Population genomics:: Whole-genome analysis of polymorphism and divergence in Drosophila simulans

被引：511

作者：

Begun, David J. ^{[1
,2
]}

Holloway, Alisha K. ^{[1
,2
]}

Stevens, Kristian ^{[1
,2
]}

Hillier, LaDeana W. ^{[3
]}

Poh, Yu-Ping ^{[1
,2
,4
,5
]}

Hahn, Matthew W. ^{[6
,7
]}

Nista, Phillip M.

Jones, Corbin D. ^{[8
,9
]}

Kern, Andrew D. ^{[1
,2
,10
]}

Dewey, Colin N. ^{[11
]}

Pachter, Lior ^{[12
,13
]}

Myers, Eugene ^{[13
]}

Langley, Charles H. ^{[1
,2
]}

机构：

[1] Univ Calif Davis, Dept Ecol & Evolut, Davis, CA 95616 USA

[2] Univ Calif Davis, Ctr Populat Biol, Davis, CA 95616 USA

[3] Washington Univ, Genome Sequence Ctr, St Louis, MO USA

[4] Natl Tsing Hua Univ, Inst Mol & Cellular Biol, Hsinchu 300, Taiwan

[5] Acad Sinica, Res Ctr Biodivers, Taipei 115, Taiwan

[6] Indiana Univ, Dept Biol, Bloomington, IN USA

[7] Indiana Univ, Sch Informat, Bloomington, IN USA

[8] Univ N Carolina, Dept Biol, Chapel Hill, NC USA

[9] Univ N Carolina, Caolina Ctr Genome Sci, Chapel Hill, NC USA

[10] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[11] Univ Wisconsin, Dept Biostat & Med Informat, Madison, WI USA

[12] Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA

[13] Univ Calif Berkeley, Dept Comp Sci, Berkeley, CA 94720 USA

来源：

PLOS BIOLOGY | 2007年 / 5卷 / 11期

关键词：

D O I：

10.1371/journal.pbio.0050310

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2534 / 2559

页数：26

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