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Published online on March 19, 2007, 10.1073/pnas.0700890104
PNAS | March 27, 2007 | vol. 104 | no. 13 | 5698-5703


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BIOLOGICAL SCIENCES / POPULATION BIOLOGY
Extreme genomic variation in a natural population

Kerrin S. Small*, Michael Brudno{dagger}, Matthew M. Hill*, and Arend Sidow*,{ddagger}

*Departments of Genetics and Pathology, Stanford University Medical Center, Stanford, CA 94305-5324; and {dagger}Department of Computer Science, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5S 3G4

Communicated by Robert H. Waterston, University of Washington, Seattle, WA, January 31, 2007 (received for review September 7, 2006)

Whole-genome sequence data from samples of natural populations provide fertile grounds for analyses of intraspecific variation and tests of population genetic theory. We show that the urochordate Ciona savignyi, one of the species of ocean-dwelling broadcast spawners commonly known as sea squirts, exhibits the highest rates of single-nucleotide and structural polymorphism ever comprehensively quantified in a multicellular organism. We demonstrate that the cause for the extreme heterozygosity is a large effective population size, and, consistent with prediction by the neutral theory, we find evidence of strong purifying selection. These results constitute in-depth insight into the dynamics of highly polymorphic genomes and provide important empirical support of population genetic theory as it pertains to population size, heterozygosity, and natural selection.

ciona | genome | heterozygosity | population size

Author contributions: K.S.S. and A.S. designed research; K.S.S., M.B., and M.M.H. performed research; M.B. and M.M.H. contributed new reagents/analytic tools; K.S.S. and A.S. analyzed data; and K.S.S. and A.S. wrote the paper.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/cgi/content/full/0700890104/DC1.

{ddagger}To whom correspondence should be addressed. E-mail: arend{at}stanford.edu

© 2007 by The National Academy of Sciences of the USA


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