It isn't just the pattern of similarities that evidence common descent and evolution. The differences also provide us with big pieces of evidence.
The inspiration for this post comes from EvoGrad and Stephen Schaffner, from whom I will be borrowing various figures. Ebersberger et al. (2002) published on this subject, and could have served as direct or indirect inspiration for EvoGrad and Schaffner.
With credit given, let's move on to the evidence.
Mutations are heritable changes, specifically heritable changes in the DNA sequence of a genome. The type of mutation I will be discussing is a substitution mutation where one base is swapped out for a different base. For example:
AGGCTAATCG --original AGGGTAATCG --mutated
There are two main types of substitutions: transitions and transversions. They are called this because if the mutation is between two similar bases it is a transition, and a transversion if it is between two dissimilar bases. The two classes of bases are purines and pyrimidines. For clarity's sake, I like to refer to them as one ring and two ring bases, as shown in the picture below:
Due to the biochemistry of genetics, transitions tend to happen more often than transversions. That is, substitutions occur more often between bases that have the same number of rings. Even though there are two possible transversion mutations per base compared to just one possible transition, we still see more transitions than transversions.
Evograd compiled a total of 220,000 de novo (i.e. new mutations detected in experiments in green) human mutations from various papers and compared them to 78.6 million substitutions found in the existing human population (i.e. the standing variation in the human population in blue) from public databases. This is what that comparison looks like:
Like I stated earlier, transitions outnumber transversions in this figure. The first set of bars are the transitions, and the other three sets of bars are the transversions. Also, the rate at which these mutations occur in real time matches the standing variation in the human population. In other words, this is smoking gun evidence that the process we observe creating mutations in real time is responsible for the variation we see in the human population. The fingerprint produced by the natural process of mutation is measurable and present in the human population.
But what if we do the same thing for a comparison of the human and chimp genome? The model for common descent and evolution states that humans and chimps share a common ancestor. Therefore, this model predicts that our lineages started from the same ancestral genome and population. As our lineages diverged, the same process of mutation should have created differences between those lineages. Therefore, if this model is correct then we should see the same fingerprint when we compare the human and chimp genomes.
Wouldn't you know it, there's that fingerprint. In fact, let's extend it out to other primates:
There's that same fingerprint, just as we would expect from common ancestry and evolutionary mechanisms.
This is smoking gun evidence for common ancestry. This evidence is exactly what we would expect to see if our models are true.