Introduction

I didn't make a big deal of it in what we just went over, but in deriving the Jukes-Cantor equation I used the phrase ``substitution rate'' instead of the phrase ``mutation rate.'' As a preface to what is about to follow, let me explain the difference.

• Mutation rate refers to the rate at which changes are incorporated into a nucleotide sequence during the process of reproduction, i.e., the probability that an allele in an offspring differs from the copy of that in its parent from which it was derived. Mutation rate refers to the rate at which mutations arise.

• An allele substitution occurs when a newly arisen allele completely replaces other alleles in a population in which it arises, i.e., when a newly arisen allele becomes fixed in a population. Substitution rate refers to the rate at which allele substitutions occur.

As we'll see, mutation rates and substitution rates are related - substitutions can't happen unless mutations occur, after all - , but it's important to remember that they refer to different processes.