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- Title
Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.
- Authors
Jackson, Benjamin C.; Campos, José L.; Haddrill, Penelope R.; Charlesworth, Brian; Kai Zeng
- Abstract
Four-fold degenerate coding sites formamajor component of the genome, and are often used tomake inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genomepolymorphismdata set from D. simulans. We analyzed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism data set from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitutionpattern inboth lineages is probablydue to an ancestral reduction in selectionintensity, andisunlikely tobe the result of an increase inmutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, weshow that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution.
- Subjects
DROSOPHILA evolution; GENETIC polymorphisms; GENETIC code; INTRONS; GENE conversion; INSECTS
- Publication
Genome Biology & Evolution, 2017, Vol 9, Issue 1, p102
- ISSN
1759-6653
- Publication type
Article
- DOI
10.1093/gbe/evw291