Estimation of the neutral mutation rate in a finite population from DNA sequence data.

The sampling theory for the infinite site model taking into account the phylogenetic relationship between the alleles is developed for those cases in which two or three alleles are observed in the sample. From this theory a maximum likelihood estimate of theta = 4N mu can be obtained. Unlike the maximum likelihood estimate of theta based on the infinite allele model or the number of segregating sites, this estimate of theta is a function of the frequencies of the alleles. This method is used to estimate theta for mitochondrial DNA in Drosophila melanogaster and D. virilis from data obtained by Shah and Langley (1979. Nature (London) 281, 696-699) using restriction endonucleases.