Molecular homologies reflect functional similarities, not common descent.
Molecular similarities exist not only in functional aspects of organisms, but also in nonfunctional aspects, such as neutral mutations in the genome, or amino acid substitutions that make no difference to the structure of a protein. Molecular investigations of evolutionary relationships rely heavily upon these nonfunctional aspects.
In general, evolutionary trees generated by these techniques have been a good match to evolutionary trees constructed through the fossil and other data. There are even times when fossil finds have confirmed evolutionary relationships suggested by molecular data that would not have been expected on the basis of the appearance of an organism alone.
Last updated: 21 Mar 2008
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