We analyzed DNA variation at the acidic chitinase (
ChiA) locus of
Arabis gemmifera and among its eight related species. Nucleotide diversity (π) of the entire locus in
A. gemmifera was 0.0032, which was one third that of
A. thaliana. In
A. gemmifera, an excess of unique polymorphisms yielded significantly negative results with the tests of Tajima and Fu and Li. The McDonald and Kreitman test revealed that the ratio of nucleotide replacement to synonymous changes in
A. gemmifera was significantly greater than those between
A. gemmifera and
A. glabra,
A. gemmifera and
A. griffithiana, A. gemmifera and
A. korshinskyi,
A. gemmifera and
A. wallichii, and
A. gemmifera and
A. himalaica. These results indicated that the neutrality assumption, the equilibrium population assumption, or both, could not be applied to the
ChiA locus of
A. gemmifera. The small size and relative isolation of local subpopulations of
A. gemmifera could explain the excess of unique polymorphisms and the high proportion of replacement changes. The specific sampling scheme of this study, where one strain each was sampled from each local subpopulation might also have led to an excess of singletons. Interspecific comparison among
Arabidopsis,
Arabis and
Cardaminopsis species showed that
Ka was always lower than
Ks, providing evidence against the adaptive evolution of
ChiA. However,
Ka/Ks was greater between closely related species than between more distant related species.
ChiA had a higher level of replacement divergence and a lower level of synonymous divergence compared than did
Adh. We suggest that both the mutation rate at the nucleotide level and the selective constraints at the protein level are lower in
ChiA than in
Adh.
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