About the Authors

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

Alexander Braunstein

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

Gareth Malsen

Affiliation Wellcome Trust Sanger Institute, Cambridge, United Kingdom

Stijn Van Dongen

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

Paul P. Gardner

Affiliation Wellcome Trust Sanger Institute, Cambridge, United Kingdom

Anders Krogh

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

Thomas D. Otto

Affiliation Wellcome Trust Sanger Institute, Cambridge, United Kingdom

Arnab Pain

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

Matthew Berriman

Affiliation Wellcome Trust Sanger Institute, Cambridge, United Kingdom

Jon McAuliffe

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

Emmanouil T. Dermitzakis

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

Daniel C. Jeffares

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

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.