Does a tree-like phylogeny only exist at the tips in the prokaryotes?

Does a tree-like phylogeny only exist at the tips in the prokaryotes? ››: On the basis of too much horizontal gene transfer? They suggest so, given that deep-branching trees can't be reliably constructed from complete genomes but known clades do form bifurcating phylogenies. Not sure about this -- evidence of the accuracy of phylogenetics is itself a carefully constructed tree/web. I wonder if datasets like this can estimate a historical rate of horizontal tranfer based on the transition from tree-to-net as we move back through time adding deeper "branches". But what is the disruptive effect on a tree of any single horizontal transfer (meaning, what unanticipated messiness might result from your algorithm and have you proven that the degree of messiness correlates with the degree of non-vertical transmission)?; [Permalink…23-Dec-04…Deserving memes…]

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