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

By D. Begun, A. K. Holloway, Kristian Stevens, LaDeana W. Hillier, Yu-Ping Poh, Matthew W. Hahn, Phil Nista, Corbin D. Jones, Andrew D. Kern, Colin N. Dewey and 3 more. PLoS Biology, 2007

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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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/4333c881c27e7f96fe3e6ee0bf83f19df5843c9b

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Citations in the corpus

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Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags (2010, background): “Depending upon demographic factors such as population size and structure, and the strength and nature of selection [117,118], blocks of linkage disequilibrium (LD) can be as small as a few hundred base pairs (as in flies [105]) to several dozens of kilobases (kb) (as in dogs [119]).”
Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow (2014, background): “Consequently, this means that linked selection in extant populations will not cause the appearance of ‘islands’ of high divergence in d XY , although linked selection in ancestral populations can actually lower the value of d XY (Begun et al. 2007).”
Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation (2013, background): “In accord with this expectation, it is found that diversity increases with recombination rate and decreases with the density of functional sites (Begun et al., 2007; Shapiro et al., 2007).”
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data (2009, background): “The analysis of DNA polymorphisms is a powerful approach to understand the evolutionary process and to establish the functional significance of particular genomic regions (Nielsen, 2005; Rosenberg and Nordborg, 2002; Begun et al. , 2007).”
Divergent selection and heterogeneous genomic divergence (2009, background): “For example, loci under divergent selection and those tightly physically linked to them may exhibit stronger differentiation than neutral regions with weak or no linkage to such loci.”