I would expect a high degree of similarity between species for genes that code for building blocks such as
-keratins protein that are used to make hair, horns, nails, claws and hooves of mammals, because any change to the gene that affects how the protein is formed would change the protein.
This is simple back-thinking the issue: if the same protein is being used by two different organisms, then each has a gene to code for making it that results in the same protein. Such genes could be copied and mutated, but to achieve the same end result there has to be preserved the section that codes for the construction of the protein.
We also know that all life is based on a limited number of basic proteins, thus the genes that produce those proteins will need to be highly similar. Hair proteins are similar, bone proteins are similar, skin proteins are similar, etc etc.
In addition the basic "body plan" is also similar with number and placement of bones, organs and the like.
You could make an (probably bad) analogy to building a house and a five story apartment building using brick, wood, glass, metals and such. The instructions needed to make bricks, make mortar, make 2x4's, make nails, make glass, make pipes and ducts, etc. etc. would be the same for both building. Likewise the basic construction process used to build walls and windows and doors and floors would be the same, the only difference would be the repetitions, sizes and placement of each element -- the architectural plans. Summing up all the instructions necessary to build all the elements from scratch would mean that the regulatory (architectural) proportion would be fairly small compared to the structural proportion.
Thus I would expect parts of genomes that code for building proteins to be highly similar across species, but I would expect increasing differences in parts of the genomes that code for how to assemble those proteins for increasingly different organisms.
Enjoy.
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