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There are a variety of measures of tree similarity implemented in the TreeDist R package. (Your phylogenies appear to be from the R ape package, so hopefully you are somewhat familiar with R.) Other tools include treedist from Joe Felsenstein, which computes Robinson-Foulds and the Branch Score Distance (which sounds closely related to your interests, ...


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I don't know whether this is actually used in phylogeny, but if you restrict the problem to cases where the topologies are the same, each tree can be described as a point in a n-dimensional space where n is the number of branches, and each axis represents the (possibly normalized) length of one of the branches. You can then compute distances between points (...


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Not with fossils. Very very few organisms ever fossilize and most of the organisms tissues are not represented in fossils. Less than 0.01% of all animal SPECIES have left a single fossil and most of those have not been found yet. Because of how incomplete the fossil record is we can never say a species is definitively part of a lineage. in fact the basic ...


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This phenomenon appears to be called "pseudoextinction", with dinosaurs as the classic example of an ancestor (of modern avians). We know tons and tons about dinosaurs and avians, such that we can be pretty damn sure that modern avians are the descendants of dinosaurs. Granted, almost by definition no fossil evidence could yield conclusive evidence ...


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