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The other aspect of the tree of life that were really struggling to handle is that fact that, among microorganisms in particular, there is a lot of lateral transfer of genes and sometimes whole genomes.
Most biologists are aware of the acquisitions of chloroplasts and mitochondria early in eukaryotic evolution, but just in the past 10 years, other labs have discovered two additional acquisitions of chloroplasts. So not only do we have to deal with non-vertical events where entire organisms are engulfed, but there are also all the lateral gene transfer events which dont fit the model of the tree.
Scientists acknowledge lateral gene transfer as a phenomenon, and then we draw our trees anyway. So I think the next paradigm shift will be figuring out how to capture the combination of lateral and vertical events on depictions of the tree of life.