1. Fruit bats (Family: Pteropodidae) are animals of great ecological and economic importance, yet their populations are threatened by ongoing habitat loss and human persecution. A lack of ecological knowledge for the vast majority of Pteropodid bat species presents additional challenges for their conservation and management. 2. In Australia, populations of flying-fox species (Genus: Pteropus) are declining and management approaches are highly contentious. Australian flying-fox roosts are exposed to management regimes involving habitat modification, either through human-wildlife conflict management policies, or vegetation restoration programs. Details on the fine-scale roosting ecology of flying-foxes are not sufficiently known to provide evidence-based guidance for these regimes and the impact on flying-foxes of these habitat modifications is poorly understood. 3. We seek to identify and test commonly held understandings about the roosting ecology of Australian flying-foxes to inform practical recommendations and guide and refine management practices at flying-fox roosts. 4. We identify 31 statements relevant to understanding of flying-fox roosting structure, and synthesise these in the context of existing literature. We then contribute contemporary data on the fine-scale roosting structure of flying-fox species in south-eastern Queensland and north-eastern New South Wales, presenting a 13-month dataset from 2,522 spatially referenced roost trees across eight sites. 5. We show evidence of sympatry and indirect competition between species, including spatial segregation of black and grey-headed flying-foxes within roosts and seasonal displacement of both species by little red flying-foxes. We demonstrate roost-specific annual trends in occupancy and abundance and provide updated demographic information including the spatial and temporal distributions of males and females within roosts. 6. Insights from our systematic and quantitative study will be important to guide evidence-based recommendations on restoration and management and will be crucial for the implementation of priority recovery actions for the preservation of these species into the future.

1. The COVID-19 pandemic has highlighted the importance of efficient sampling strategies and statistical methods for monitoring infection prevalence, both in humans and reservoir hosts. Pooled testing can be an efficient tool for learning pathogen prevalence in a population. Typically pooled testing requires a second phase follow up procedure to identify infected individuals, but when the goal is solely to learn prevalence in a population, such as a reservoir host, there are more efficient methods for allocating the second phase samples. 2. To estimate pathogen prevalence in a population, this manuscript presents an approach for data integration with two-phased testing of pooled samples that allows more efficient estimation of prevalence with less samples than traditional methods. The first phase uses pooled samples to estimate the population prevalence and inform efficient strategies for the second phase. To combine information from both phases, we introduce a Bayesian data integration procedure that combines pooled samples with individual samples for joint inferences about the population prevalence. 3. Data integration procedures result in more efficient estimation of prevalence than traditional procedures that only use individual samples or a single phase of pooled sampling. 4. The manuscript presents guidance on implementing the first phase and second phase sampling plans using data integration. Such methods can be used to assess the risk of pathogen spillover from reservoir hosts to humans, or to track pathogens such as SARS-CoV-2 in populations.