From the guide:

Different traits have different methods of mutations, feathers, down and tail genes can mutate into a brand new gene each 5 generations, eyes can be mixed to create new genes. Beak and feet require filling out a mixed linage tree of two specific traits to unlock. No mutations are guarantied they only happen if their prerequisites are met and on a chance percentage.

When pengis with two specfic eye traits breed, they have a chance to give a new eye trait.

Often, but not always, special edition Pengis can pass a new eye instead of it's shown eyes, other times, it can pass the new eyes it has.

Sometimes there are dare rewards that are new eyes, dares are time limited “challenges” where you need to find pengis with certain traits in order to possibly receive a dare reward as an egg.

Starter traits come from starter eggs bought in starter packs (or as hidden genes on SEs that are bought.)

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