BLAST

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Chapter 2: Biological Sequences

Molecular Clocks

If you compare the sequences from related organisms, it is clear that certain posi-

tions don’t change much over time while others change very rapidly. For example,

parts of the ribosomal RNA are identical in every organism sequenced to date, from

bacteria to humans. These subsequences are so important that if they change, the

organism dies. Clearly, these are under intense selective pressure. There are other

sites, such as third codon positions, that are only mildly affected by selection and

tend to drift. There are even sequences, such as viral coat proteins, in which selec-

tion acts to promote variation, and these change very rapidly. Regardless of the

underlying mechanism, it is possible to use the rate of change as a molecular clock.

If you know the mutation rate for a particular sequence, you can use it to determine

how long ago two sequences diverged. Suppose you have the same protein sequence

from both cats and dogs, and there are 10 differences between them. From the fossil

record, you estimate that cats and dogs had a common ancestor 50 million years ago.

Now when you compare the cat sequence to the same sequence in humans, you find

12 differences. You can now estimate that carnivores and humans shared a common

ancestor