioning (Cadotte et al., 2008; Cadotte, 2013). Linking biodiversity with the direct benefits provided to humans through ecosystem services have proven to be more complex (Cardinale et al., 2012; Balvanera et al., 2014), though there is now evidence of the direct correlation between biodiversity and some provisioning and regulating ecosystem services (Harrison et al. 2014). Protecting biodiversity is therefore a major concern for humanity. Biodiversity is under threat due to climate change and human induced impact, to the point that the earth has been described as being in the midst of a major sixth extinction event (Kolbert, 2014; Ceballos et al., 2015). Reducing biodiversity loss both now and in the future are urgent conservation priorities and key components of the Aichi targets for 2020 by parties to the United Nations Convention on Biological Diversity (Pereira et al., 2013), especially after the failure to meet 2010 targets. To manage biological resources effectively given predicted future human impacts and climate change we need to collectively improve our capacity to assess biodiversity, both now and in the future. Increasing knowledge of biodiversity patterns and what causes areas of rich biodiversity to form are vital steps towards prioritizing where and why we should focus future conservation efforts. Methods to measure biodiversity have typically focused at the species level, using metrics such as species richness that simply count the number of species present within a given area. The degree of endemism present may also be inferred if the known ranges of species are incorporated with this data. Species richness and endemism are the fundamental measurements of biodiversity which are currently used for conservation efforts at most scales, for example, defining the world’s biodiversity hotspots (Myers et al., 2000) or establishing protected areas. Despite the wealth of biodiversity knowledge that is now available to scientists and conservation planners, several problems remain when using traditional methods for assessing biodiversity. Knowledge about biodiversity remains insufficient because the majority of species have still not been described (the Linnean shortfall), and the distributions of most are not fully understood or have significant sampling gaps, especially at local scales (the Wallacean shortfall) (Whittaker et al., 2005). These shortfalls are a serious problem for conservation planning in poorly developed regions of the world which often support high biodiversity but lack the appropriate infrastructure to document and assess it (Bini et al., 2006). Although traditional measures have provided a solid basis for biodiversity assessment and conservation, it has become increasingly clear that species diversity alone misses out on the full patterns of biodiversity present. Biodiversity is optimally represented by the full set of nested clades representing phylogenetic relationships and genetic diversity at all levels within the tree of life, and not just species (Mishler et al., 2014). However, even if we were to describe all of the species on earth and fully account for their distributions we would still have a problem due to a lack of available phylogenetic information for most organisms (the Darwinian shortfall, Diniz-Filho et al., 2013). Therefore, the documentation of biodiversity with molecular 3 tools and techniques provides the basis for understanding the diversity within and between organisms, and is crucial to integrate the information they can provide to complement traditional measures in future biodiversity assessment and conservation, especially in highly diverse tropical regions. Molecular tools for estimating biodiversity The low cost and effort of generating sequence data has led to a proliferation of molecular based biodiversity assessment techniques for rapid biodiversity assessment. One of the most common, DNA barcoding, is a tool that uses a standardized locus of DNA (typically between 400 and 800 base pairs in length) which can be easily amplified and sequenced across a wide range of organisms, showing variability within and between species. Massive online digital libraries of sequences from known species serve as the standard to match an unknown sample, allow its identification (Moritz & Cicero, 2004; Hebert & Gregory, 2005; Lahaye et al., 2008; Nagy et al., 2012), and in vertebrates is typically the mitochondrial 16S rRNA or cytochrome oxidase subunit 1 (COI) genes (Vences et al., 2005). To gain more detailed data, extra loci such as recombinant nuclear genes may be chosen to supplement barcoding genes to increase phylogenetic signal and resolution, or fast evolving loci such as microsatellites may be used for microevolutionary processes acting at the level of populations such as allele frequency changes over time (Tautz & Schlötterer, 1994). With the advent of high throughput Next Generation Sequencing (NGS) techniques and their increasing affordability, it has now become feasible to conduct both macroevolutionary (phylogenomics) and microevolutionary (population genomics) research with unprecedented amounts of sequence data, in the order of thousands to millions of base pairs, for a relatively small cost (Lemmon & Lemmon,

Load more