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You can only build a tree based on who you know and then if you find something new, it can rearrange the relationships among the other taxa. I think that weve actually made a lot of progress on the tree of life, and that the next real challenge is going to be turning back to the organisms themselves and doing the really hard work of the cell biology to then understand what the tree tells us about major transitions in evolution and major innovations across the tree.
Finding new taxa, grinding them up, and getting their DNA is much less challenging. 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.