To find the most rapidly evolving regions in the yeast genome we compared most of chromosome III from three closely related lineages of the wild yeast Saccharomyces paradoxus. Unexpectedly, the centromere appears to be the fastest-evolving part of the chromosome, evolving even faster than DNA sequences unlikely to be under selective constraint (i.e., synonymous sites after correcting for codon usage bias and remnant transposable elements). Centromeres on other chromosomes also show an elevated rate of nucleotide substitution. Rapid centromere evolution has also been reported for some plants and animals and has been attributed to selection for inclusion in the egg or the ovule at female meiosis. But Saccharomyces yeasts have symmetrical meioses with all four products surviving, thus providing no opportunity for meiotic drive. In addition, yeast centromeres show the high levels of polymorphism expected under a neutral model of molecular evolution. We suggest that yeast centromeres suffer an elevated rate of mutation relative to other chromosomal regions and they change through a process of “centromere drift,” not drive.


  • Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. EU444725, EU444726, and EU444121EU444533.

  • 1 Present address: Faculty of Life Sciences, University of Manchester, Oxford Rd., Manchester M13 9PT, United Kingdom.

  • 2 Present address: Department of Entomology, The Natural History Museum, Cromwell Rd., London SW7 5BD, United Kingdom.

  • Communicating editor: D. Begun

  • Received October 30, 2007.
  • Accepted February 8, 2008.
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