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PMID: 17988176 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.

PLoS biology ·Vol. 5 ·No. 11 ·2007-11-06 ·Pages e310

Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH

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.

MeSH Terms
Animals Chromosome Mapping Drosophila/classification,genetics Drosophila Proteins/genetics Evolution, Molecular Genetic Variation Genetics, Population Genome, Insect Genomics Linkage Disequilibrium Models, Genetic Molecular Sequence Data Polymorphism, Genetic X Chromosome
Chemicals
Drosophila Proteins
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Begun David J
Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America. [email protected]
Holloway Alisha K
Stevens Kristian
Hillier Ladeana W
Poh Yu-Ping
Hahn Matthew W
Nista Phillip M
Jones Corbin D
Kern Andrew D
Dewey Colin N
Pachter Lior
Myers Eugene
Langley Charles H
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Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
DOI
10.1371/journal.pbio.0050310
Email
[email protected]
Published
2007-11-06
Pages
e310
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC2062478
Subset
IM
Grants
NHGRI NIH HHS · R01 HG002942 · United States
NHGRI NIH HHS · R01HG2107-3 · United States
NIGMS NIH HHS · R01 GM071926 · United States
NHGRI NIH HHS · R01-HG02362-03 · United States
NHGRI NIH HHS · R01 HG002107 · United States
NHGRI NIH HHS · HG02942-01A1 · United States
NHGRI NIH HHS · R01 HG002362 · United States
Databases
GENBANK
AAEU01000000
External Links
PubMed source DOI: 10.1371/journal.pbio.0050310 PMC Full Text View journal details
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