It is entirely possible that secreted effector proteins have evolved under different selective constraints in host-adapted vs host-generalist serovars of Salmonella, but the analysis of D(N) alone doesn't demonstrate this. To detect different selective pressures, it would be much more informative to use the usual dN/dS approach. This is particularly crucial in the present study, since we already know the serovars are not equally divergent.

It was reported in 2007 that approximately a quarter of the Typhi and Paratyphi A genomes have been recombined relatively recently in their evolutionary history. The central observation of this study was that, while most Salmonella enterica serovars showed pairwise nucleotide divergence of ~1.1% across their genomes, the distribution of nucleotide divergence between Typhi and Paratyphi A was different: about 3/4 of the genome looked like any other pair of serovars, i.e. 1.1% divergence, while the other quarter was much less divergent, ~0.1%. The authors then used models to demonstrate that the most likely explanation for this is convergence due to recombination between Typhi and Paratyphi A, rather than recent divergence of the serovars. The paper is available in PubMed Central:
"A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?"
Xavier Didelot, Mark Achtman, Julian Parkhill, Nicholas R. Thomson and Daniel Falush
Genome Res. 2007 January; 17(1): 61–68
PMCID: PMC1716267
http://www.pubmedcentral....

The recombination between Typhi and Paratyphi A needs to be taken into account when interpreting the data presented in the present study. The authors here focus only on D(N), the measure of non-synonymous SNPs between different pairs of serovars... low D(N) between Typhi and Paratyphi A for a particular gene is interpreted as a different evolutionary constraint in these human-adapted serovars compared to the host-generalist serovars considered. However, most of the genes discussed in this paper have particularly low levels of divergence between Typhi and Paratyphi A, suggesting they were exchanged via recombination - e.g. 0-0.6% in sipD, sseC, sseD, sseF. In contrast sifA has 2.1% nucleotide divergence, suggesting it was not recombined between Typhi and Paratyphi A, which is probably why it has a higher D(N). Without normalising to D(S), i.e. calculating dN/dS, it is impossible to say whether the similarities observed between Typhi and Paratyphi A genes is due to selective pressures associated with their host-restriction, or simply chance recombination. The latter would be an example of convergent evolution, which may or may not have provided a selective advantage for the recombinant strain. For example, the nucleotide sequence for sipD is identical in Typhi and Paratyphi A, which says nothing about selection on non-synonymous SNPs, especially given the background information about recombination. Furthermore, dN/dS between Typhimurium and Enteritidis sequences of sipD is 0.30, whereas dN/dS between Typhi and Enteritidis is similar at 0.33, and Typhi-Typhimurium is 0.35 (calculated using the online dN/dS tool SNAP at http://hcv.lanl.gov/conte...).