Open access paper, too, from PLOS:
A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.
So, even a tree of cellular lineages is not an unproblematic concept. Students of animals and plants have long accepted that incomplete lineage sorting, introgression, and full-species hybridization pose difficulties for the sorts of trees that Darwin might have had us draw. But it is microbes, with their promiscuous willingness to exchange genes between widely separated branches of any “tree,” that have most seriously jeopardized the neo-Darwinian synthesis, in the oversimplified form that we have often presented it to the public . More sophisticated understandings do remain possible  and should be debated in a more conceptually and science-historically self-aware context . – Doolittle WF, Brunet TDP (2016) What Is the Tree of Life? PLoS Genet 12(4): e1005912. doi:10.1371/journal.pgen.1005912 (public access) More.
Translation: It’s just not working anymore. Wasn’t that what Copernicus told the Pope when the Pope sent letters around asking for help reforming the Ptolemaic calendar?: The calendar doesn’t work because the theory is a mess. We heard that from Dava Sobel’s book, Galileo’s Daughter.
Can we strike a deal for “the leaf of life”? Yes, it raises all sorts of questions, but at least that thing looks like, well, …
The tree of life is mostly a complete mystery (so then how do we know it’s a tree?)
Kirk Durston on the new tree of life
Tree of life morphs into … leaf?
Maybe the Tree of Life is more of an art exhibit than a science pursuit?
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