DNA is not only the molecule that stores information about the physical characteristics of individuals, but also the molecule that stores a record of evolution in past generations. From generation to generation, mutations accumulate in the DNA. If these mutations occur within genes, natural selection may act upon the organism that has the mutation. Natural selection may reduce the frequency of a harmful mutation in a population, although it may never eliminate it, or it may increase the frequency of a beneficial mutation. Natural selection does not affect the frequency of a mutation that has no effect on the function of the organism (a neutral mutation). Mutations that occur in the noncoding DNA will also be unaffected by natural selection. Neutral genetic mutations, and mutations in the noncoding DNA, accumulate in the DNA as it is passed from one generation to another. A comparison between the coding and noncoding regions of DNA indicates that there are more differences between humans and mice in their noncoding DNA than in their genetic DNA.

Organisms that are part of a single population interbreed and share genes. Although each organism in a population is genetically unique, all are genetically similar because they draw their genes from a single gene pool. But when a population is separated into two populations, new and different mutations occur in each of the populations. The new mutations present in one population are not found in the other. Over time, the DNA of the two gene pools becomes different. The longer the populations are separated, the greater the differences in their DNA. If the populations diverge enough to become separate species, the DNA is even more different; DNA of two different genera are even more different; the DNA of two families even more different; and so on. By quantifying how different the DNA is between two organisms, scientists can determine how much evolutionary divergence has occurred since their separation. If scientists assume that mutations occur at a constant rate, these mutations constitute a molecular clock. The DNA molecules have been keeping a cumulative record of the passage of time that helps scientists to reconstruct evolutionary history.

Because neutral mutations and mutations in the noncoding DNA are not related to the structure and function of organisms, comparisons of DNA and comparisons of anatomy provide independent data for the reconstruction of evolutionary relationships. DNA nucleotides, just like the physical characteristics of organisms, can be used as data in phylogenetic analysis. Usually, phylogenetic reconstructions of evolutionary history based upon DNA correspond closely to phylogenetic reconstructions based upon physical traits, thus providing independent confirmation of the evolutionary patterns. This could scarcely have happened unless evolution really occurred. The DNA confirmation of evolution is one of the best sources of evidence against creationism. A creationist could explain the evolutionary patterns of neutral and noncoding DNA only by claiming that a Supreme Being created mutations that had an evolutionary pattern but were otherwise useless. . .

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