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<blockquote data-quote="l_raty" data-source="post: 3356237" data-attributes="member: 24811"><p>This sequence (GenBank <a href="http://www.ncbi.nlm.nih.gov/nuccore/HM535648" target="_blank">HM535648</a>/<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_014341.1" target="_blank">NC_014341</a>, by Yang et al. 2010 [<a href="https://tspace.library.utoronto.ca/bitstream/1807/64525/1/zr10045.pdf" target="_blank">pdf</a>]), although obviously bad, has been used recurrently in subsequent publications.</p><p></p><p><em>E.g.</em>: Jetz et al. 2012 [<a href="http://bbcd.bio.uniroma1.it/bbcd/sites/default/files/file%20lezioni/BirdDiversification.pdf" target="_blank">pdf</a>], Ma et al. 2015 [<a href="http://www.bioline.org.br/pdf?zr14009" target="_blank">pdf</a>], Wu et al. 2015 [<a href="http://www.avianres.com/content/pdf/s40657-015-0010-5.pdf" target="_blank">pdf</a>], Gibb et al. 2015 [<a href="http://gbe.oxfordjournals.org/content/7/11/2983.full.pdf" target="_blank">pdf</a>] (the existence of a problem is acknowledged in this paper; but as the sequence indeed appears chimaeric, its simple inclusion in an analysis is in fact quite problematic), and now Peng et al. 2016 [<a href="http://www.tandfonline.com/doi/pdf/10.1080/23802359.2015.1137802" target="_blank">pdf</a>]. Having been used in Jetz et al. 2012, the sequence also affects the <a href="https://species.mol.org/species/Pseudopodoces_humilis" target="_blank">"Map of Life" website</a>, presumably giving <em>Pseudopodoces</em> an artificially high evolutionary distinctness. It also presumably biased the analyses of Holt & Jønsson 2014 [<a href="http://sysbio.oxfordjournals.org/content/63/6/1010.full.pdf" target="_blank">pdf</a>; <a href="http://dx.doi.org/10.5061/dryad.qd3pd" target="_blank">data</a>]. This sequence was also harvested from GenBank by BOLD (twice, as it was present in GenBank under two different accession numbers; in BOLD: <a href="http://boldsystems.org/index.php/Public_RecordView?processid=CYTC4940-12" target="_blank">CYTC4940-12</a>/<a href="http://boldsystems.org/index.php/Public_RecordView?processid=CYTC3544-12" target="_blank">CYTC3544-12</a>; the barcode region of its COI gene is embedded in the barcode cluster <a href="http://boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAC1536" target="_blank">BOLD:AAC1536</a>, which otherwise includes only eastern <em>Phoenicurus ochruros</em> sequences).</p><p></p><p>The mitochondrial genome of <em>Pseudopodoces humilis</em> has been resequenced by Xin et al. "2015" (=in press; Genbank <a href="http://www.ncbi.nlm.nih.gov/nuccore/KP001174.1" target="_blank">KP001174</a>; [<a href="https://www.researchgate.net/publication/271224278" target="_blank">pdf</a>]). (This last sequence seems OK.)</p><p></p><p>------</p><p>(PS - Nick: Although I don't doubt your conclusions, the values you quote are a bit odd. <em>Tarsiger</em>, <em>Ficedula</em> and <em>Phoenicurus</em> differ in COI sequence by ~10%: I don't see how a sequence that is a 100% match for one, could be a 99% match for the other two. Didn't you take these values from the "Query cover" column in the BLAST results, instead of the "Ident" column?)</p></blockquote><p></p>
[QUOTE="l_raty, post: 3356237, member: 24811"] This sequence (GenBank [URL="http://www.ncbi.nlm.nih.gov/nuccore/HM535648"]HM535648[/URL]/[URL="http://www.ncbi.nlm.nih.gov/nuccore/NC_014341.1"]NC_014341[/URL], by Yang et al. 2010 [[URL="https://tspace.library.utoronto.ca/bitstream/1807/64525/1/zr10045.pdf"]pdf[/URL]]), although obviously bad, has been used recurrently in subsequent publications. [I]E.g.[/I]: Jetz et al. 2012 [[URL="http://bbcd.bio.uniroma1.it/bbcd/sites/default/files/file%20lezioni/BirdDiversification.pdf"]pdf[/URL]], Ma et al. 2015 [[URL="http://www.bioline.org.br/pdf?zr14009"]pdf[/URL]], Wu et al. 2015 [[URL="http://www.avianres.com/content/pdf/s40657-015-0010-5.pdf"]pdf[/URL]], Gibb et al. 2015 [[URL="http://gbe.oxfordjournals.org/content/7/11/2983.full.pdf"]pdf[/URL]] (the existence of a problem is acknowledged in this paper; but as the sequence indeed appears chimaeric, its simple inclusion in an analysis is in fact quite problematic), and now Peng et al. 2016 [[URL="http://www.tandfonline.com/doi/pdf/10.1080/23802359.2015.1137802"]pdf[/URL]]. Having been used in Jetz et al. 2012, the sequence also affects the [URL="https://species.mol.org/species/Pseudopodoces_humilis"]"Map of Life" website[/URL], presumably giving [I]Pseudopodoces[/I] an artificially high evolutionary distinctness. It also presumably biased the analyses of Holt & Jønsson 2014 [[URL="http://sysbio.oxfordjournals.org/content/63/6/1010.full.pdf"]pdf[/URL]; [URL="http://dx.doi.org/10.5061/dryad.qd3pd"]data[/URL]]. This sequence was also harvested from GenBank by BOLD (twice, as it was present in GenBank under two different accession numbers; in BOLD: [URL="http://boldsystems.org/index.php/Public_RecordView?processid=CYTC4940-12"]CYTC4940-12[/URL]/[URL="http://boldsystems.org/index.php/Public_RecordView?processid=CYTC3544-12"]CYTC3544-12[/URL]; the barcode region of its COI gene is embedded in the barcode cluster [URL="http://boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAC1536"]BOLD:AAC1536[/URL], which otherwise includes only eastern [I]Phoenicurus ochruros[/I] sequences). The mitochondrial genome of [I]Pseudopodoces humilis[/I] has been resequenced by Xin et al. "2015" (=in press; Genbank [URL="http://www.ncbi.nlm.nih.gov/nuccore/KP001174.1"]KP001174[/URL]; [[URL="https://www.researchgate.net/publication/271224278"]pdf[/URL]]). (This last sequence seems OK.) ------ (PS - Nick: Although I don't doubt your conclusions, the values you quote are a bit odd. [I]Tarsiger[/I], [I]Ficedula[/I] and [I]Phoenicurus[/I] differ in COI sequence by ~10%: I don't see how a sequence that is a 100% match for one, could be a 99% match for the other two. Didn't you take these values from the "Query cover" column in the BLAST results, instead of the "Ident" column?) [/QUOTE]
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