In my theory, mutations accumulate in the non-coding, non-regulatory part of the genome, until a ’tipping point’ is reached, where the genome becomes bistable, potentially encoding another proteome with a different layout of gene boundaries, introns, and regulatory elements.

Environmental stress causes a switchover to another “interpretation” of the genome, leading to the sudden appearance of a new species.

Before the switchover, the secondary state of the genome is latent, and can spread in a population through inheritance. The switchover may occur simultaneously in several individuals, so they can find compatible mates.

The switchover changes chromatin structure, exposing fragile sites and microhomologies leading to chromosome breaks and rearrangements, and ultimately to a new karyotype. The rearrangement is stereotypical, predisposed by the sequence, and facilitated by epigenetic markings, so it yields the same karyotype in each individuals.

In the ‘latent’ phase, accumulation mutations in the ‘junk’ DNA, new features can develop by extremely unlikely series of mutations, amplified by the anthropic selection.