Phylogenomics of Melastomataceae: rooting out discordance across organellar and nuclear genomes

Melastomataceae are a megadiverse, worldwide family, comprising about 173 genera and almost 6000 species distributed mostly in the tropics. Although molecular phylogenetics have clarified major tribal relationships over the past few decades, deeper nodes within the family remain difficult to resolve with only a few number of plastid and nuclear loci, highlighting the need for genomic-scale data including major representatives across the family to resolve these recalcitrant nodes. In this study, we reconstructed a phylogenetic tree for Melastomataceae comprising all tribes and more than 90% of the generic diversity, based on hundreds of loci sampled across nuclear, chloroplast and mitochondrial genomes. This represents the most taxonomically comprehensive phylogenetic study of the family to date, particularly with respect to major lineages of Melastomataceae. We inferred phylogenies for each genome compartment and assessed topological discordance among them. We further evaluated the nuclear gene tree discordance and quantified the relative contribution of incomplete lineage sorting and reticulation. We also reconstructed ancestral chromosome number evolution to identify polyploidization events. We recovered robust phylogenies congruent with previous analyses, but relationships and branch support recovered at deeper nodes varied across genome compartments. Our nuclear genomic dataset resulted in highly supported phylogenetic relationships across the entire tree. Plastid and mitochondrial topologies were mostly concordant, but were highly discordant with nuclear topologies, especially in the backbone relationships of the family. Most nuclear gene tree discordance at deep nodes of Melastomataceae can be attributed to gene tree estimation error and ILS, but reticulation events at deep and shallow levels also play a role. Gene duplication and polyploidization events introduce additional conflict within closely related major clades, highlighting the complex evolutionary radiation of the family.