I was wondering the same, so I'm glad he asked it and happy you answered it. But it seems some DNA fragments would be more important/preserved than others, and it looks as though selective breeding would treat highly conserved sequences the same as any sequence, and what is conserved in the new species might leave out something that was present in the old...
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Yeah, not all gene sequences are created equal. Those that control neuron growth in your brain and spine, for example, are clearly more important than those that control your eye color. In recreating these species, those genes which differ from the gene sequences shared with the related species are of the most immediate concern.