Chloroplastic and Nuclear Markers Reveal the Phylogeny of Passiflora Species from Boyacá, Colombia

Passiflora species are recognized for their intense evolutionary dynamics within the chloroplast genome (cp), serving as a primary model for studying structural variations in natural populations. This study investigates the phylogenetic relationships of 47 Passiflora accessions from Boyacá, Colombia, utilizing a multilocus approach with chloroplast genes (trnL), non-coding regions (psbA-trnH), and nuclear markers (ITS). Multiple sequence alignments identified fragment sizes of ~264 bp (trnL), ~333 bp (psbA-trnH), and ~706 bp (ITS), each displaying distinct nucleotide compositions. Evolutionary patterns and substitution rates were evaluated using the Maximum Likelihood approach in IQ-TREE, with best-fit models selected via the Bayesian Information Criterion (BIC). The analysis revealed that transitional substitution rates consistently exceeded transversions across all markers, with the trnL region exhibiting a notably high G-to-A substitution rate of 22.15. These genomic data resolved robust evolutionary proximity between P. edulis f. edulis and P. edulis f. flavicarpa, while highlighting significant genetic divergence from P. ligularis and P. maliformis. The results demonstrate that while these specific markers effectively clarify lineage relationships, an integrated multi-marker system is essential to provide a precise understanding of the complex evolutionary divergence patterns in Andean Passiflora, offering a foundational genetic background for regional biodiversity conservation.