The emergence of infectious diseases is increasing globally, whilst biodiversity is being lost at an unprecedented rate. The amphibian chytrid fungus (Batrachochytrium dendrobatidis) has driven the extinction of more species than any other known pathogen. This loss was particularly severe among Neotropical amphibians, with several infamous extinctions from Costa Rica. Although chytrid has been attributed to all enigmatic population declines in Costa Rica, its presence has only been investigated from a few populations. Alongside chytrid, another pathogen, ranavirus (Ranavirus spp.), is considered a significant threat to amphibian populations. Very little is known about ranaviruses outside of temperate regions, but its recent confirmation from Costa Rica has provided an opportunity to investigate both pathogens amongst declining amphibian populations. The aim of this thesis was to improve the knowledgebase of chytrid and ranaviruses in the tropics, using Costa Rica as a model system, investigate cryptic diversity among local amphibian hosts and to optimise and determine suitable diagnostics that could be used to aid ranavirus research globally. The Área de Conservación Guanacaste (ACG), northern Costa Rica was chosen as my main study location for the investigation of hosts and pathogens. The ACG is comprised of high habitat diversity that is representative of multiple tropical habitats. Samples from the ACG were used to compare four ranavirus assays to determine appropriate diagnostics. Museum specimens collected between 1976 and 1989 were used to examine how long ranaviruses have been present in northern and central Costa Rica and whether they were present during outbreaks of chytrid. The presence of ranavirus was also examined amongst highly threatened amphibian populations in tropical regions of Australia. I identified six candidate species of amphibian, indicating current inventories of Neotropical amphibians to be incomplete. Among the populations of these candidate species, ranavirus and chytrid are present. Chytrid was commonly found in wet forest habitats, whereas ranavirus was detected among all habitat types. However, ranavirus prevalence increased with temperature. Both pathogens were non-randomly distributed among host taxonomic families and ranavirus was detected in Costa Rican reptile species, representing the first detection of this pathogen from this group in Central America. Comparisons of ranavirus diagnostics indicated some assays to exhibit poor sensitivity and generate false positives. Using this information and a highly sensitive assay I detected ranavirus from populations sampled from prior to and during amphibian declines. Infected individuals included extinct and severely declined species. I also detected this pathogen from the order Gymnophiona, which, to my knowledge, has not been found infected with ranavirus previously. Additionally, I detected ranavirus from highly threatened Australian amphibian populations. Future research priorities should include the description of candidate species identified here using morphometrics, bioacoustics and nuclear DNA. If confirmed as true species, their conservation status should be assessed. The results of pathogen surveys among Costa Rican populations will allow researchers to identify areas and taxa more likely to be infected within the tropics. My findings from comparing ranavirus assays will facilitate the generation of highly accurate results, hence improve estimates of distribution and impacts of ranavirus. My thesis has improved the knowledge of both hosts and ranaviruses in Costa Rica, but also in tropical systems more generally, and will help guide future researchers with the effective detection of ranaviruses from these under-studied systems.

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Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.