Are there choices in the darkness? habitat selection and environmental filtering shape invertebrate communities in semi-arid caves

Habitat selection governs subterranean organism distributions, where environmental gradients and restricted resources impose strong constraints, suggesting many cave-dwelling species respond primarily to fine-scale microhabitat variation rather than broad spatial patterns. To evaluate this hypothesis, we examined environmental drivers of invertebrate richness and community composition across 24 limestone caves in a tropical semi-arid region. Adopting a multi-scale framework, we quantified landscape attributes, cave-level habitat features, and local microhabitat conditions, recording 336 invertebrate species representing 40 orders and 106 families, including 38 obligate subterranean taxa. Our findings demonstrate that these communities are governed by a hierarchy of localized environmental filters, while regional spatial processes exert a negligible footprint. At the mesoscale, cave identity and internal sectors heavily determine community composition, overriding geographic distance and maintaining high species turnover. Across internal gradients, non-troglobitic and troglobitic fauna display an inverse spatial sorting between scales. For non-troglobitic communities, species richness declines sharply toward deeper zones, a negative effect intensified at the microscale where these organisms respond positively to trophic resource availability. Conversely, obligate troglobitic richness is constrained by moisture availability at the mesoscale but becomes solely and positively driven by distance from the entrance at the microscale, as specialized species track deep, buffered microhabitats to avoid competitive interactions in high-energy zones. Together, our results confirm that niche-based environmental filtering structures these assemblages, positioning each cave as an ecologically singular unit. Consequently, Brazilian environmental licensing cannot rely on regional offsetting, since individual caves are not ecological substitutes, and fine-scale inventories are critical to prevent biodiversity loss.