Fig. 1

Progress of h-PHI removing recombinant taxa among mother–child sequences. The h-PHI test removed the sequence contributing most to the PHI signal in each iteration, recalculating the overall PHI score after each removal as the homoplasy relationships changed depending on the current sample. Datasets with many recombinants started at a lower Pr(PHI) value and had more taxa removed (Table 1). The colored lines show the iterative progress, and the dashed line indicates Pr(PHI) = 0.05, above which the iterative removal process stopped