The phylogenetic analysis uses 14 protein-coding genes and two ribosomal RNA genes to reconstruct relationships within the Poecilosclerida order. While the study employs robust maximum likelihood methods, it excludes mitochondrial genomes deemed “too divergent or too similar” (Methods section). This subjective pruning of data could bias the results by removing potentially informative sequences, especially in a group with complex evolutionary histories like sponges. Could the authors clarify the specific criteria or thresholds used to define sequences as “too divergent or too similar”? Additionally, were sensitivity analyses performed to evaluate how the inclusion or exclusion of these genomes affected the phylogenetic topology?
