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This result suggests that signal peptides might be under relaxed purifying selection.
These genes may be under relaxed purifying selection or possibly positive selection.
The higher evolutionary rate of signal peptide part compared to mature protein provides an indication that signal peptide parts may be under relaxed purifying selection, indicative of the signal peptides not being secreted into host cells.
Alternatively, when coenzyme B12 or its precursors are available in the environment, some or all the ORFs coding for proteins involved in its synthesis may be under relaxed purifying selection.
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In any case, it is difficult to imagine that all the genes in this study are under relaxed purifying selection in parasites.
The previous results from a different lineage within the N. tetrasperma species complex found a higher Ka/ Ks ratio for a set of N. tetrasperma genes located within the nonrecombining region but not for a set of genes from outside of this region, consistent with the genes within the nonrecombining region being under relaxed purifying selection (Whittle and Johannesson 2011; Whittle et al. 2011b).
Most of the codons in genes are under purifying selection, and many, including some positively selected sites (ω close to 1), identified codons were under relaxed purifying or neutral selection (Fig. S5 and Table 5).
> -wrap-foot> Nonsubstitutionubstitution patterns are not significantly different between complete genes in functional operons and complete genes in partly inactivated operons as would be expected for genes under relaxed purifying selection (fig. 4).
Thus, a false inference of positive selection is likely for genes under relaxed purifying selection when the overlapping gene is under strong purifying selection.
Thus, we conclude that FOXE1 is likely to have evolved either under relaxed purifying selection or restricted positive selection in a few specific residues in the avian lineage.
These genes are most likely the result of positive selection; while both positive selection and relaxed purifying selection can lead to elevated dN/dS ratios, genes under relaxed purifying selection would also be expected to have a higher rate of amino acid substitution than is seen here.
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