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Research Article

Long- and Short-Term Selective Forces on Malaria Parasite Genomes

  • Sanne Nygaard,

    Affiliations: Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark, Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark, Center for Social Evolution, University of Copenhagen, Copenhagen, Denmark

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  • Alexander Braunstein,

    Affiliations: Statistics Department, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, Google, Inc., Mountain View, California, United States of America

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  • Gareth Malsen,

    Affiliation: Wellcome Trust Sanger Institute, Cambridge, United Kingdom

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  • Stijn Van Dongen,

    Affiliation: RNA Genomics, European Bioinformatics Institute, Cambridge, United Kingdom

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  • Paul P. Gardner,

    Affiliation: Wellcome Trust Sanger Institute, Cambridge, United Kingdom

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  • Anders Krogh,

    Affiliations: Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark, Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark

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  • Thomas D. Otto,

    Affiliation: Wellcome Trust Sanger Institute, Cambridge, United Kingdom

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  • Arnab Pain,

    Affiliations: Wellcome Trust Sanger Institute, Cambridge, United Kingdom, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia

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  • Matthew Berriman,

    Affiliation: Wellcome Trust Sanger Institute, Cambridge, United Kingdom

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  • Jon McAuliffe,

    Affiliation: Statistics Department, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

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  • Emmanouil T. Dermitzakis mail,

    d.jeffares@ucl.ac.uk (DJ); emmanouil.dermitzakis@unige.ch (ED)

    Affiliations: Wellcome Trust Sanger Institute, Cambridge, United Kingdom, Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland

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  • Daniel C. Jeffares mail

    d.jeffares@ucl.ac.uk (DJ); emmanouil.dermitzakis@unige.ch (ED)

    Affiliations: Wellcome Trust Sanger Institute, Cambridge, United Kingdom, Department of Genetics, Evolution and Environment, University College London, United Kingdom

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  • Published: September 09, 2010
  • DOI: 10.1371/journal.pgen.1001099

About the Authors

Sanne Nygaard, Anders Krogh
Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
Sanne Nygaard, Anders Krogh
Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
Sanne Nygaard
Center for Social Evolution, University of Copenhagen, Copenhagen, Denmark
Alexander Braunstein, Jon McAuliffe
Statistics Department, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
Alexander Braunstein
Google, Inc., Mountain View, California, United States of America
Gareth Malsen, Paul P. Gardner, Thomas D. Otto, Arnab Pain, Matthew Berriman, Emmanouil T. Dermitzakis, Daniel C. Jeffares
Wellcome Trust Sanger Institute, Cambridge, United Kingdom
Stijn Van Dongen
RNA Genomics, European Bioinformatics Institute, Cambridge, United Kingdom
Arnab Pain
Computational Bioscience Research Center, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
Emmanouil T. Dermitzakis
Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
Daniel C. Jeffares
Department of Genetics, Evolution and Environment, University College London, United Kingdom

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: ETD DCJ. Performed the experiments: SN AB GM DCJ. Analyzed the data: SN SvD PPG TDO JM ETD DCJ. Contributed reagents/materials/analysis tools: AK TDO AP MB JM DCJ. Wrote the paper: SN ETD DCJ. Identified and characterized CEs, ran SISSIz, identified SNPs, conducted polymorphism analysis, collated analysis: DCJ. Conducted divergence and constraint analysis, integrated genome annotations and alignments, ran RNAz: SN. Created alignments: AB JM. Obtained and mapped P. falciparum reads to the reference: GM. Assisted with RNA-Seq transcriptome analysis: TDO. Contributed suggestions for analysis: AP MB. Initiated the study, assisted with data analysis: ETD.