Arabidopsis evolution study pulled

Plant biologists have withdrawn a study on linkurl:__Arabidopsis thaliana__;http://www.the-scientist.com/article/display/54194/ evolution published in a 2004 issue of __Science__, saying one of its conclusions was marred by contamination, according to a retraction appearing today (Apr. 10) in the journal. The original linkurl:paper,;http://www.sciencemag.org/cgi/content/abstract/306/5704/2081 authored by then North Carolina State University genomicist linkurl:Michael Purugganan;http://www.the-s

Bob Grant
Bob Grant

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Apr 9, 2008
Plant biologists have withdrawn a study on linkurl:__Arabidopsis thaliana__;http://www.the-scientist.com/article/display/54194/ evolution published in a 2004 issue of __Science__, saying one of its conclusions was marred by contamination, according to a retraction appearing today (Apr. 10) in the journal. The original linkurl:paper,;http://www.sciencemag.org/cgi/content/abstract/306/5704/2081 authored by then North Carolina State University genomicist linkurl:Michael Purugganan;http://www.the-scientist.com/article/display/13399/ and a team of international colleagues, suggested self-pollination had evolved in __A. thaliana__ after a period of rapid evolution - or a selective sweep - after the most recent ice age. It has been cited more than 40 times, according to ISI. The team pulled the paper because of "spurious PCR amplification by the primers and/or by DNA contaminations," according to the published retraction. Purugganan told __The Scientist__ that in four out of the 21 __A. thaliana__ samples the team genotyped, DNA contamination caused PCR primers to amplify a gene allele (__ΨSCR1__) that in actuality was absent from a particular...
a 2004 issue of __Science__, saying one of its conclusions was marred by contamination, according to a retraction appearing today (Apr. 10) in the journal. The original linkurl:paper,;http://www.sciencemag.org/cgi/content/abstract/306/5704/2081 authored by then North Carolina State University genomicist linkurl:Michael Purugganan;http://www.the-scientist.com/article/display/13399/ and a team of international colleagues, suggested self-pollination had evolved in __A. thaliana__ after a period of rapid evolution - or a selective sweep - after the most recent ice age. It has been cited more than 40 times, according to ISI. The team pulled the paper because of "spurious PCR amplification by the primers and/or by DNA contaminations," according to the published retraction. Purugganan told __The Scientist__ that in four out of the 21 __A. thaliana__ samples the team genotyped, DNA contamination caused PCR primers to amplify a gene allele (__ΨSCR1__) that in actuality was absent from a particular haplotype. "We thought we were getting something when in fact we were amplifying some contaminated DNA," Purugganan said. After the publication of the __Science__ paper in December 2004, Purugganan and his postdoc at the time, Kentaro Shimizu, began hearing "second-hand from colleagues" that they were not finding the __ΨSCR1__ in __A. thaliana__ samples they were genotyping. "When we heard this," Purugganan recalls, "we said, 'We've got to figure this out.'" Purugganan and Shimizu realized their error after a few months of reanalyzing the data, and concluded that the extent of the DNA contamination was likely minor but enough to change the conclusion that self-pollination, or selfing, evolved only once throughout the entire __A. thaliana__ species. "It was probably minute amounts [of DNA] that were in the buffer or something," Purugganan said. "We still believe there was a selective sweep, but it was not species wide." Shimizu, Purugganan and colleagues published an linkurl:updated study;http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-294X.2007.03605.x this January in an issue of __Molecular Ecology__, in which they reanalyzed the botched data and concluded that only the European population of __Arabidopsis__ experienced the selective sweep. "We realized that the data were showing us that there was not just one origin of selfing in __Arabidopsis__," Purugganan said. "The picture that is emerging now is that selfing has evolved multiple times. It becomes a really fascinating story now." Purugganan, who is now at New York University, said that discovering the errors in his 2004 Science paper led to a new view of the evolution of self-pollination in __A. thaliana__, in which the phenomenon evolved once in European and at least one separate time in African and Asian populations. "By looking at something and knowing there was an error, we were not only able to correct it," said Purugganan, "it's actually more interesting than the original story."

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