At the crossroads of two biodiversity hotspots; the biogeographic patterns of Shimba Hills, Kenya Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Beryl Akoth Bwong von Kenia Basel, 2017 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. em. Dr. Peter Nagel (Fakultätsverantwortlicher) PD. Dr. Simon P. Loader (Dissertationsleiter) PD. Dr. Stefan Lötters (Korreferent) Basel, den 20. Juni 2017 Prof. Dr. Martin Spiess (Dekan) ii TABLE OF CONTENTS Introduction 1 Biogeography 2 Amphibians as exemplar taxa for understanding phylogeographic history of an area 4 The Shimba Hills 4 Objective 6 Chapter overview 6 Additional outputs 8 Refferences 9 Chapter 1 15 Amphibian diversity in Shimba Hills National Reserve, Kenya: A comprehensive list of specimens and species Chapter 2 43 Genetic, morphological and ecological variation in the congeners Hyperolius mitchelli Loveridge, 1953 and Hyperolius rubrovermiculatus Schiøtz, 1975 from East Africa. Chapter 3 98 Three new species of Callulina (Amphibia: Anura: Brevicipitidae) from East Africa with conservation and biogeographical considerations for the whole genus. Chapter 4 122 Phylogeography of amphibians of Shimba Hills, Kenya. Synthesis 186 iii Acknowledgements 194 Supplementary Materials 197 Chapter 1 198 Chapter 2 212 Chapter 4 218 iv Introduction 1 Biogeography Until Wallace’s pivotal contribution in 1876, our understanding of animal and plant species distribution was generally based on non-scientific principals. With Wallace (1876), the distribution of organisms could be understood from a historical perspective and this contribution heralded the birth of the science of biogeography. Since its original conception, biogeography has broadened its understanding from a purely historical science to incorporate current determinants of the patterns of species distribution. Biogeography seeks to answer the questions of why species are distributed where they are or put simply, why some areas have more species than others. Patterns of diversity distributions are determined by a number of factors, both current as well as historical. For example, environmental and geological history of an area (Crowe & Crowe, 1982; Fjeldsaå & Lovett, 1997; Ricklef, 2003; Dornelas, et al., 2006; Dimitrov et al., 2012), individual species ecology and physiology determines the ranges and abundance of species in an area (Duellman & Trueb, 1986; Hamilton, 1982; Hugget, 2004). Understanding patterns of species diversity also include taking into consideration dispersal ability and adaptability of species to past changes in the environment and how this influences the distribution of species through time (Farrel et al., 1992; Latham & Ricklefs, 1993). Therefore, historical and ecological processes both contribute to our understanding of biogeographic patterns. The biogeographic field that focuses on historical causes of biodiversity patterns is known as historical biogeography. It is concerned with evolutionary processes spanning millions of years back in time. More recent historical determinants of biodiversity patterns at the intra-specific level can also be investigated, and this is called phylogeography (Avise et al., 1987). Phylogeography is a branch of historical biogeography that deals with the analysis of the relationship between population genetic structure and geography (see also Avise, 2000; Arbogast & Kenagey, 2001; Avise, 2004). Phylogeographic studies aim to characterise the roles played by recent environmental and historical factors that shaped the present diversity patterns (Zink, 2002; Lomolino et al., 2004). Such studies employ the use of molecular markers to examine both recent and deeper phylogeographic history of a species or an area (Avise, 1987, Avise, 2000; Zink, 2007). Phylogeographic studies were previously based on mitochondrial molecular markers as these genes are rapidly evolving and hence suitable for examining events in the recent past (Avise, 1987). However latest advances in the discipline of molecular biology has seen a rise in the use of other markers, from partial sequences such as chloroplast from plants and nuclear genes which are slow evolving and better suited for deeper phylogeographic history (Janzen et al., 2002), to genome wide comparisons (Davey & Blaxter, 2010; Macher et al., 2015). Phylogeographic studies may be conducted on single wide ranging species to understand how genetic diversity is 2 distributed within its range (Zink, 2000) while the study of genetic diversity of several wide ranged co- occurring species constitute comparative phylogeography (Bermingham & Moritz, 1998). Comparative phylogeography investigates if members of a community have responded in concert to historical biogeographic factors and therefore if present genetic patterns can be explained by particular geographic processes (Zink, 1996; Avise, 2004). Further, the availability of information on the evolution rates of various molecular markers has made it even possible to estimate dates of population separations, thus through comparative phylogeography, it is possible to reconstruct the recent biogeographic history of an area (Bermingham & Moritz, 1998). For a long time phylogeography has been the main method through which genetic patterns within species has been investigated. However advancements in other related fields such as bioinformatics and molecular biology has seen the incorporation of other tools such as spatial data in phylogeographic analysis. The advancements in the field of Geographical Information System (GIS) for example have seen the incorporation of spatial information in various fields of studies where previously this was not possible. One such area is the application of Species Distribution Modelling (SDM) in phylogeographic interpretations (Carstens & Richards, 2006; Chan, et al., 2011). Species distribution models also known as bioclimatic models, estimate potential species distributions by deriving environmental envelopes from distributions and projecting into an interpolated potential climate of an area (Pearson, 2007; Waltari & Guralnick, 2009). These models are based on the assumption that the ecological niche of a species determines its distribution (Nogués-Bravo, 2009). Species distribution models are produced by combining current environmental parameters and known occurrence data of a species fitted to a model to predict current distributions (Hugall, et al., 2002; Elith & Leathwick, 2009). When projected to past climates, SDM can also be used to generate potential suitable habitats in past climatic conditions, i.e., the paleo- distributions of species (Hugall, et al., 2002; Carstens & Richards, 2007). Paleo-distribution modelling have proved useful as alternative ways of establishing historical factors determining the current genetic structuring in species (Elith & Leathwick, 2009). This is true especially in taxa that lack good fossil representation like amphibians. Paleo-distribution modelling has been used extensively to provide a priori hypotheses or validate results from phylogeographic analysis. Paleo-distribution models shed light on the effects of past climatic conditions on the current patterns of species distribution therefore providing independent means to understand the current phylogeographic patterns of a species or an area (see Carstens & Richards, 2007; Waltari et al., 2007; Buckley et al., 2010; Ahmadzadeh et al., 2013). In addition, for studies involving co-distributed species, concordance in phylogeographic structures are often 3 interpreted to mean a concerted response to a similar vicariance events with the assumption that the species must have also been co-distributed in the past and therefore SDM provides ways to test such assumptions (Guissan & Thuiller, 2005; Miller, 2010). Amphibians as exemplar taxa for understanding phylogeographic history Amphibians are favourable candidates for phylogoegraphic studies because of a number of physiological and ecological reasons. They are less vagile and have high affinity/philopatry to their breeding sites leading to populations with highly structured genetics over short geographical distances (Avise, 2004; Zeisset & Beebee, 2008). Amphibians are sensitive to small changes in the climate which may be attributed to divergence within some species (Graham et al., 2004; Buckley & Jets, 2007) and have diverse physiological adaptations (Duellman & Trueb, 1986) that enable them to respond idiosyncratically to environmental and geologic processes. Additionally amphibians are relatively common and easily sampled in breeding sites during the wet periods (Duellman & Trueb, 1986). Moreover amphibian phylogeography has been demonstrated as suitable for understanding historical aspects of species distribution (Zeisset & Beebee, 2008). Specifically for this study amphibians were selected due to the presence of wide spread species in our study site and adjacent areas which are important in establishing the historical genetic exchange among the sites or areas. In addition the apparently mixed assemblages of amphibians recently reported in Shimba Hills of Kenya-SHK (Bwong et al., in press) make them good model taxon for understanding the biogeographic history of Shimba Hills. The Shimba Hills The Shimba Hills of Kenya (here after SHK) is geographically located at the cross roads of two major