Or through its course in history the genes used in the beginning have been deleted or changed for modification as time moved on so it would not be a reliable source?
It's because they
do change that we're able to establish phylogenetic (DNA-based) evolutionary trees. We use genes that are "highly conserved", by which we mean they:
1)Have identical function throughout the species in which they are found, and
2) Perform a crucial function, such that drastic mutation is usually fatal to the organism and therefore experience mutational change only very slowly
Using such genes we can construct trees of evolutionary ancestry. One such recent project compared genes for the major ribosomal subunit, and contributed to this:
The node at the very center, of course, is the Last Universal Common Ancestor, or "LUCA."