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Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

Begun, David J. and Holloway, Alisha K. and Stevens, Kristian and Hillier, LaDeana W. and Poh, Yu-Ping and Hahn, Matthew W. and Nista, Phillip M. and Jones, Corbin D. and Kern, Andrew D. and Dewey, Colin N. and Pachter, Lior and Myers, Eugene and Langley, Charles H. (2007) Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biology, 5 (11). Art. No. e310. ISSN 1545-7885. PMCID PMC2062478. doi:10.1371/journal.pbio.0050310.

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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.

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Pachter, Lior0000-0002-9164-6231
Additional Information:© 2007 Begun et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: March 19, 2007; Accepted: September 26, 2007; Published: November 6, 2007. DJB was supported by National Institutes of Health (NIH) Grant R01 GM071926. CHL was supported by NIH R01HG2107–3 and NIH HG02942-01A1. AKH was supported by a National Science Foundation (NSF) Postdoctoral Fellowship in Biological Informatics (Grant No. 0434670). MWH and PMN were supported by an Indiana University-Purdue University Collaborations in Life Sciences and Informatics Research grant to MWH. MWH was also supported by an NSF Postdoctoral Fellowship in Biological Informatics while he was at UC-Davis. CDJ was supported by NSF grant DEB 0512106. ADK was supported by a Howard Hughes Predoctoral Fellowship. Y-P. Poh was supported by a graduate student fellowship (Academica Sinica) and Grant NSC 9402917-1-007–011. LP and CD were supported by NIH R01-HG02362–03 and NSF grant CCF 03–47992. Generation of the D. simulans and D. yakuba sequences was supported by grants from the National Human Genome Research Institute. We gratefully acknowledge the following members of the Washington University Medical School Genome Sequencing Center: Asif T. Chinwalla, Holland Cordum, Lucinda A. Fulton, Robert S. Fulton, Elaine M. Mardis, Joanne Nelson, John Osborne, Kymberlie H. Pepin, Patrick Minx, John Spieth, Rick Wilson, Jian Xu, Shiaw-Pyng Yang, and especially Sandra W. Clifton for her role in shepherding this project. D. Barbash and H. Lindfors provided assistance in the laboratory at UC-Davis. J. Anderson alerted us to the possibility that the sim4 and sim6 libraries could be cross-contaminated and also provided many useful comments on the paper. We also thank M. Noor, T. Mitchell-Olds, and three anonymous reviewers for comments. Author Contributions: The project was conceived by DJB and CHL. The D. yakuba assembly was produced by LWH. The D. yakuba/D. melanogaster alignment was by CND and LP. KS created the D. simulans assembly used in the analysis; its quality was evaluated by AKH and empirically tested by CDJ. An early version of the D. simulans assembly was by produced by EM. Population genetic analysis was performed by AKH, YPP, CHL, DJB, MWH, PMN, CDJ, KS, and ADK. The paper was written by DJB, AKH, and CHL, with assistance from several co-authors. Accession Numbers: The GenBank ( accession number for D. yakuba is AAEU01000000 (version 1) and for the D. simulans w501 whole-genome shotgun assembly is TBS-AAEU01000000 (version 1). The authors have declared that no competing interests exist.
Funding AgencyGrant Number
NIHR01 GM071926
NSF Postdoctoral Fellowship0434670
Indiana University-Purdue UniversityUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Academia SinicaUNSPECIFIED
National Science Council (Taipei)9402917-1-007–011
National Human Genome Research InstituteUNSPECIFIED
Issue or Number:11
PubMed Central ID:PMC2062478
Record Number:CaltechAUTHORS:20170307-114846354
Persistent URL:
Official Citation:Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh Y-P, Hahn MW, et al. (2007) Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biol 5(11): e310. doi:10.1371/journal.pbio.0050310
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74852
Deposited By: George Porter
Deposited On:07 Mar 2017 20:45
Last Modified:11 Nov 2021 05:30

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