SRP459985 PRJNA1015739 ddRad raw sequences of Plathymenia reticulata samples from Cerrado, Atlantic Forest and the ecotonal region between them This data refers to the raw data used in the study Genomic signatures of ecological divergence between savanna and forest populations of a Neotropical tree (doi.org/10.1093/aob/mcad120) authored by Muniz et al. 2023. The study investigated two ecotypes of the tree Plathymenia reticulata, one from Cerrado and the other from Atlantic Forest which have a hybrid zone in the ecotonal zone of Atlantic Forest/Cerrado. The ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analyzed with ddRadSeq. The study evaluated the genomic divergence, the genotipic classes of the hybrids and SNPs under putative selection.