Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
Creators
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1.
University of California, Davis
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2.
Washington University in St. Louis
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3.
National Tsing Hua University
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4.
Academia Sinica
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Indiana University Bloomington
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6.
University of North Carolina at Chapel Hill
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7.
University of California, Santa Cruz
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8.
University of Wisconsin–Madison
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9.
University of California, Berkeley
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.
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 (http://www.ncbi.nlm.nih.gov/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.Attached Files
Published - journal.pbio.0050310.PDF
Supplemental Material - 151547.zip
Files
151547.zip
Additional details
Identifiers
- PMCID
- PMC2062478
- Eprint ID
- 74852
- Resolver ID
- CaltechAUTHORS:20170307-114846354
Funding
- NIH
- R01 GM071926
- NIH
- R01HG2107–3
- NIH
- HG02942-01A1
- NSF Postdoctoral Fellowship
- 0434670
- Indiana University-Purdue University
- NSF
- DEB-0512106
- Howard Hughes Medical Institute (HHMI)
- Academia Sinica
- National Science Council (Taipei)
- 9402917-1-007–011
- NIH
- R01-HG02362–03
- NSF
- CCF-0347992
- National Human Genome Research Institute
Dates
- Created
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2017-03-07Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field