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Mendelian ponies could have a single gene with 3 alleles, E/U/P, with EE, EU and EP earth, UU and PP respectively unicorn and pegasus and UP either unicorn or pegasus at random (i.e. depending on other genes). If the two parents are EU and EP they are earth but offspring of all three types is possible. An even simpler model: one gene with two alleles, earth and fancy, earth dominant, fancy ponies become unicorns or pegasi depending on rainbow intensity or other non-genetic factors.

In the Dune case a very Mendelian concern with preserving a few important mutations in very narrow bloodlines could be combined with a secondary requirement for high IQ, physical fitness etc. that could be (inefficiently) satisfied by focusing on "well bred" aristocracy that benefits from marrying genetically far above average people.

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