While Darwin argued for a single Tree — probably the most powerful image he introduced into biological perception — he was always cagey about the structure of its root. Life was “originally breathed [‘by the Creator,’ added in the 2nd edition of the Origin] into a few forms or into one” (1859, 490). There’s a world of (inferential / phylogenetic) difference, however, between divinely created first life and naturally arising first life, when the single most important question in the latter scenario concerns the probability of abiogenesis. “A few forms” that independently evolved (say) ribosomal structure, versus a single origin for the ribosome, would entail radically different consequences for phylogenetic reconstruction.
Move the red bead of the probability of abiogenesis down its wire, away from zero and towards one, and funny things happen to the structure of the monophyletic tree of life. The tree comes apart from the bottom, and the fracturing process rapidly climbs up into the branches.