Ecological processes maintaining landscape genetic variation and metacommunity structure in natural landscapes have traditionally been studied in isolation. Their integrated study may inform on whether major ecological processes affect species or landscapes differently, yielding a more cohesive understanding of the spatial organization of biodiversity. Here, we investigated the relative importance of spatial and environmental drivers on cladoceran metacommunity structure and the landscape genetic structure of its most widespread member, Daphnia magna, in soda pans of the Seewinkel region in Austria, covering the entire habitat network. These temporary pans exhibit strong environmental gradients, with wind serving as a key dispersal agent among them. Our study shows both parallels and divergences in the relative impacts of environmental sorting and spatial connectivity on landscape genetic versus metacommunity structure. The metacommunity primarily reflects environmental structuring, while spatial signals dominate in the D. magna metapopulation. The weaker environmental signal in Daphnia suggests that environmental gradients are not a key driver of landscape genetic structure in neutral markers. Prevailing wind direction was an important driver both in metacommunity and landscape genetic structure. This suggests its pivotal role across the two levels of ecological organization via determining connectivity among pans, thereby affecting dispersal and colonization rates, influencing both local species and genetic composition.
