Museomic phylogenomics of Orthosiinae (Apocynaceae) integrating targeted sequencing and morphology

Abstract

Museum collections offer valuable resources for phylogenetic research, especially in taxonomically challenging groups. Here, we present a phylogenetic study of the South American Apocynaceae subtribe Orthosiinae, based on sequencing 835 nuclear genes and chloroplast genomes from ~120 species using a family‐specific probe set and multiple herbarium samples per species. Our results confirm generic relationships within Orthosiinae with Monsanima (2 species) sister to Scyphostelma (>50 species), and Jobinia (25 species) +  Orthosia (55 species). Data were processed with the HybPhyloMaker pipeline, providing a reproducible framework for phylogenetic reconstructions using concatenation and coalescent‐based methods. The final dataset comprised 204 samples, 810 nuclear genes (1.2 Mb) and complete chloroplast genomes (0.16 Mb) after excluding samples with signals of admixture. Phylogenetic analysis identified several cryptic lineages with little morphological differentiation, highlighting the need for further systematic research in the Andes. Evolutionary placement of 107 additional samples confirmed Monsanima as sister to the rest of Orthosiinae. Divergence‐time estimates placed the crown age of Orthosiinae at ~13 Ma. Morphological analysis revealed high variability in leaf and floral traits traditionally used for taxon delimitation but also identified floral characters that are diagnostic for generic identification. Ancestral state reconstructions show no clear directional changes in leaf morphology, whereas several floral traits tend to evolve toward smaller sizes along the youngest branches of the phylogeny. Our integrated museomic approach contributes to a better understanding of evolutionary patterns and taxonomic relationships in this still understudied lineage of South American Apocynaceae.