But in this topic we are discussing if features in the genome indicates realtionshipos between species, so possible effects of a pre-flood environment don't apply.
Consider that genes code for proteins, and every three bases of a genes sequence represents one amino acid of a protein. This is the codon (I realise you probably know this already). However, most amino acids are represented in the genome by more than one codon, in fact there can be anywhere up to six different codons. Therefore there can be a great deal of variation in a genes sequence that will produce the same protein ”design’. This allows for mutations to accrue without changing the protein.
Now we can look at this sequence variation in genes that maintain basic cell function in all organisms, such as cytochromes B or C, and map the variation in gene sequences between species. Now within a kind as it diversifies into different species you’d expect this variation to show relationships as mutations are inherited, just as in a familial relationship. But you wouldn’t expect to fit species of different kinds into a familial relationship of variation, since the kinds were created separately and mutations are random. However that is not what we see, and the variation that is present in all species is consistent with them all being related. So for example the variation of cytochrome B between humans and Chimpanzees is less than the variation between Chimpanzees and Gorillas so it’s possible to build up a pattern of relationship between these apes.
This is only addressing the question of relationships between species. The question of how changes in the genomes can result in the variety of phenotypes we see I will leave to another post.
Also I note that I’ve used the terms kind and species and I know in the past this has created arguments over definitions, but it’s not really relevant to what I’m trying to discuss.