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  1. Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
    • Ying Zhen,
    • Christian D. Huber,
    • Robert W. Davies,
    • and Kirk E. Lohmueller
    Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
    ...nonsynonymous mutations in humans, mice, and Drosophila melanogaster by examining patterns of polymorphism and divergence. We develop a novel composite likelihood framework to test whether these parameters differ across species. Overall, we reject a model with the same p+ and s+ of beneficial mutations across...
  2. Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
    • Viola Nolte,
    • Ram Vinay Pandey,
    • Robert Kofler,
    • and Christian Schlötterer
    Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
    ...Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana Viola Nolte , Ram Vinay Pandey , Robert Kofler and Christian Schlötterer 1 Institut für Populationsgenetik...
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  3. Research: Genome-wide signals of positive selection in human evolution
    • David Enard,
    • Philipp W. Messer,
    • and Dmitri A. Petrov
    Genome Res. June 2014 24: 885-895; Published in Advance March 11, 2014, doi:10.1101/gr.164822.113
    ...design of Hernandez et al. (2011) (also implemented in Drosophila by Sattath et al. 2011) is strongly biased against finding signatures of positive selection in the human and all other s with sharply variable levels of genomic constraint. This is because, as we show in the Results, nonsynonymous...
  4. Research: Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
    • Asher D. Cutter and
    • Jae Young Choi
    Genome Res. August 2010 20: 1103-1111; Published in Advance May 27, 2010, doi:10.1101/gr.104331.109
    ...a signature of more effective purifying selection in high-recombination regions of the genome. Finally, we identify an emerging contrast between widespread adaptive hitchhiking effects in species with large outcrossing populations (e.g., Drosophila ) versus pervasive background selection effects...
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  5. Research: Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans
    • Dee R. Denver,
    • Dana K. Howe,
    • Larry J. Wilhelm,
    • Catherine A. Palmer,
    • Jennifer L. Anderson,
    • Kevin C. Stein,
    • Patrick C. Phillips,
    • and Suzanne Estes
    Genome Res. December 2010 20: 1663-1671; Published in Advance October 29, 2010, doi:10.1101/gr.108191.110
    ...scores for all possible pairwise combinations of C. elegans genes that were found to harbor a MA12 or recovery-line mutation based on numerous underlying feature data sources (yeast two-hybrid experiments, microarray data, etc.) from C. elegans, Drosophila melanogaster, and Saccharomyces cerevisiae...
  6. LETTER: Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
    • Romain A. Studer,
    • Simon Penel,
    • Laurent Duret,
    • and Marc Robinson-Rechavi
    Genome Res. September 2008 18: 1393-1402; Published in Advance June 18, 2008, doi:10.1101/gr.076992.108
    ...GO +: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments . Nucleic Acids Res. 35 : W91 – W96 . ↵ Andolfatto, P. ( 2007 ) Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila...
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  7. ERRATUM: Erratum Genome Res. January 2008 18: 197
    ...genome;18/1/197 1088-9051 Erratum Erratum Genome Research 17: 1755–1762 (2007) Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster   Peter Andolfatto Corrected values of π S and Ka were plotted in Figure 1B, not residuals, as reported in the text...
  8. Review: Population genetic inference from genomic sequence variation
    • John E. Pool,
    • Ines Hellmann,
    • Jeffrey D. Jensen,
    • and Rasmus Nielsen
    Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
    ...of the human generated by reduced representation shotgun sequencing. Nature 407: 513–516. Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149–1152. Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster...
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