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

Year: 2007
Type: article
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.
Source: PLoS Biology
DOI: 10.1371/journal.pbio.0050310
Authors: David J Begun, Alisha K Holloway, Kristian Stevens, LaDeana W Hillier, Yu-Ping Poh, Matthew W Hahn, Phillip M Nista, Corbin D Jones, Andrew D Kern, Colin N Dewey, Lior Pachter, Eugene Myers, Charles H Langley
Institutions: University of California, Davis, Washington University in St. Louis, National Tsing Hua University, Biodiversity Research Center, Academia Sinica, Academia Sinica, Indiana University Bloomington, Indiana University, University of North Carolina at Chapel Hill, University of California, Santa Cruz, University of Wisconsin–Madison, University of California, Berkeley
Language: English
Subfield: Genetics
Open Access status: gold
Estimated APC paid: $5,500
Funders: National Science Foundation, Purdue University, National Science Council, National Institutes of Health, National Human Genome Research Institute, National Institute of General Medical Sciences
Awards: CAREER: Comparison and Annotation of Multiple Whole Genomes, G1851494342, G2382515120, G2761153153, G3152554797, G3154946093, LINKAGE DISEQUILIBRIUM MAPPING OF COMPLEX-TRAIT GENES, G5520316217, Genetic Analysis of Complex Adaptive Traits, Postdoctoral Research Fellowship in Biological Informatics for FY 2005, G83040846, Cross-species gene finding and annotation
OpenAlex ID: W2126334905
FWCI: 31.49
Cites: 140
Cited by: 626
Related to: 10