Lithobiomes Heterogeneity and Geographic Distance Shape the Landscape Genomics Within Brazilian Mountain Systems

Lithological heterogeneity, climatic gradients, and geographic distance may shape the genetic structure of montane plant species, but their combined effects remain underexplored in Neotropical ecosystems. To investigate the genetic patterns and the underlying processes in different lithobiomes of southeastern Brazil, we evaluate the genomic landscape of Paepalanthus calvus (Eriocaulaceae), a rare case of a species restricted to different lithobiomes in campos de altitude and campos rupestres. Using genome-wide SNP data and different edaphoclimatic datasets, we identified two major genetic clusters corresponding to the established rocky ecosystems, with further substructure reflecting the lithological heterogeneity among the campos rupestres. Genomic variation was primarily predicted by geographic distance followed by biophysical predictors at the ground level, while climatic factors at the atmospheric level showed limited influence. We identified 36 SNPs putatively located in regions linked to selective genes, primarily associated with spatial and biophysical predictors. Our findings thus demonstrate the significance of ecogeographic isolation and population responses to environmental heterogeneity in driving genetic differentiation within fragmented montane environments. These patterns highlight the importance of lithobiomes-specific processes in shaping biodiversity and provide new insights into the evolutionary dynamics of these rocky ecosystems.