In recent years, large clearings (>1000 ha) accounted for gradually smaller amounts of total annual deforestation
in the Brazilian Amazon, whereas the proportion of small clearings (<50 ha) nowadays represents
more than 80% of annual deforestation. Despite the ubiquity of small clearings in fragmented
Amazonian landscapes, most fragmentation research has focused on the effects of large-scale deforestation,
leading to a poor understanding of the impacts of smaller barriers on Amazonian vertebrates. We
capitalized on the periodical re-isolation of experimental forest fragments at the Biological Dynamics
of Forest Fragments Project in the Central Amazon as a before-after-control-impact experiment to investigate
the short-term effects of small clearings on bat assemblages. Over the course of three years we
sampled six control sites in continuous forest, the interiors and edges of eight forest fragments as well
as eight sites in the surrounding matrix. Sampling took place both before and after the experimental
manipulation (clearing of a 100 m wide strip of regrowth around each fragment), resulting in ~4000
bat captures. Species were classified as old-growth specialists and habitat generalists according to their
habitat affinities and a joint species distribution modeling framework was used to investigate the effect
of fragment re-isolation on species occupancy. Following fragment re-isolation, species richness declined
in all habitats other than fragment edges and, although responses were idiosyncratic, this decline was
more pronounced for forest specialist than for generalist species. Additionally, fragment re-isolation
led to a reduction in the similarity between assemblages in modified habitats (fragment interiors, edges
and matrix) and continuous forest. Sampling of controls in continuous forest both prior to and after reisolation
revealed that much of the variation in bat species occupancy between sampling periods did not
arise from fragment re-isolation but rather reflected natural spatiotemporal variability. This emphasizes
the need to sample experimental controls both before and after experimental manipulation and suggests
caution in the interpretation of results from studies in which the effects of habitat transformations are
assessed based solely on data collected using space-for-time substitution approaches