The hypothesis we are testing is straightforward: is biochemistry responsible for the differences between individuals within a species and between species? To test this hypothesis we look for the same pattern of transition, transversion, and CpG mutations.
“Genomewide average frequencies for various nucleotide differences between chimpanzees and humans ( A ) and among humans ( B ). Ti = transitions.”
Ebersberger et al. (2002)
We can see the same pattern in the chart above. (B) is the comparison between human genomes, and we see that the CpG mutations dominate. (A) is the comparison between chimp and human DNA, and we see the same pattern of specific types of substitution mutations as those seen in the comparison between humans.
@glipsnort (aka Steve Schaffner) has a very similar chart that excludes the CpG mutations so that we can see the relationships between the types of mutations with lower rates:
Again, transitions outnumber transversions in both the human-human comparison and the human-chimp comparison, and the same trends are seen in both.
This also extends to comparisons of more distantly related species. I will leave out the graphs here to keep the clutter down, but you can check them out here.
The evidence supports our hypothesis. The evidence is consistent with biochemistry and common descent producing the differences between genomes. Does this mean that God is not guiding these mutations? NO!! Science has no way of proving or disproving this claim. What we can say is that the evidence is consistent with our hypothesis. Period.
It is this type of evidence that has led scientists to conclude that mutation is the cause for differences between species. This isn’t assumed. This is a supported conclusion. Evolution explains why we see these differences as much as any other scientific theory explains how nature works.