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Retraction of Shimizu et al., Science 306 (5704) 2081-2084.

Science 11 April 2008:
Vol. 320. no. 5873, p. 176
DOI: 10.1126/science.320.5873.176a
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Letters

Retraction

In the Report "Darwinian selection on a selfing locus" (1), we concluded that a species-wide selective sweep was associated with the rise of selfing in A. thaliana. We have reinvestigated the sequence and structure of alleles at the S pseudo locus and now find that spurious PCR amplification by the primers and/or by DNA contaminations resulted in our report of the PsiSCR1 and PsiSCR2/3 sequence from the accessions with haplotype B (CS902 ecotype) and haplotype C (CS1044, CS6751, and CS6764 ecotypes). Instead, haplogroup C either does not have an SCR allele, or if it is present it is so divergent as to be undetectable by PCR or Southern blotting. In CS902, which has a haplotype group B at the S pseudolocus, we and other groups (2) have isolated a distinct and novel SCR allele. When these corrections are made to the data, the species-wide nature of the selective sweep can no longer be supported.

We have, however, conducted further experiments and reanalysis to characterize these alleles and resolved discrepancies with previous studies (2, 3). We describe this reanalysis in a paper in the journal Molecular Ecology (4). In this paper, we report that PsiSCR1 and its derivative alleles spread to 94% frequency in a collection of 297 accessions. We conclude that a selective sweep did occur but was confined to European populations of A. thaliana, and that selfing appears to have evolved independently within this species. Moreover, our finding of three SRK haplotype groups, plus the very low diversity in the PsiSCR1 locus in most of the European accessions is still supported. Nevertheless, given that one of our previous conclusions is no longer tenable and in the interests of maintaining the integrity of the scientific literature, we retract the Report. Dr. Purugganan, as the senior author of the paper, takes full responsibility for these genotyping errors and apologizes for any difficulties it may have caused.

P. Awadalla (1) did not sign this Retraction because he does not support the interpretation of K.K.S. and M.D.P. above and thereafter (4) as sufficient evidence of a European sweep, and he was not involved in any data collection (1, 4). However, he agrees that Shimizu et al. (1) should be retracted.

Kentaro K. Shimizu
Institute of Plant Biology
University of Zurich
Zurich, Switzerland

Jennifer M. Reininga
Institute for Genome Sciences and Policy
Duke University
Durham, NC 27708, USA

*In the 2004 Report, Jennifer M. Reininga's name was listed as Jennifer M. Cork.

Ana L. Caicedo
Department of Biology
University of Massachusetts
Amherst, MA 01003, USA

Charlotte A. Mays
Department of Genetics
North Carolina State University
Raleigh, NC 27695, USA

Richard C. Moore
Department of Botany
Miami University
Oxford, OH 45056, USA

Kenneth M. Olsen
Department of Biology
Washington University
St. Louis, MO 63130, USA

Stephanie Ruzsa
Department of Genetics
North Carolina State University
Raleigh, NC 27695, USA

Graham Coop
Department of Human Genetics
University of Chicago
Chicago, IL 60637, USA

Carlos D. Bustamante
Department of Biological Statistics and Computational Biology
Cornell University
Ithaca, NY 14853, USA

Michael D. Purugganan
Department of Biology
New York University
New York, NY 10003, USA

References

  1. K. K. Shimizu et al., Science 306, 2081 (2004).
  2. C. Tang et al., Science 317, 1070 (2007).
  3. S. Sherman-Broyles et al., Plant Cell 19, 94 (2007).
  4. K. K. Shimizu, R. Shimizu-Inatsugi, T. Tsuchimatsu, M. D. Purugganan, Mol. Ecol. 17, 704 (2008).




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Science. ISSN 0036-8075 (print), 1095-9203 (online)