title: Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences.
abstract: BACKGROUND
  Several lines of evidence suggest that codon usage in the Drosophila saltans and D. willistoni lineages has shifted towards a less frequent use of GC-ending codons. Introns in these lineages show a parallel shift toward a lower GC content. These patterns have been alternatively ascribed to either a shift in mutational patterns or changes in the definition of preferred and unpreferred codons in these lineages.
  
  
  CONCLUSIONS
  To gain additional insight into this question, we quantified background substitutional patterns in the saltans/willistoni group using inactive copies of a novel, Q-like retrotransposable element. We demonstrate that the pattern of background substitutions in the saltans/willistoni lineage has shifted to a significant degree, primarily due to changes in mutational biases. These differences predict a lower equilibrium GC content in the genomes of the saltans/willistoni species compared with that in the D. melanogaster species group. The magnitude of the difference can readily account for changes in intronic GC content, but it appears insufficient to explain changes in codon usage within the saltans/willistoni lineage.
  
  
  CONCLUSIONS
  We suggest that the observed changes in codon usage in the saltans/willistoni clade reflects either lineage-specific changes in the definitions of preferred and unpreferred codons, or a weaker selective pressure on codon bias in this lineage.
authors.affiliation: Department of Biological Sciences, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA. ndsingh@stanford.edu
authors.forename: Nadia D
authors.initials: ND
authors.lastname: Singh
authors.forename: Peter F
authors.initials: PF
authors.lastname: Arndt
authors.forename: Dmitri A
authors.initials: DA
authors.lastname: Petrov
mesh_terms: D000818:Animals; D001482:Base Composition; D003062:Codon / Q000235:genetics*; D004330:Drosophila / Q000145:classification* / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics* / Q000378:metabolism; D020862:GC Rich Sequence / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D016296:Mutagenesis / Q000235:genetics; D010802:Phylogeny; D013045:Species Specificity
chemical_list: D003062:Codon; D029721:Drosophila Proteins