Phylogenetic trees

One increasingly popular objection to the historical Adam is based on comparative genomics. But from what I've read, comparative genomics skewers many traditional phylogenetic trees by reconnecting the dots in a different order. For instance:

http://blog.drwile.com/?p=1008

So comparative genomics is forcing Darwinians to rewrite various chapters in their backstory of evolution (i.e. phylogenetic trees). And as we continue to map ever more genomes of ever more species, I assume that revisionism will only expand. 

Before the advent of genomics, phylogenetic trees inferred from comparative anatomy and reconstructing the fossil record. Fossils and homologies. 

But as a result of comparative genomics, we're told that some species which were previously thought to be more closely related to each other are now thought to be less closely related to each other while some species which were previously thought to be less closely related to each other are now thought to more closely related to each other. In other words, I believe that comparative genomics is quietly rewriting the story of what's an ancestor to what. That what used to be considered a common ancestor is in fact more distant. 

So even though the "headline" trumpets new evidence for evolution, comparative genomics is challenging the narrative behind-the-scenes.