Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes

<h4>Premise</h4>The species-rich flora of Tropical Andes underwent multiple rapid and recent diversifications, yet resolving their evolutionary histories remains challenging despite increasing phylogenomic data. Here, we examined phylogenomic conflict in Brachyotum (Melastomataceae) to identify sources preventing its resolution.<h4>Methods</h4>We sequenced multiple nuclear loci through target capture and plastid loci through genome skimming for approximately two thirds of Brachyotum species. We analyzed nuclear loci with concatenated maximum-likelihood, multispecies coalescent (MSC), and phylogenetic network approaches, whereas plastid loci were analyzed with a concatenated maximum-likelihood.<h4>Results</h4>Topological conflict was widespread among gene trees. Brachyotum was inferred as monophyletic by concatenated nuclear and ASTRAL approaches, but as paraphyletic by BEAST and phylogenetic network analyses, the latter involving four introgression events. Plastid analyses also recovered paraphyly. Across analyses, the backbone of Brachyotum showed low branch support, and individual nuclear loci yielded markedly divergent topologies across inference methods.<h4>Conclusions</h4>Despite pervasive gene tree discordance, the signal for multiple introgression events is robust. Cytonuclear discordance between plastid and nuclear data further supports introgression. Our results suggest that current phylogenomic approaches may not fully capture the evolutionary complexity of Brachyotum, a challenge that may extend to other rapid Andean plant radiations.