Key points in the article
1) The gene linked with hearing is known as prestin
2) There are a limited number of ways that prestin can change to make it responsive to high frequencies (When expressed)
3) There was a selective pressure which conserved these limited number of mutations that occured that made individuals of both species better at hearing high frequencies.
With these points in mind its innevitable that we should find similar genes in bats and dolphins. Given the nature of this gene it would be suprising if we'd found that there was a significant different between them.
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Of course there is an important lesson to be learned from this research and that is that when determined how related various species are from their genes care should be taken in interpretation of results. Of course this is already addressed as they don't just rely on one gene to make these phylogenetic tree's.
As for your alternative theory I don't think it warrants serious consideration.
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