Certain highly similar DNA segments have been found that, while on the one hand are too similar when compared across the different species, on the other hand are limited to only one group of species. These highly similar segments are found in vertebrates, invertebrate chordates, nematodes, and arthropods, but they generally are restricted to those groups. That is, highly similar segments are found in the vertebrates, another set of highly similar segments are found in the invertebrates, and so forth.
These various segments seem to play the same types of regulatory roles across the vertebrates, invertebrate chordates, nematodes, and arthropods. Also, they share certain sequence properties. For instance, the vertebrate segments share striking nucleotide frequency patterns with the invertebrate segments.
So what does all this mean? To make sense out of the data from an evolutionary perspective we must believe that these thousands of sequences had to evolve independently and relatively rapidly in the vertebrates, invertebrate chordates, nematodes, and arthropods. This independent process of evolution produced all these sequences with similar functions across these disparate groups of species, and according to the same striking nucleotide frequency patterns. Amazing.
But that is not all. Then, after all these heroics, the evolution of these DNA segments, within each group, must have come to a mysterious and abrupt stop. These similarities within the groups make little sense on evolution. As one paper put it:
it is difficult to reconcile their extreme conservation with our current understanding of enhancer function.
It is yet another pattern that is the opposite of what evolution expected.