Dataset Information

Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.

ABSTRACT: In Drosophila, many studies have examined the short- or long-term evolution occurring across synonymous sites. Few, however, have examined both the recent and long-term evolution to gain a complete view of this selection. Here we have analyzed Drosophila ananassae DNA polymorphism and divergence data using several different methods, and have identified evidence of positive selection favoring preferred codons in both recent and long-term evolutionary time scale. Further in D. ananassae, the strength of selection for preferred codons was stronger on the X chromosome compared to the autosomes. We show that this stronger selection is not due to higher gene expression of X-linked genes. Analysis of the selectively neutral introns indicated that the X chromosome also had a preference for GC over AT nucleotides, potentially from GC-biased gene conversions (gcBGCs) that can also affect the base composition of synonymous sites. Thus selection for preferred codons and gcBGC both seem to be partially responsible for shaping the D. ananassae synonymous site evolution.

SUBMITTER: Choi JY

PROVIDER: S-EPMC5002260 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Publications

Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.

Choi Jae Young JY Aquadro Charles F CF

Journal of molecular evolution 20160801 1-2

In Drosophila, many studies have examined the short- or long-term evolution occurring across synonymous sites. Few, however, have examined both the recent and long-term evolution to gain a complete view of this selection. Here we have analyzed Drosophila ananassae DNA polymorphism and divergence data using several different methods, and have identified evidence of positive selection favoring preferred codons in both recent and long-term evolutionary time scale. Further in D. ananassae, the stren ...[more]

PMID: 27481397

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Project description:Evolution of protein sequences is largely governed by purifying selection, with a small fraction of proteins evolving under positive selection. The evolution at synonymous positions in protein-coding genes is not nearly as well understood, with the extent and types of selection remaining, largely, unclear. A statistical test to identify purifying and positive selection at synonymous sites in protein-coding genes was developed. The method compares the rate of evolution at synonymous sites (Ks) to that in intron sequences of the same gene after sampling the aligned intron sequences to mimic the statistical properties of coding sequences. We detected purifying selection at synonymous sites in approximately 28% of the 1,562 analyzed orthologous genes from mouse and rat, and positive selection in approximately 12% of the genes. Thus, the fraction of genes with readily detectable positive selection at synonymous sites is much greater than the fraction of genes with comparable positive selection at nonsynonymous sites, i.e., at the level of the protein sequence. Unlike other genes, the genes with positive selection at synonymous sites showed no correlation between Ks and the rate of evolution in nonsynonymous sites (Ka), indicating that evolution of synonymous sites under positive selection is decoupled from protein evolution. The genes with purifying selection at synonymous sites showed significant anticorrelation between Ks and expression level and breadth, indicating that highly expressed genes evolve slowly. The genes with positive selection at synonymous sites showed the opposite trend, i.e., highly expressed genes had, on average, higher Ks. For the genes with positive selection at synonymous sites, a significantly lower mRNA stability is predicted compared to the genes with negative selection. Thus, mRNA destabilization could be an important factor driving positive selection in nonsynonymous sites, probably, through regulation of expression at the level of mRNA degradation and, possibly, also translation rate. So, unexpectedly, we found that positive selection at synonymous sites of mammalian genes is substantially more common than positive selection at the level of protein sequences. Positive selection at synonymous sites might act through mRNA destabilization affecting mRNA levels and translation.

Dataset Information

Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.

Publications

Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.

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