Maria Pinilla Vargas

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.

Habitat stability is important for maintaining biodiversity by preventing species extinction, but this stability is being challenged by climate change. The tropical alpine ecosystem is currently one of the ecosystems most threatened by global warming, and the flora close to the permanent snow line is at high risk of extinction. The tropical alpine ecosystem, found in South and Central America, Malesia and Papuasia, Africa, and Hawaii, is of relatively young evolutionary age, and it has been exposed to changing climates since its origin, particularly during the Pleistocene. Estimating habitat loss and gain between the Last Glacial Maximum (LGM) and the present allows us to relate current biodiversity to past changes in climate and habitat stability. In order to do so, (i) we developed a unifying climate‐based delimitation of tropical alpine regions across continents, and (ii) we used this delimitation to assess the degree of habitat stability, that is, the overlap of suitable areas between the LGM and the present, in different tropical alpine regions. Finally, we discuss the link between habitat stability and tropical alpine plant diversity. Our climate‐based delimitation approach can be easily applied to other ecosystems using our developed code, facilitating macro‐comparative studies of habitat dynamics through time.