Nulceotide diversity (pi) and sequence diversity (theta) are same value

Question

[klively497]

I have a project where I am comparing conservation of a gene between two species. I have only one sequence of the gene for each species. I ran DNA Polymorphism tests on DnaSP and got the same value for pi and theta. Why would this be?

[Joe]

Old thread, but at a guess, I would imagine this is just insufficient data. I don't know the maths offhand to say why exactly but intuitively, if you only have 1 x 2 = 2 sequences, one per genome, then it's impossible to say much if anything about the diversity, since your options are for a given nucleotide/amino acid:

• Both match (identical sites)
• 1 sequence matches
• Neither sequence matches

Or, to think of it just in terms of the sequences, if you only have 2, they either are, or aren't identical. There is no 'diversity' to be had here.