Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes

Resumen

The phylogenetic relationships within Lepanthes, a highly diverse miniature orchid genus in the Neotropics, have remained unresolved until this study. Using living collections and publicly available data, we examined major taxonomic groups, evolutionary lineages, and biogeographic origins. We applied genome skimming to sequence 10 chloroplast genomes, recovered up to 86 plastome coding genes from GenBank, and amplified matK and rITS genes for 26 species. The chloroplast genomes (~157,185-158,260 bp) contained 136 genes, and six hypervariable regions, including parts of ycf1, were identified as potential DNA barcodes. Our findings revealed that Carl Luer’s subgeneric groups are not monophyletic, highlighting morphological homoplasy. Six evolutionary clades were identified, although the phylogeny’s backbone remains unresolved, requiring nuclear markers for further clarity. Two Marsipanthes species (L. attenboroughii and L. caprimulgus) are closely related to East Andean Lepanthes species, suggesting ancestral origins in southern Ecuador or northern Peru, followed by Andean dispersal. PCA analysis showed sepal dimensions are key for species differentiation. Despite limited species sampling, this study captures significant taxonomic, geographic, and morphological diversity, offering initial insights into Lepanthes evolution. Our results provide a foundation for future research using the molecular tools identified here.

Citation: Arias, T., Moreno, J.S., Reyes, S., Llano Almario, M., Serna, A., Iturralde, G.A., Valencia J., Baquero, L. & Zuluaga, A. 2025. Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes. Revista Jard. Bot. Nac. Univ. Habana 46(Número especial 1): 68.  

Trabajo presentado en el XIII Congreso Latinoamericano de Botánica. Sesión Sistemática, Filogenia, Biogeografía y Evolución.