Plastome phylogenomics of the Diverse Neotropical Orchid Genus Lepanthes with Emphasis on Subgenus Marsipanthes (Pleurothallidinae: Orchidaceae)

The first successful resolution of phylogenetic relationships within main lineages in the diverse Neotropical orchid genus Lepanthes Sw. is presented here. Genome skimming produced ten newly sequenced chloroplast genomes, with additional plastome coding genes (17–86) retrieved from GenBank, alongside 26 amplified matK and rITS genes, enabling phylogenetic reconstruction. The Lepanthes plastomes (157,185 − 158,260 bp, 37.15% GC content) contained 136 annotated genes, including 86 protein-coding, 42 tRNA, and 8 rRNA genes. Six hypervariable regions, including parts of the ycf1 gene, were identified as potential DNA barcodes. Phylogenetic analyses revealed that Carl Luer’s subgeneric classifications are non-monophyletic, reflecting significant morphological homoplasy. PCA and correlation analyses confirmed widespread homoplasy in continuous morphological characters. Six major clades were identified, though backbone resolution remains unresolved at two nodes of the phylogeny, requiring the use of nuclear markers or expanded sampling. Subgenus Marsipanthes species are non-monophyletic and constitute an East Andean early divergent clade with species from subgenus Lepanthes , while some derived Biogeographic Choco Marsipanthes clades were recovered, forming a polytomy with species from subgenus Lepanthes . The genus likely originated in southern Ecuador or northern Peru, dispersing across the Andes into the broader Neotropics. Although only a subset of Lepanthes diversity was sampled, the study captures significant taxonomic, geographic, and morphological variation. It provides foundational insights into the genus’s evolution, along with tools and hypotheses that can be expanded upon in future research to further refine our understanding of its evolutionary history.