Any explanation for the origin of biological structures has to take several facts into account.
1) Common descent. Wherever new structures come from, they arise in the context of descent from earlier species. The genetic evidence for common descent is inescapable.
2) New structures often arise gradually. Where we have an extensive fossil record, we can often trace the gradual appearance of some new feature. For example, we have nice fossil records of intermediate forms of whale blowholes and mammalian middle ear bones.
3) Genuinely new structures are actually rare in the history of life. Both blowholes and middle ear bones, for example, are modifications of earlier structures, as are tetrapod limbs, bat and bird wings, whale flippers, and so on.
So, besides evolution of new features through mutation, what other explanations are being offered to explain new structures?