Locus-Specific Decoupling of Base Composition Evolution at Synonymous Sites and Introns along the Drosophila melanogaster and Drosophila sechellia Lineages
| Autor: | Vanessa L. Bauer DuMont, Mark Wright, Nadia D. Singh, Charles F. Aquadro |
|---|---|
| Rok vydání: | 2009 |
| Předmět: |
0106 biological sciences
Genetics 0303 health sciences biology Intron Locus (genetics) biology.organism_classification 010603 evolutionary biology 01 natural sciences Drosophila sechellia 03 medical and health sciences base composition Molecular evolution Homogeneous Melanogaster Drosophila Drosophila melanogaster Research Articles substitution rates Ecology Evolution Behavior and Systematics Recombination 030304 developmental biology |
| Zdroj: | Genome Biology and Evolution |
| ISSN: | 1759-6653 |
| DOI: | 10.1093/gbe/evp008 |
| Popis: | Selection is thought to be partially responsible for patterns of molecular evolution at synonymous sites within numerous Drosophila species. Recently, "per-site" and likelihood methods have been developed to detect loci for which positive selection is a major component of synonymous site evolution. An underlying assumption of these methods, however, is a homogeneous mutation process. To address this potential shortcoming, we perform a complementary analysis making gene-by-gene comparisons of paired synonymous site and intron substitution rates toward and away from the nucleotides G and C because preferred codons are G or C ending in Drosophila. This comparison may reduce both the false-positive rate (due to broadscale heterogeneity in mutation) and false-negative rate (due to lack of power comparing small numbers of sites) of the per-site and likelihood methods. We detect loci with patterns of evolution suggestive of synonymous site selection pressures predominately favoring unpreferred and preferred codons along the Drosophila melanogaster and Drosophila sechellia lineages, respectively. Intron selection pressures do not appear sufficient to explain all these results as the magnitude of the difference in synonymous and intron evolution is dependent on recombination environment and chromosomal location in a direction supporting the hypothesis of selectively driven synonymous fixations. This comparison identifies 101 loci with an apparent switch in codon preference between D. melanogaster and D. sechellia, a pattern previously only observed at the Notch locus. |
| Databáze: | OpenAIRE |
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