About the Authors

David J Begun

To whom correspondence should be addressed. E-mail: djbegun@ucdavis.edu (DJB); akholloway@ucdavis.edu (AKH); chlangley@ucdavis.edu (CHL)

Affiliations Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America , Center for Population Biology, University of California Davis, Davis, California, United States of America

Alisha K Holloway

To whom correspondence should be addressed. E-mail: djbegun@ucdavis.edu (DJB); akholloway@ucdavis.edu (AKH); chlangley@ucdavis.edu (CHL)

Affiliations Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America , Center for Population Biology, University of California Davis, Davis, California, United States of America

Kristian Stevens

Affiliations Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America , Center for Population Biology, University of California Davis, Davis, California, United States of America

LaDeana W Hillier

Affiliation Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America

Yu-Ping Poh

Affiliations Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America , Center for Population Biology, University of California Davis, Davis, California, United States of America , Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan Authority , Research Center for Biodiversity, Academica Sinica, Taipei, Taiwan Authority

Matthew W Hahn

Affiliations Department of Biology, Indiana University, Bloomington, Indiana, United States of America , School of Informatics, Indiana University, Bloomington, Indiana, United States of America

Phillip M Nista

Affiliation Department of Biology, Indiana University, Bloomington, Indiana, United States of America

Corbin D Jones

Affiliations Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America , Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America

Andrew D Kern

Affiliations Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America , Center for Population Biology, University of California Davis, Davis, California, United States of America , Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America

Colin N Dewey

Affiliation Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America

Lior Pachter

Affiliations Department of Mathematics, University of California, Berkeley, California, United States of America , Department of Computer Science, University of California, Berkeley, California, United States of America

Eugene Myers

Affiliation Department of Computer Science, University of California, Berkeley, California, United States of America

Charles H Langley

To whom correspondence should be addressed. E-mail: djbegun@ucdavis.edu (DJB); akholloway@ucdavis.edu (AKH); chlangley@ucdavis.edu (CHL)

Affiliations Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America , Center for Population Biology, University of California Davis, Davis, California, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

The project was conceived by DJB and CHL. The D. yakuba assembly was produced by LWH. The D. yakuba/D. melanogaster alignment was by CND and LP. KS created the D. simulans assembly used in the analysis; its quality was evaluated by AKH and empirically tested by CDJ. An early version of the D. simulans assembly was by produced by EM. Population genetic analysis was performed by AKH, YPP, CHL, DJB, MWH, PMN, CDJ, KS, and ADK. The paper was written by DJB, AKH, and CHL, with assistance from several co-authors.