title: Population genomic analysis of base composition evolution in Drosophila melanogaster.
abstract: The relative importance of mutation, selection, and biased gene conversion to patterns of base composition variation in Drosophila melanogaster, and to a lesser extent, D. simulans, has been investigated for many years. However, genomic data from sufficiently large samples to thoroughly characterize patterns of base composition polymorphism within species have been lacking. Here, we report a genome-wide analysis of coding and noncoding polymorphism in a large sample of inbred D. melanogaster strains from Raleigh, North Carolina. Consistent with previous results, we observed that AT mutations fix more frequently than GC mutations in D. melanogaster. Contrary to predictions of previous models of codon usage in D. melanogaster, we found that synonymous sites segregating for derived AT polymorphisms were less skewed toward low frequencies compared with sites segregating a derived GC polymorphism. However, no such pattern was observed for comparable base composition polymorphisms in noncoding DNA. These results suggest that AT-ending codons could currently be favored by natural selection in the D. melanogaster lineage.
authors.affiliation: Institute of Molecular and Cellular Biology, National Tsing Hua University, Taiwan, Republic of China. elfinpoh@gmail.com
authors.forename: Yu-Ping
authors.initials: YP
authors.lastname: Poh
authors.forename: Chau-Ti
authors.initials: CT
authors.lastname: Ting
authors.forename: Hua-Wen
authors.initials: HW
authors.lastname: Fu
authors.forename: Charles H
authors.initials: CH
authors.lastname: Langley
authors.forename: David J
authors.initials: DJ
authors.lastname: Begun
mesh_terms: D000818:Animals; D001482:Base Composition; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D049750:Genome, Insect; D009154:Mutation; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D011153:Population / Q000235:genetics; D020506:Untranslated Regions
chemical_list: D020506:Untranslated Regions