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What if she was born as a 'freak' and people were unable to determine if it was male or female
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Incest isn't labeled bad from a genetic standpoint because of that, it's more the shrinking of the gene pool and bringing out recessive diseases. Unless the gene for genital misgrowth was already in the family that is. I'm not sure incest is even that picky, you could just as well inherit a good recessive gene (it just wouldn't be as noticable, no-one maps the British royal family's genes for keeping their hair unil old or anything).
Now having six toes, that is something Yasu could have inherited.
Did the phonecalls in ep 5 start after Battler solved the epitaph? Because that would explain how he knew in the first place, much like how Yasu knows about the cliff dive (Natsuhi should have made some serious inquiries into Genji...)
Also cut Natsuhi some slack, she faked Kinzos murder pretty cleverly.