Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.
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.
Begun
David J
DJ
Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America. djbegun@ucdavis.edu
Holloway
Alisha K
AK
Stevens
Kristian
K
Hillier
Ladeana W
LW
Poh
Yu-Ping
YP
Hahn
Matthew W
MW
Nista
Phillip M
PM
Jones
Corbin D
CD
Kern
Andrew D
AD
Dewey
Colin N
CN
Pachter
Lior
L
Myers
Eugene
E
Langley
Charles H
CH
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
D029721:Drosophila Proteins