Patterns of molecular variation and evolution in Drosophila americana and its relatives

• Published in: Genetics (Austin) Vol. 176; no. 4; pp. 2293 - 2305
• Main Authors: Maside, X, Charlesworth, B
• Format: Journal Article
• Language: English
• Published: United States Genetics Soc America 01-08-2007; Genetics Society of America; Copyright © 2007 by the Genetics Society of America
• Subjects: amino acid substitution; Animals; Base Composition; Changes; Chromosomes; Codon - genetics; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; Drosophila; Drosophila - classification; Drosophila - genetics; Drosophila americana; Drosophila ezoana; Drosophila littoralis; Drosophila montana; Drosophila Proteins - genetics; Drosophila virilis; evolution; Evolution, Molecular; Female; Genes, Insect; genetic polymorphism; Genetic Variation; Genetics; Investigations; Methods; Molecular Sequence Data; nucleotide sequences; Phylogeny; RNA, Untranslated - genetics; silent polymorphism; Species Specificity; Studies; X Chromosome - genetics
• ISSN: 0016-6731; 1943-2631; 1943-2631
• DOI: 10.1534/genetics.107.071191

We present the results of a survey of DNA sequence variability at X-linked and autosomal loci in Drosophila americana and of patterns of DNA sequence evolution among D. americana and four other related species in the virilis group of Drosophila. D. americana shows a typical level of silent polymorphism for a Drosophila species, but has an unusually low ratio of nonsynonymous to silent variation. Both D. virilis and D. americana also show a low ratio of nonsynonymous to synonymous substitutions along their respective lineages since the split from their common ancestor. The proportion of amino acid substitutions between D. americana and its relatives that are caused by positive selection, as estimated by extensions of the McDonald-Kreitman test, appears to be unusually high. We cannot, however, exclude the possibility that this reflects a recent increase in the intensity of selection on nonsynonymous mutations in D. americana and D. virilis. We also find that base composition at neutral sites appears to be in overall equilibrium among these species, but there is evidence for departure from equilibrium for codon usage in some lineages.