Scripts and data for multistate occupancy models

Monitoring programs are pivotal to establishing sound management. Due to economical, logistic, and time limitations, monitoring programs often gather naïve occupancy or abundance data but overlook differences among life-history stages. However, species occurrence does not necessarily mean successful reproduction and population viability, and it is unclear to what extent monitoring programs that do not consider separately adult presence and reproduction provide effective management indications. Unfortunately, collecting data on certain life stages requires high sampling effort, leading to a trade-off between model reliability and resources needed for monitoring. Assessing differences between adult-only and more complete monitoring programs is fundamental to identify the strategy that best informs on the ecological processes. Here, we collected data on presence and reproduction of amphibians in 207 waterbodies in Italy in 2017–2022. We then used multistate occupancy models to test whether environmental features affect differently adult occurrence and breeding probabilities of multiple amphibian species. We capitalized on the opportunity to assess optimal sampling efforts by modeling the detection probabilities of adults and reproduction across multiple species. Lastly, we identified the optimal monitoring strategy under different scenarios of resource availability, comparing adult-only monitoring vs. jointly assessing the occurrence of adults and reproduction. In many cases, the main drivers of adult occurrence and reproduction did not coincide, as most investigated ecological variables affected one life-stage or the other. We provide quantitative estimates of the sampling effort needed to reliably appraise the occurrence of adults/reproduction and their drivers. When scarce resources are available, monitoring adults was the optimal strategy for species with low detection probability of eggs and larval life stages. Conversely, with more resources, monitoring both adults and reproduction emerged as the best strategy for all the considered species. Integrated monitoring of adults and reproduction is essential to comprehensively identify effective conservation measures for amphibians.

We provide the RData file containing detection/non-detection data of different life-stages of seven amphibian species from 2017 to 2022, environmental variables potentially related to occupancy and/or reproduction, and factors potentially related to detection probabilities ("amphibian_multistate_dataset.Rdata").

Additionally, we provide the script used to run the multistate occupancy models ("amphibian_multistate_models.R") and model outputs for each species ("results.zip").