Fig. 3. UML species discovery results—B clade, 100% data completeness.The cladogram shows the ML tree topology and the position of the alphanumerically labeled clades. Each column represents the results of a UML dimensionality reduction plus clustering method. Horizontal bars within each column represent the proportion of times an individual was assigned to a given cluster across replicates, with different colors representing different clusters. Horizontal bars are aligned to the tips of the cladogram. Within each method (column), clusters were compared pairwise across replicates via normalized mutual information (NMI), and the replicate with the highest average NMI was chosen as the reference replicate. Cluster labeling (coloring) was then standardized to the reference replicate via the Hungarian method. Cluster labeling is not standardized between different methods.