Tajima's D T and Fu and Li's F were nonsignificant (D T = 0.183, p > 0.05 and F = 1.151, p > 0.10), suggesting that genetic variation of COI is under selective neutrality or in drift-mutation equilibrium.
The DoS is expected to be zero under selective neutrality, negative under purifying selection, and positive under positive selection.
The underlying paradigm of this approach is that most of the functional regions are assumed to be under selective constraint, which in turn reduces the rate of evolution relative to neutrality.
Allozyme markers and morphological traits may be under selective constraint in natural populations in contrast with SSR markers which are usually described following the neutrality hypothesis.
This program calculates the goodness-of-fit between an observed distribution of changes in amino acid physiochemical properties and an expected distribution that each amino acid replacement is equally likely under selective neutrality.
Indeed, in the simplest case, some amino acids are permitted at a site (under selective neutrality) and some are forbidden (under strong negative selection) - which would lead to a strong correlation.
For this D, application of Jukes-Cantor formula [ 4], (eq. 4.2) produces the following value of the per-site number of nucleotide substitutions per a selectively neutral site: (11) Indeed, under selective neutrality the rate of evolution is equal to mutation rate, so that K1/2, neutral = 6 μτ neutral with I = 4, and τ neutral = ln2/ 8 μ) in this case.
In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality.
However no values of Tajima's D varied significantly from values expected under selective neutrality, and only 3 of the 14 values of Fu's Fs were statistically significant.
Using control regions under selective neutrality or presumed constant selective pressures across the species, shared and private polymorphism was used to establish a divergence time of roughly 1.3 MYA and a consistent, if asymmetric, gene flow [ 42].
