Most zooplankton species inhabiting seasonal ponds produce dormant stages to overcome the dry seasons. Zooplankton specimens emerging from the sediment contribute to the ecological dynamics of these ecosystems, because they constitute important energy sources for higher trophic levels in aquatic food webs. In contrast to snapshot studies of the active communities, studying the ecological correlates of the distribution of the egg bank can help identify the potential drivers of zooplankton composition. We tested the association of local (habitat structure and water chemistry), climatic and spatial predictors with the alpha and beta diversity of zooplankton hatchling communities in subtropical seasonal ponds. Incubation experiments were conducted with sediment samples from 11 ponds distributed along an approximately 500‐km latitudinal gradient in southern Brazil. We assessed the patterns for the total community, Cladocera only and Rotifera only. The alpha diversity of the total community and Cladocera were primarily related to substrate heterogeneity. Annual rainfall and substrate heterogeneity jointly influenced the beta diversity of the total community. Annual rainfall solely influenced the beta diversity of Cladocera, while substrate heterogeneity influenced the overall beta diversity of Rotifera. Overall, the distinct relationships of the total hatchling community and Cladocera and Rotifera with the explanatory datasets suggest differing sensitivities of the zooplankton groups to impacts in habitat structure and climatic conditions in subtropical seasonal ponds.
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