My best guess :
A schizophrenic man had a sex change and married his adopted brother. The "marriage" is a genuine marriage, but is between a man, a (newly-made) woman with the same parents but no blood relation, and the male alter-ago of the transexual. No clue about the chromosome part, maybe part of the surgery involved cutting one off.
Just in case this is somehow not the correct answer (though I wrote this before reading the 3rd hint...),
I do think two of the 'men' are the same person, somehow. I think in fact 46 of their chromosomes are identical and the 45 reference is a red herring. If they're identical to the atomic level surely it's impossible for them to be two different people?
Also,
Pretty sure sex change is involved somehow. The question even says at marriage they were men, which is ambiguous as to when they were men.