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.

Beaks (and feet) are the hardest mutations to get, it requires the parents each have the prerequisite traits going back 3 generations. Which parent in each generation that has which trait doesn't matter, so long as each set of parents has both traits represented.

Beaks are often passed from SEs, though not all SEs have new beaks.

Beaks currently do not come as dare rewards, this may change in the future.

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

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