title: Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
abstract: The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans.
authors.affiliation: Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America. djbegun@ucdavis.edu
authors.forename: David J
authors.initials: DJ
authors.lastname: Begun
authors.forename: Alisha K
authors.initials: AK
authors.lastname: Holloway
authors.forename: Kristian
authors.initials: K
authors.lastname: Stevens
authors.forename: Ladeana W
authors.initials: LW
authors.lastname: Hillier
authors.forename: Yu-Ping
authors.initials: YP
authors.lastname: Poh
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
authors.forename: Phillip M
authors.initials: PM
authors.lastname: Nista
authors.forename: Corbin D
authors.initials: CD
authors.lastname: Jones
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Kern
authors.forename: Colin N
authors.initials: CN
authors.lastname: Dewey
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
authors.forename: Eugene
authors.initials: E
authors.lastname: Myers
authors.forename: Charles H
authors.initials: CH
authors.lastname: Langley
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004330:Drosophila / Q000145:classification / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D049750:Genome, Insect; D023281:Genomics; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D014960:X Chromosome
chemical_list: D029721:Drosophila Proteins