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Figure 1

Two examples of imprecise intron losses. (A) The gene lost both an intron and a 21-bp-long downstream exon. The downstream intron was intact and did not lose any nucleotides; its splicing was supported by > 10 RNA-Seq reads. The splicing of the target intron in was also supported by > 10 RNA-Seq reads and by EST asmbl_392.tomatov23pasa_pasa4. The assembly of the variation site in was supported by nine different Whole Genome Shotgun (WGS) reads. (B) The gene lost a 204-bp-long intron, a 22-bp-long segment from an upstream exon and a 9-bp-long segment from a downstream exon. This deletion occurred in the 3'-UTR and did not inactivate the gene, as supported by >10 RNA-Seq reads. The successful splicing of the target intron in was supported by > 10 RNA-Seq reads. The assembly of the variation site in was supported by > 10 WGS reads. For details of the RNA-Seq and WGS reads and other intron losses, see Additional file 2 and Additional file 3 .

The species A. thaliana diverged from its relative Arabidopsis lyrata less than ten million years ago [ 18 ]. In comparing the genomes of these species, we found 17 IILs in A. thaliana (Additional file 3 ). A close examination of 114 cases of intron loss from A. thaliana that were reported in a previous study [ 19 ] revealed that 104 of these cases, which occurred in 98 genes, were PILs, two were IILs, and eight lacked support due to insufficient numbers of RNA-Seq reads. The two cases of IILs were included in our 17-case dataset of IILs.

Transcriptome data showed that all of the variant genes in our study were still actively expressed (Additional files 2 and 3 ). A close examination of these genes did not reveal any premature stop codons that were introduced by intron loss mutations. The IIL genes are unlikely to be pseudogenized. Indels caused by IILs in coding sequences are more likely to be selected against. It is possible that the IILs that we observed were recent events that would soon be eliminated. This possibility could be excluded if the variations that we observed in one species were also found to exist in another. For this reason, we investigated whether tomato’s wild relative, Solanum pimpinellifolium , shares intron variations with tomato. In S. lycopersicum , there are five IILs and five PILs. We surveyed the orthologous genes in the genome of S. pimpinellifolium and found all ten of the variations. Therefore, all of the intron losses that we observed in S. lycopersicum have been fixed during evolution.

Taking advantage of the availability of genome sequences corresponding to multiple A. thaliana lines, we also tested whether the intron variations that were observed in A. thaliana have been fixed during evolution. By surveying 17 IIL genes in 180 lines of A. thaliana from Sweden [ Clearance Looking For Outlet Find Great distressed cutout brogues Black Marsèll xaHDvR
], we found that all 17 cases of IILs had been fixed. Similarly, by surveying 104 PILs in 180 lines of A. thaliana , we found that 101 cases of PIL have been fixed during evolution and only three PILs remained polymorphic, in genes AT1G48420 , AT3G23080 , and AT4G00350 . However, the allele frequencies of these three PILs were high: 97.7% for AT1G48420 , 36.1% for AT3G23080 and 97.2% for AT4G00350 .

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Early this year, a British tabloid ran a hyperbolic article on climate change, claiming that world leaders had been "duped" by climate data that had been manipulated. It wasn't unusual for the outlet or the article's author to make badly misleading claims about climate research, and our own investigation into the underlying disagreement showed that the piece actually boiled down to a dispute about how best to archive data. These sorts of misrepresentations happen dozens of times a year.

But something unusual did eventually happen as a response to the article in the Mail on Sunday : a UK press watchdog determined that the article breached the Editor's Code of Conduct. Mail on Sunday was subsequently ordered to prominently display the inaccuracies above the article itself.

The judgement was handed down by IPSO, the UK's Independent Press Standards Organization (IPSO). It maintains an Editor's Code of Conduct , which sets standards for handling a variety of issues; the one relevant here is the section on accuracy . The Mail on Sunday belongs to IPSO and agrees to be bound by its rulings.

(The Mail on Sunday is an editorially independent sister publication to the higher-profile Daily Mail . While they don't share staff, their outlook is substantially similar, and no distinction is made between the two when articles are posted on the Daily Mail website.)

The article in question was published back in February. It focuses on a paper by NOAA scientists that revised the agency's climate history to reflect updated work on sea surface temperatures. The result was a slight change to the upward trend over the most recent decades. This had the effect of eliminating the statistical significance of an apparent slowdown in the rate of warming around the start of this century.

For those invested in the idea that warming had slowed down, this scientific finding was extraordinarily inconvenient. The list of people who refused to accept the result includes the head of the House Science Committee, Lamar Smith (R-Tex.), who responded by subpoenaing NOAA scientists and their e-mails and accusing them of fraud . So the scientific results were already the subject of some political controversy.

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