One of the central pillars of the standard evolutionary model is the belief that all living species evolved from a common ancestor through a gradually unfolding tree of life.
The changes involved in adapting a generic mammalian template into a whale are certainly not all simple, independent, single-letter changes.
A bottleneck of two, or a first pair at our origin older than 500,000 years, is possible.
In order for evolution to have occurred as the orthodox theory describes, the intricate embryonic development stages of species must have evolved.
The claim that they found that the expression of dorsoventral transcription factors evolved independently in certain bilaterian lineages is not even wrong.