First what do we mean when we talk about the molecular evidence for evolution? The “Molecular” refers to DNA and RNA but could also be used to refer to proteins as well given that these are often the end products of DNA. With that out of the way you will no doubt have heard that we share some 96% of our DNA with Chimpanzees, what does this mean? Well to put this into some context it is also widely reported that we share about 75% percent with Pumpkins. When numbers such as these are bandied about it is used to impress upon people how related we are to various other organisms that we share our planet with. What is actually being measured here is the level of similarity shown between genes that seem to serve the same functions in different organisms.
By looking at how similar these stretches of DNA are between species we can make inferences about common ancestors and how long ago we may have split from them. In effect we are trying to create a map of the so called “Tree of Life“. Getting back to the chimps this measure of 96% similarity isn’t really an absolute measure of how much of our DNA is the same as theirs, rather is is more a measure of how closely the genes we have in common resemble each other.
So Chimps and humans have genes in common and these genes show substantial similarity, how does this imply common descent? By itself this is compelling evidence, if we are not related there is no reason to think we would be similar in this way at all as even if the same proteins are used in each animal there are numerous different gene sequences that would lead to the same or very similar protein. However we also have evidence of genes that are broken in humans being broken in chimps in the exact same way which is highly unlikely if there was no common ancestor that had bequeathed each lineage with the mistake.
To understand the following example I need side track somewhat to explain a little about viruses, it’s relevant trust me and I’ll make it quick. Viruses as I’m sure you know are basically packets of genetic material that force their way into cells and take over the machinery to make copies of themselves. Some viruses actually insert their own DNA into our Genome in order to do their little hijacking act these are the Retroviruses. These stretches of virus Can then become a permanent part of the genome for that cell. If the cell infected happens to be a germ line cell, ie a sperm or egg, then this insertion becomes hereditary and is transmitted to the next generation. If this happens then the inherited virus DNA is referred to as an Endogenous Retrovirus or ERV.
Thus ERVs can be considered to be “mistakes” in the genome of in individual or species. As the insertion of the virus DNA is both rare and random there is no reason outside of common decent (shared ancestry) that two species would have the same ERVs. There are at least seven common insertions between chimps and humans showing quite conclusively that there was a point in the past where our species had not yet diverged.
Cladogram of ERVs in related species