Excess of Nonsynonymous Polymorphism at Acph-1 in Different Gene Arrangements of Drosophila subobscura

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Abstract
Nucleotide variation in the Acph-1 gene region was analyzed in a natural population of Drosophila subobscura from Bizerte (Tunisia). The lines studied differed in their gene arrangement for segment I of the O chromosome: 21 lines were O3+4+8, 21 were O3+4+23, and 3 were O3+4. According to chromosomal phylogenies, O3+4 is a central arrangement from which O3+4+8 and O3+4+23 originated. Strong genetic differentiation at Acph-1 was detected among the different arrangements, which is reflected in strong linkage disequilibrium between the variants at informative polymorphic sites and the type of arrangement. Estimates of silent nucleotide diversity are slightly lower within O3+4+23 (pisilent = 0.0166) than within O3+4+8 (pisilent = 0.0228) or O3+4 (pisilent = 0.0234). In contrast, nonsynonymous nucleotide diversity estimates (around 0.1%) are similar in the three arrangements. Most nonsynonymous rare variants are singletons, which results in highly significant Tajima's neutrality tests within the young O3+4+8 and O3+4+23 arrangements. This test is not significant for nonsynonymous mutations within a large Spanish O3+4 sample. In addition, a significant and marginally significant excess of nonsynonymous polymorphism was detected by the McDonald and Kreitman test within O3+4+23 and O3+4+8, respectively. This excess results in a rather high neutrality index (NI = 5.25) when both arrangements are jointly analyzed, in contrast to its value within the old O3+4 arrangement (NI = 1.74). The pattern of variation at Acph-1 within the young arrangements is unusual for nuclear genes and has the same characteristics previously detected in most genes of the mitochondrial genome. Assuming that most nonsynonymous mutations at Acph-1 are under weak negative selection, a smaller effective size of the young arrangements relative to O3+4 might explain the observed results. The relatively low frequency of O3+4+8 and O3+4+23 in the distribution area of D. subobscura, the more recent origin of these arrangements relative to O3+4 and the suppression of recombination in heterokaryotypes might contribute to the relatively small effective size of the young arrangements. Therefore, present results indicate that the differences in effective size and recombination caused by chromosomal arrangements are modulating nonsynonymous variation at Acph-1.

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