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Species loss in fragile insular communities can alter the composition and stability of local assemblages. Climate change or anthropogenic pressures are sometimes attributed to the loss of Caribbean bats, but other factors are elusive to document. We studied time-scaled changes in bat assemblage composition from a palaeontological excavation in Cueva Matos, Puerto Rico. Over 800 individual fossils were identified to species, and charcoal was used to develop an AMS¹⁴C chronology. Although three bat species live in the cave today, fossils comprise 10 species. These included five extirpated species from the cave and three no longer present on the island. Losses centred around 2460–4470 kya. Notably, we document the first record ofMormoops megalophyllaas extirpated from Puerto Rico. Nearly 90% of the extirpated bats in Cueva Matos prefer to roost in hot caves where temperatures may reach 40℃. However, these temperatures are currently not held in any cave chamber. Our findings suggest that structural changes in the cave resulted in the loss of heat traps and likely led to a sudden shift in the bat assemblage composition at this cave, which is now void of hot cave specialist bats. 

The absence of terrestrial apex predators on oceanic islands led to the evolution of endemic secondary apex predators like birds, snakes and crocodiles, and loss of defence mechanisms among species. These patterns are well documented in modern and Quaternary terrestrial communities of the West Indies, suggesting that biodiversity there assembled similarly through overwater dispersal. Here, we describe fossils of a terrestrial apex predator, a sebecid crocodyliform with South American origins from the late Neogene of Hispaniola that challenge this scenario. These fossils, along with other putative sebecid specimens from Cuba and Puerto Rico, show that deep-time Caribbean ecosystems more closely resembled coeval localities in South America than those of today. We argue that Plio-Pleistocene extinction of apex predators in the West Indies resulted in mesopredator release and other evolutionary patterns traditionally observed on oceanic islands. Adaptations to a terrestrial lifestyle documented for sebecids and the chronology of West Indian fossils strongly suggest that they reached the islands in the Eocene–Oligocene through transient land connections with South America or island hopping. Furthermore, sebecids persisted in the West Indies for at least five million years after their extinction in South America, preserving the last populations of notosuchians yet recovered from the fossil record.