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

@article{citeulike:2016790, 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.}, author = {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. }, citeulike-article-id = {2016790}, doi = {10.1371/journal.pbio.0050310}, journal = {PLoS Biology}, keywords = {drosophila, molecular\_evolution, species\_divergence}, month = {November}, number = {11}, pages = {e310+}, posted-at = {2008-01-20 16:53:21}, priority = {2}, title = {Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans}, url = {http://dx.doi.org/10.1371/journal.pbio.0050310}, volume = {5}, year = {2007} }

TY - JOUR ID - citeulike:2016790 L3 - citeulike-article-id:2016790 TI - Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans JF - PLoS Biology VL - 5 IS - 11 SP - e310 N2 - 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. KW - drosophila KW - molecular_evolution KW - species_divergence AU - Begun, David AU - Holloway, Alisha AU - Stevens, Kristian AU - Hillier, Ladeana AU - Poh, Yu-Ping AU - Hahn, Matthew AU - Nista, Phillip AU - Jones, Corbin AU - Kern, Andrew AU - Dewey, Colin AU - Pachter, Lior AU - Myers, Eugene AU - Langley, Charles PY - 2007/11/01/ UR - http://dx.doi.org/10.1371/journal.pbio.0050310 ER -