It's pretty hard to hand wave away something that admits it is based upon evolutionary construct. When the trees are based upon evolutionary belief and defined by it, it's admitting the bias.Phylogenetic trees are by definition trees that represent hereditary ancestry. Nobody ever said otherwise. However, that doesn't change the fact that the trees themselves are algorithmic constructs based on underlying data.
It's also worth noting that phylogenetic trees do have real-world application (such as pathogen tracking) and in at least once instance I know of have been used as evidence in a criminal trial.
So if you're attempting to blindly hand-wave them away just because you don't like what they represent, you're being about as silly as I was when I was denying the moon.
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