'Junk' DNA doesn't actually contain genes. By definition, a gene encodes a functional polypeptide or RNA. This is different from alleles that are neutral for vi

'Junk' DNA doesn't actually contain genes. By definition, a gene encodes a functional polypeptide or RNA. This is different from alleles that are neutral for viability. An example of such an allele might be connected earlobes -- this phenotype is genetically determined, but unless there's sexual selection I'm not aware of, you are correct that we wouldn't necessarily expect the alleles involved in this phenomenon to go away. However, they might as a result of an accident of history or genetic drift.