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I wouldnt be surprised if the discovery of new lineages shifts the tree around. 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.