Eighteen museum specimens of the extinct great Auk were used to amplify coxI, a

Question

Eighteen museum specimens of the extinct great Auk were used to amplify coxI, a mitochondrial gene for cytochrome oxidase. DNA sequence analysis of 600 nucleotides of coxI revealed 5 alleles and the number of nucleotide differences between them are shown below, as well as the number of times each allele was found in the sample.

A B C D E Number
A        4
B 4                3
C 2 3             6
D 2 4 1         3
E 5 3 3 2         2

What is the nucleotide diversity () of coxI in the Great Auk based on this sample

Explanation / Answer

The formula for nucleotide diversity () is given as:

=[# of total differences/# of pairwise comparisons]/size of sequence

where the # of pairwise comparisons= [n*(n-1)]/2

So

# of total differences=(4+2+3+2+4+1+5+3+3+2)=29

# of pairwise comparisons=(5*4)/2=10

Size of the sequence is 600 nt

Now we just plug these numbers into the equation:

=[29/10]/600=.00483

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