Yes, these transitions could happen by undirected naturalistic processes because they occur at the level of species or genus.
According to Behe, and I think it is a reasonable position, the edge is between the levels of family and genus. Here is what he said in Darwin Devolves: « As a first approximation, Darwinian processes (or for that matter any other nonintelligently planned process) cannot produce descendants that differ from their ancestor at the level of family or higher »
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