Positive and Negative Selection in the β-Esterase Gene Cluster of the Drosophila melanogaster Subgroup

Abstract

We examine the pattern of molecular evolution of the beta-esterase gene cluster, including the Est-6 and psiEst-6 genes, in eight species of the Drosophila melanogaster subgroup. Using maximum likelihood estimates of nonsynonymous/synonymous rate ratios, we show that the majority of Est-6 sites evolves under strong (48% of sites) or moderate (50% of sites) negative selection and a minority of sites (1.5%) is under significant positive selection. Est-6 sites likely to be under positive selection are associated with increased intraspecific variability. One positively selected site is responsible for the EST-6 F/S allozyme polymorphism; the same site is responsible for the EST-6 functional divergence between species of the melanogaster subgroup. For psiEst-6 83.7% sites evolve under negative selection, 16% sites evolve neutrally, and 0.3% sites are under positive selection. The positively selected sites of psiEst-6 are located at the beginning and at the end of the gene, where there is reduced divergence between D. melanogaster and D. simulans; these regions of psiEst-6 could be involved in regulation or some other function. Branch-site-specific analysis shows that the evolution of the melanogaster subgroup underwent episodic positive selection. Collating the present data with previous results for the beta-esterase genes, we propose that positive and negative selection are involved in a complex relationship that may be typical of the divergence of duplicate genes as one or both duplicates evolve a new function.

Protein fossils live on as RNA

“…In particular, a small but significant number of the 'reads' found using the Solexa sequencing technology 1,4 can be intersected with some 70 pseudogenes, for an average of roughly 12 reads each. Finally, there is strong evidence that for several genes -particularly the β-esterase gene and its pseudogene -a duplicated pseudogene forms a functional complex with its parent gene, with regulatory consequences 15 .…”

Molecular Evolution of Glutathione S-Transferases in the Genus Drosophila

“…1; however, to formally test whether adaptive models fit the patterns of sequence divergence better than neutral models, we used two standard PAML comparisons (model M2a vs. M1a and M8 vs. M7; Yang and Nielsen 2002;Lynn et al 2005;Balakirev et al 2006). Of 22 sets of GSTs subjected to site-specific CODEML analyses, only GstD1 was found significant after Bonferroni correction for multiple tests (P-value ¼ 0.0014, which is ,0.05/22; Table 1).…”

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

“…In general, identifying various kinds of selection are classic focal points for evolutionary biologists, and codon models are also proving invaluable in studies of pathogenic drug resistance, disease progression, and epidemics dynamics, important in vaccine design and treatment strategies (Lemey, Derdelinckx, et al 2005;Lemey, Van Dooren, and Vandamme 2005;Chen and Lee 2006;Kosakovsky Pond, Frost, et al 2006;Seoighe et al 2007;Carvajal-Rodriguez et al 2008;Kosakovsky Pond et al 2008). Using codon models to study the evolution of gene families is also well documented (Bielawski and Yang 2003;Aguileta et al 2004;Balakirev et al 2006;Studer et al 2008). Whereas selection studies are still predominant, plenty of other applications are emerging.…”