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Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
Authors:David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun  David J Begun
Institution:1 Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America, 2 Center for Population Biology, University of California Davis, Davis, California, United States of America, 3 Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America, 4 Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan Authority, 5 Research Center for Biodiversity, Academica Sinica, Taipei, Taiwan Authority, 6 Department of Biology, Indiana University, Bloomington, Indiana, United States of America, 7 School of Informatics, Indiana University, Bloomington, Indiana, United States of America, 8 Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America, 9 Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America, 10 Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America, 11 Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America, 12 Department of Mathematics, University of California, Berkeley, California, United States of America, 13 Department of Computer Science, University of California, Berkeley, California, United States of America
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.
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