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Bats are implicated in the emergence of many zoonotic diseases, including the coronaviruses (CoVs) responsible for deadly outbreaks of severe acute respiratory syndrome (SARS) in 2002-2003, and Middle East respiratory syndrome (MERS) which first emerged in 2012. Despite an increased interest in bat CoVs since the SARS epidemic, little research has examined bat CoVs from a disease ecology perspective. In this thesis, I investigated the epidemiology and ecology of CoVs and bats that host them in Ghana, West Africa. I captured bats at several colonies regularly over two years. Samples were screened for CoVs, which were found to be widespread in insectivorous cave-dwelling bats of the genera Hipposideros and Nycteris. A novel CoV related to MERS-CoV was detected at high prevalence in slit-faced bats, Nycteris cf. gambiensis, supporting suggestions of a bat origin of MERS-CoV. I examined population and individual-level risk factors for infection with four CoVs in Nycteris cf. gambiensis, Hipposideros abae, and H. cf. ruber. I found a strong seasonal effect on CoV infection rates, and a strong association with age, whereby juvenile bats are at greater risk of infection, as well as evidence for higher risk with low body condition. These findings provide new insights into the ecological, demographic and temporal processes that influence CoV infection dynamics in bats, with implications for public health management to prevent virus spillover to humans and domestic animals. In the second half of my thesis, I examined the evolution of cryptic species, and genetic and acoustic diversity in CoV-hosts Hipposideros caffer and H. ruber. Using mitochondrial DNA and microsatellite loci, and acoustic and morphological data, I showed that mitochondrial DNA clades represent distinct species, with no evidence of interbreeding between groups. I then used mitochondrial sequence data to date lineage divergence, and explore the historical and evolutionary processes that may have given rise to diversity in these taxa. Further, I characterised spatial patterns of intraspecific genetic diversity in the three species corresponding to H. cf. ruber (H. sp. B, C, and D). Comparison shows stark contrasts in the spatial patterns of genetic variation of these species, despite them having diverged relatively recently and apparently having highly similar ecological and natural history traits. I discuss the implications of these results for disease surveillance and spread, wildlife management, and the evolutionary processes that generate and maintain diversity.The findings of this thesis add to knowledge of bat CoV ecology and epidemiology, aswell as to the evolution and patterns of diversity within a relatively widespread, but understudied,group of Afrotropical bats that are natural CoV hosts. The results are discussed in the context ofzoonoses, wildlife management and disease prevention, and the evolution of cryptic species inbats. The findings of this thesis add to knowledge of bat CoV ecology and epidemiology, as well as to the evolution and patterns of diversity within a relatively widespread, but understudied, group of Afrotropical bats that are natural CoV hosts. The results are discussed in the context of zoonoses, wildlife management and disease prevention, and the evolution of cryptic species in bats. I discuss the implications of these results for

We investigated bats of the Hipposideros caffer complex from Ghana in order to resolve their cryptic diversity. We confirmed presence of four previously established mtDNA lineages and demonstrated significant divergence among them based on nuclear microsatellites, frequency distribution of echolocation calls, and external morphometry. We showed that H. caffer complex in West Africa consists of at least four distinct species and highlighted the potential presence of further cryptic species. Levels of biodiversity are globally underestimated, especially in tropical ecosystems. This is particularly so for bats compared to other mammalian taxa, due to morphological conservatism. Here, we investigate West African bats of the Hipposideros caffer complex, an insectivorous bat group occurring throughout the Afrotropics. From samples collected in Ghana, we aim to resolve the cryptic diversity identified by mitochondrial (mt) DNA using nuclear genetic, acoustic, and external morphometric data. We confirmed the presence of four previously established mtDNA lineages within the H. caffer complex and found significant genetic divergence among lineages based on nuclear microsatellite data and significant differences in frequencies of echolocation calls and morphometric measures. From these new data, we conclude that H. caffer complex in West Africa consists of at least four distinct species. While the small‐sized species from coastal savanna could be assigned to H. caffer tephrus, the taxonomic identity of the three sympatric, similarly sized species pertaining to H. ruber from the forest zone of Central Ghana is yet to be assessed., publishedVersion

Additional file 1: Table 1. International Classification of Diseases, Tenth Edition, Australian Modification (ICD-10-AM) diagnostic and Australian Classification of Health Interventions, Eighth Edition (ACHI) procedure codes for anaemia and bleeding disorders used in this study. Table 2. Rates of diagnoses and procedures identified by hospital and data source, New South Wales, 2011-2015.