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Good question. I don't think it's perfectly understood, but it sounds like a recessive inhibitor combined with the pti-1L gene. I found this quote on stubs "The last two genes came from a study on Rhode Island Reds (Crawford, 1990). It was mentioned that these stub genes may be partially sex-limited, as stubs expression was more prominent in males. Other studies indicated a polygenic basis for the stubs trait (ie, multiple genes involved, acummulative effect on expression). "
So maybe there is a mutation within feathered shanked varieties, a separate gene, that inhibits expression in two doses, but not in one (recessive). When bred to a non-feathered variety (ameraucana) the inhibitor and the pti-1L both drop to one dose, but because the pti-1L is dominant, the feathers express and the inhibitor is rendered inactive. Does that make sense?