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Finally, we selected sixteen microsatellites with high polymorphism, stability, and conformity with neutral selection for our research (Additional file 1: Table S1).
For a neutral selection of the coefficients of the differences, we use Eq. (5) in this study.
Ka/Ks = 1 is referred to as "neutral selection", meaning that natural selection does not have any forces acting on the protein (Hurst [2002]).
Values significantly ≪1.0 indicate purifying selection, whereas neutral selection theoretically yields a value of ∼1.0.
The Dn/Ds ratio of the concatenated MLST sequences yielded 0.0588, indicating neutral selection.
Dn/Ds < or = 1 indicates purifying or neutral selection, favouring amino acid substitutions [26].
The log-likelihood values from the M1a (neutral selection) and M2a (positive selection) models and the M7 (neutral selection) and M8 (positive selection models were used to perform a likelihood ratio test (LRT).
Randomized WTCCC and HapMap data was produced to detect deviations from neutral selection in Fig. 1 and Fig. S1.
No positively selected site was found and the mean Dn/Ds ratio corroborated the existence of neutral selection.
To confirm the occurrence of neutral selection on ibeA sequences derived from STC95 strains a SLAC analysis was carried out.
In addition, sites under positive or neutral selection are likely to adapt to drug pressures and should be avoided as targets.
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