Taxonomic revision and phylogenetic insights of Peperomia subgenus Multipalmata from Central America

This dataset contains the alignment files and phylogenetic tree files generated for a Sanger-based plastid phylogeny used to reconstruct a phylogeny of Peperomia subg. Multipalmata from Central America in context with the taxon-rich dataset of Frenzke et al. (2015). The data include alignments of the trnK intron, matK gene, and trnK–psbA spacer, which were extracted, cleaned, and processed through standard phylogenetic workflows (MAFFT, PASTA, Phyx trimming) and used to infer maximum-likelihood phylogenies in IQ-TREE2. These files correspond to the final trimmed alignments and resulting tree topologies used in the manuscript to evaluate the phylogenetic placement of P. clandestina and to compare it with the 194 accessions from Frenzke et al. (2015).