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I've done a major rewrite, let me know if it sucks. I tried to give some examples that highlight some of the possibilities and problems associated with DNA barcoding. I'm not sure if my referencing is right though as I've never really written a Wikipedia article before. I think the Criticisms section still needs some serious work, more references are needed. Mdhowe 04:38, 3 January 2006 (UTC)
Moved to DNA barcoding instead of DNA barcode, as this will be a more common search string. Evolver 18:34, 4 September 2005 (UTC)
The "criticisms" section, in particular, reads like a personal statement and justification on the part of the editor responsible, as it makes claims and gives figures none of which are backed up by citations - naming anonymous "critics" and then rebutting them looks very much like a "straw man" approach, and is therefore not in keeping with WP:NPOV. Given the large number of critics and the variety of their criticisms, this article would be far more balanced in its presentation if this section were expanded and referenced to a much greater degree. This is not my area of expertise, but I am familiar enough with it (and the debate surrounding it) to recognize that the article is presently giving short shrift to the criticisms and shortcomings of the technique and its applications. Right now, it reads more like a sales pitch. Dyanega 23:23, 29 May 2007 (UTC)
I have attempted finding the references. The "96% of eukaryotes" seems to be a mis-statement of this below. Shyamal 11:09, 28 September 2007 (UTC)
“ | In these initial analyses, 96% of test species were correctly assigned at the phylum level and 100% of insects were placed correctly at the ordinal level (Hebert et al. 2003a). | ” |
We thus consider that the application of COI barcodes in delphinid cetaceans should be done with caution; not only has the cytochrome b gene been shown to be phylogenetically more informative, but relying only on mitochondrial DNA genes alone may be problematic.
An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree.
The problem here is not that your criticisms are unwarranted - far from it - but that it's very difficult to incorporate these references into the article except in the context of "original research", which is not permitted. Without published criticisms of barcoding that use these same arguments and examples, there really is no way to introduce this information - unless these references criticize the use of mtDNA for reconstructing species trees. Since that is what barcoding is being used for, that WOULD merit inclusion in this article, even if barcoding per se was not mentioned. Dyanega ( talk) 17:31, 9 April 2008 (UTC)
The tag for the criticism section - suggesting that the section should be merged into the main text did not seem to fit in with the aim of balancing the pros and cons of the technique, something that the separation. The current treatment in the article is definitely better than it used to be - but suggestions could go here. Shyamal ( talk) 02:57, 18 February 2008 (UTC)
Merge this article with Consortium for the Barcode of Life? JmCor ( talk) 05:26, 20 August 2010 (UTC)
These are the questions for which I sought answers when I came to the article. To my surprise, these obvious questions are not answered. I remain curious. DrHow ( talk) 22:00, 5 February 2015 (UTC)
Is metabarcoding (sometimes called metagenetics, sometimes WRONGLY called metagenomics) a topic for this page or should it have its own page? Any thoughts? On one hand its very similar to DNA barcoding in the broad sense. On the other it employs a slightly different strategy where its not relating a sequence to the organism it came from, but rather estimating the species composition of a mixed (e.g. environmental) sample. Its becoming a widely used term and ought to be in wikipedia somewhere. If nobody replies I'll probably start a new page, though I don't have strong feelings. XCalPab ( talk) 21:04, 28 November 2015 (UTC)
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I have just finished a bit of a tidy up of this article with additional information and references, but one thing remains. In the "criticisms" section, I removed a paragraph commencing "The DNA barcoding debate resembles the phenetics debate of decades gone by..." since this is based on a 2005 reference, only 2 years on from Hebert's initial paper, and does not reflect the views of 2018 so far as I can ascertain. However the majority/all citations for this section date from the period 2004-2006, with nothing later than 2007. In any case I think the sentence ending "it may not be effective for the majority of known organisms." is misleading. I am sure this section could do with an update but need someone more familiar with the subject to do it. Tony 1212 ( talk) 07:18, 28 July 2018 (UTC)
Hi I represent the DNAqua-Net COST-action, a research network on barcoding and will in March 2019 run a Ph.D. course at the Swedish University of Agricultural Sciences where editing this page will be part of the exercises. I found this page heavy, not up-dated and not written in a layman’s language. Our plans are to separate the text on the organism barcoding subjects into subpages, and work on the main page to adress also a layman, and of course link the organism pages to it. We will have course teachers being active researcehr on those subjects, and helping the students to learn about the state of the art. However, before we dig in to restructuring and expanding the article, I'm most happy to receive some community suggestions on what to change. I would also especially be happy to recieve constructuve critics once we have started to encourage the students (and teachers), and not disencourage them. I have the dream that this could be a science outreach which probably is interesting a lot of different people currently. Maria Kahlert (SLU) ( talk) 13:30, 3 October 2018 (UTC)
"5) If the goal is to write a new article or expand a stub, keep in mind that this is at least as hard as learning to write for peer-reviewed publication, and that the learning process is being done very much in public. Just as you wouldn’t have a student try writing for publication without reading lots of great papers, you should have students find out what the “Good Articles” and “Featured Articles” are in your area and learn from those examples."
Hope to hear from you soon, as we all are eager to go online for real! -- Maria Kahlert (SLU) ( talk) 08:04, 21 May 2019 (UTC)
OK, have left some very brief comments on your talk page as requested (not an exhaustive review by any means but others can do this!). I suggest going ahead and then waiting for others to chime in and/or make further changes. Best regards- Tony Tony 1212 ( talk) 20:36, 21 May 2019 (UTC)
We are a group of PhD students working with Barcoding and we would like to make this Wikipedia page broader and clearer, less crowded with text. We believe that the following part, on the COI marker specifically, could be move to the Cytochrome C Oxydase subunit I Wikipedia page, under 5. Use in DNA barcoding (which is incidentally very short). This section seems too specific for a general barcoding page and we would like to focus on more general issues and several DNA markers. The text is very nicely constructed and could greatly contribute to the COI Wikipedia page instead.
"Initial criticism and current status[edit source]
In the initial years following its proposal, DNA barcoding met with spirited reaction from scientists, especially systematists, ranging from enthusiastic endorsement to vociferous opposition.[51][52] For example, some stressed the fact that DNA barcoding does not provide reliable information above the species level[citation needed], while others opined that it was inapplicable at the species level, but may still have merit for higher-level groups.[25] Others resented what they saw as a gross oversimplification of the science of taxonomy. And, more practically, some suggested that recently diverged species might not be distinguishable on the basis of their COI sequences.[53] In an early study, Funk & Omland (2003[54]) found that some 23% of animal species were polyphyletic if their mtDNA data were accurate, indicating that using an mtDNA barcode to assign a species name to an animal would be ambiguous or erroneous in those cases (see also Meyer & Paulay, 2005[55]). Some studies with insects suggested an equal or even greater error rate, due to the frequent lack of correlation between the mitochondrial genome and the nuclear genome or the lack of a barcoding gap (e.g., Hurst and Jiggins, 2005,[23] Whitworth et al., 2007,[25] Wiemers & Fiedler, 2007[56]).
Moritz and Cicero (2004[57]) questioned the efficacy of DNA barcoding by suggesting that other avian data is inconsistent with Hebert et al.'s interpretation, namely, Johnson and Cicero's (2004[58]) finding that 74% of sister species comparisons fall below the 2.7% threshold suggested by Hebert et al. These criticisms are somewhat misleading considering that, of the 39 species comparisons reported by Johnson and Cicero, only 8 actually use COI data to arrive at their conclusions. Johnson and Cicero (2004[58]) have also claimed to have detected bird species with identical DNA barcodes, however, these 'barcodes' refer to an unpublished 723-bp sequence of ND6 which has never been suggested as a likely candidate for DNA barcoding.
The criticisms given above date from the first few years following Hebert's initial (2003) papers in which the method was proposed. Writing in 2016, with 13 years elapsed since their initial proposal, Hebert and co-workers wrote:
[In animals,] DNA barcodes typically discriminate about 95% of known species; cases of compromised resolution involve sister taxa, often species that hybridize. In the many taxa where geographical variation in barcode sequences is small, a few records per species are sufficient to create an effective identification system. However, the analysis of more specimens is advantageous because it often reveals discordances that indicate misidentifications or cryptic taxa, and it also provides insights into the extent of geographical variation in barcode sequences. There are two animal phyla in which COI often fails to deliver species-level resolution, sponges and some benthic cnidarians, apparently because of their slowed rates of mitochondrial evolution. Barcoding also fails to distinguish a small fraction of species in other groups, typically sister taxa or those whose status is uncertain.[59]
In a more recent (2018) review, M. Stoeckle and D. Thaler write:
The current field of COI barcodes is no longer fragile but neither is it complete. As of late 2016 there were close to five million COI barcodes between the GenBank and BOLD databases. Objections can now be seen in the cumulative light of these data and more than a decade’s experience. There is no longer any doubt that DNA barcodes are useful and practical. The agreement with specialists encompasses most cases in several important animal domains. Many cases where DNA barcodes and domain specialists do not agree reflect geographic splits within species or hybridization between species. Others upon further investigation been attributed to mislabeling or sequence error. Some may represent bona fide exceptions to the rule that mitochondrial sequence clusters coincide with species defined by other means. In the great majority of cases COI barcodes yield a close approximation of what specialists come up with after a lot of study. Birds are one of the best characterized of all animal groups and COI barcode clusters have been tabulated as agreeing with expert taxonomy for 94% of species.[60]"
Bonnie Bailet (SLU) ( talk) 15:31, 26 March 2019 (UTC)
Hi Tony Bonnie is part of the PhD course, thus part of this "restructuring activity" we discussed earlier. Now we are doing it, and there are a lot of suggestions to move existing text of the barcoding page somewhere else. The students have together with the teachers really worked on the structure of the page, and we are all of course a bit unsure about removing/moving things. Still, we aim to do it, and hope for support to make this page more digestible. We will be back soon with more visible edits, now everything is still on our sandboxes :) Maria Maria Kahlert (SLU) ( talk) 08:34, 29 March 2019 (UTC)
Hi again, now, our joint work of DNAqua-Net researchers, teachers of PhD course PNS0169 at SLU, and the PhD-students of it, is done so far. We have restructured the main page "DNA barcoding", expanded it with more information on the method itself, updated with recent information, and lifted out the organism DNA barcoding paragraphs to seperate pages, as we feel that each organism group really has it's own challenges, methods, and different info interesting just there. We appreciate the work others have done before us, and have used the previous text as much as possible. However, as we really have restructured, it was not possible to just do edits, so I replaced the old text with our new one. We had asked the Wikicommunity in advance for advice, and you can find our conversation above. I am especially grateful to Olle Terenius, who helped us in the wide world of Wikipedia. And thanks so much Tony for the support of course as well! Hopefully, our work is useful for others. Please feel free to add work on the started stubs on missing organisms DNA pages (under "further reading"). best wishes, Maria Maria Kahlert (SLU) ( talk) 07:47, 23 May 2019 (UTC)
I came to this page after seeing a presentation at Wikimania by User:Olle Terenius (UU) about his work with PhD students which I think is an excellent initiative. Just in case there is further work planned with students on this article, I suggest that you work on improving its readability. The value for readability of this article is currently rather low at only 29 (see here: http://www.readabilityofwikipedia.com/check/DNA%20barcoding). The higher the value the better with 100 being the theoretical maximum. Readability is important for the general public but also for future translations of this article. There are great tools out there that can help in improving readability. I really like the App Hemmingway ( http://www.hemingwayapp.com/). Could be a great project for a "science communication" class in future... EMsmile ( talk) 13:05, 2 September 2019 (UTC)
This article was the subject of a Wiki Education Foundation-supported course assignment, between 9 January 2023 and 6 April 2023. Further details are available on the course page. Student editor(s): St030302 ( article contribs).
— Assignment last updated by St030302 ( talk) 19:01, 6 February 2023 (UTC)
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I've done a major rewrite, let me know if it sucks. I tried to give some examples that highlight some of the possibilities and problems associated with DNA barcoding. I'm not sure if my referencing is right though as I've never really written a Wikipedia article before. I think the Criticisms section still needs some serious work, more references are needed. Mdhowe 04:38, 3 January 2006 (UTC)
Moved to DNA barcoding instead of DNA barcode, as this will be a more common search string. Evolver 18:34, 4 September 2005 (UTC)
The "criticisms" section, in particular, reads like a personal statement and justification on the part of the editor responsible, as it makes claims and gives figures none of which are backed up by citations - naming anonymous "critics" and then rebutting them looks very much like a "straw man" approach, and is therefore not in keeping with WP:NPOV. Given the large number of critics and the variety of their criticisms, this article would be far more balanced in its presentation if this section were expanded and referenced to a much greater degree. This is not my area of expertise, but I am familiar enough with it (and the debate surrounding it) to recognize that the article is presently giving short shrift to the criticisms and shortcomings of the technique and its applications. Right now, it reads more like a sales pitch. Dyanega 23:23, 29 May 2007 (UTC)
I have attempted finding the references. The "96% of eukaryotes" seems to be a mis-statement of this below. Shyamal 11:09, 28 September 2007 (UTC)
“ | In these initial analyses, 96% of test species were correctly assigned at the phylum level and 100% of insects were placed correctly at the ordinal level (Hebert et al. 2003a). | ” |
We thus consider that the application of COI barcodes in delphinid cetaceans should be done with caution; not only has the cytochrome b gene been shown to be phylogenetically more informative, but relying only on mitochondrial DNA genes alone may be problematic.
An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree.
The problem here is not that your criticisms are unwarranted - far from it - but that it's very difficult to incorporate these references into the article except in the context of "original research", which is not permitted. Without published criticisms of barcoding that use these same arguments and examples, there really is no way to introduce this information - unless these references criticize the use of mtDNA for reconstructing species trees. Since that is what barcoding is being used for, that WOULD merit inclusion in this article, even if barcoding per se was not mentioned. Dyanega ( talk) 17:31, 9 April 2008 (UTC)
The tag for the criticism section - suggesting that the section should be merged into the main text did not seem to fit in with the aim of balancing the pros and cons of the technique, something that the separation. The current treatment in the article is definitely better than it used to be - but suggestions could go here. Shyamal ( talk) 02:57, 18 February 2008 (UTC)
Merge this article with Consortium for the Barcode of Life? JmCor ( talk) 05:26, 20 August 2010 (UTC)
These are the questions for which I sought answers when I came to the article. To my surprise, these obvious questions are not answered. I remain curious. DrHow ( talk) 22:00, 5 February 2015 (UTC)
Is metabarcoding (sometimes called metagenetics, sometimes WRONGLY called metagenomics) a topic for this page or should it have its own page? Any thoughts? On one hand its very similar to DNA barcoding in the broad sense. On the other it employs a slightly different strategy where its not relating a sequence to the organism it came from, but rather estimating the species composition of a mixed (e.g. environmental) sample. Its becoming a widely used term and ought to be in wikipedia somewhere. If nobody replies I'll probably start a new page, though I don't have strong feelings. XCalPab ( talk) 21:04, 28 November 2015 (UTC)
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I have just finished a bit of a tidy up of this article with additional information and references, but one thing remains. In the "criticisms" section, I removed a paragraph commencing "The DNA barcoding debate resembles the phenetics debate of decades gone by..." since this is based on a 2005 reference, only 2 years on from Hebert's initial paper, and does not reflect the views of 2018 so far as I can ascertain. However the majority/all citations for this section date from the period 2004-2006, with nothing later than 2007. In any case I think the sentence ending "it may not be effective for the majority of known organisms." is misleading. I am sure this section could do with an update but need someone more familiar with the subject to do it. Tony 1212 ( talk) 07:18, 28 July 2018 (UTC)
Hi I represent the DNAqua-Net COST-action, a research network on barcoding and will in March 2019 run a Ph.D. course at the Swedish University of Agricultural Sciences where editing this page will be part of the exercises. I found this page heavy, not up-dated and not written in a layman’s language. Our plans are to separate the text on the organism barcoding subjects into subpages, and work on the main page to adress also a layman, and of course link the organism pages to it. We will have course teachers being active researcehr on those subjects, and helping the students to learn about the state of the art. However, before we dig in to restructuring and expanding the article, I'm most happy to receive some community suggestions on what to change. I would also especially be happy to recieve constructuve critics once we have started to encourage the students (and teachers), and not disencourage them. I have the dream that this could be a science outreach which probably is interesting a lot of different people currently. Maria Kahlert (SLU) ( talk) 13:30, 3 October 2018 (UTC)
"5) If the goal is to write a new article or expand a stub, keep in mind that this is at least as hard as learning to write for peer-reviewed publication, and that the learning process is being done very much in public. Just as you wouldn’t have a student try writing for publication without reading lots of great papers, you should have students find out what the “Good Articles” and “Featured Articles” are in your area and learn from those examples."
Hope to hear from you soon, as we all are eager to go online for real! -- Maria Kahlert (SLU) ( talk) 08:04, 21 May 2019 (UTC)
OK, have left some very brief comments on your talk page as requested (not an exhaustive review by any means but others can do this!). I suggest going ahead and then waiting for others to chime in and/or make further changes. Best regards- Tony Tony 1212 ( talk) 20:36, 21 May 2019 (UTC)
We are a group of PhD students working with Barcoding and we would like to make this Wikipedia page broader and clearer, less crowded with text. We believe that the following part, on the COI marker specifically, could be move to the Cytochrome C Oxydase subunit I Wikipedia page, under 5. Use in DNA barcoding (which is incidentally very short). This section seems too specific for a general barcoding page and we would like to focus on more general issues and several DNA markers. The text is very nicely constructed and could greatly contribute to the COI Wikipedia page instead.
"Initial criticism and current status[edit source]
In the initial years following its proposal, DNA barcoding met with spirited reaction from scientists, especially systematists, ranging from enthusiastic endorsement to vociferous opposition.[51][52] For example, some stressed the fact that DNA barcoding does not provide reliable information above the species level[citation needed], while others opined that it was inapplicable at the species level, but may still have merit for higher-level groups.[25] Others resented what they saw as a gross oversimplification of the science of taxonomy. And, more practically, some suggested that recently diverged species might not be distinguishable on the basis of their COI sequences.[53] In an early study, Funk & Omland (2003[54]) found that some 23% of animal species were polyphyletic if their mtDNA data were accurate, indicating that using an mtDNA barcode to assign a species name to an animal would be ambiguous or erroneous in those cases (see also Meyer & Paulay, 2005[55]). Some studies with insects suggested an equal or even greater error rate, due to the frequent lack of correlation between the mitochondrial genome and the nuclear genome or the lack of a barcoding gap (e.g., Hurst and Jiggins, 2005,[23] Whitworth et al., 2007,[25] Wiemers & Fiedler, 2007[56]).
Moritz and Cicero (2004[57]) questioned the efficacy of DNA barcoding by suggesting that other avian data is inconsistent with Hebert et al.'s interpretation, namely, Johnson and Cicero's (2004[58]) finding that 74% of sister species comparisons fall below the 2.7% threshold suggested by Hebert et al. These criticisms are somewhat misleading considering that, of the 39 species comparisons reported by Johnson and Cicero, only 8 actually use COI data to arrive at their conclusions. Johnson and Cicero (2004[58]) have also claimed to have detected bird species with identical DNA barcodes, however, these 'barcodes' refer to an unpublished 723-bp sequence of ND6 which has never been suggested as a likely candidate for DNA barcoding.
The criticisms given above date from the first few years following Hebert's initial (2003) papers in which the method was proposed. Writing in 2016, with 13 years elapsed since their initial proposal, Hebert and co-workers wrote:
[In animals,] DNA barcodes typically discriminate about 95% of known species; cases of compromised resolution involve sister taxa, often species that hybridize. In the many taxa where geographical variation in barcode sequences is small, a few records per species are sufficient to create an effective identification system. However, the analysis of more specimens is advantageous because it often reveals discordances that indicate misidentifications or cryptic taxa, and it also provides insights into the extent of geographical variation in barcode sequences. There are two animal phyla in which COI often fails to deliver species-level resolution, sponges and some benthic cnidarians, apparently because of their slowed rates of mitochondrial evolution. Barcoding also fails to distinguish a small fraction of species in other groups, typically sister taxa or those whose status is uncertain.[59]
In a more recent (2018) review, M. Stoeckle and D. Thaler write:
The current field of COI barcodes is no longer fragile but neither is it complete. As of late 2016 there were close to five million COI barcodes between the GenBank and BOLD databases. Objections can now be seen in the cumulative light of these data and more than a decade’s experience. There is no longer any doubt that DNA barcodes are useful and practical. The agreement with specialists encompasses most cases in several important animal domains. Many cases where DNA barcodes and domain specialists do not agree reflect geographic splits within species or hybridization between species. Others upon further investigation been attributed to mislabeling or sequence error. Some may represent bona fide exceptions to the rule that mitochondrial sequence clusters coincide with species defined by other means. In the great majority of cases COI barcodes yield a close approximation of what specialists come up with after a lot of study. Birds are one of the best characterized of all animal groups and COI barcode clusters have been tabulated as agreeing with expert taxonomy for 94% of species.[60]"
Bonnie Bailet (SLU) ( talk) 15:31, 26 March 2019 (UTC)
Hi Tony Bonnie is part of the PhD course, thus part of this "restructuring activity" we discussed earlier. Now we are doing it, and there are a lot of suggestions to move existing text of the barcoding page somewhere else. The students have together with the teachers really worked on the structure of the page, and we are all of course a bit unsure about removing/moving things. Still, we aim to do it, and hope for support to make this page more digestible. We will be back soon with more visible edits, now everything is still on our sandboxes :) Maria Maria Kahlert (SLU) ( talk) 08:34, 29 March 2019 (UTC)
Hi again, now, our joint work of DNAqua-Net researchers, teachers of PhD course PNS0169 at SLU, and the PhD-students of it, is done so far. We have restructured the main page "DNA barcoding", expanded it with more information on the method itself, updated with recent information, and lifted out the organism DNA barcoding paragraphs to seperate pages, as we feel that each organism group really has it's own challenges, methods, and different info interesting just there. We appreciate the work others have done before us, and have used the previous text as much as possible. However, as we really have restructured, it was not possible to just do edits, so I replaced the old text with our new one. We had asked the Wikicommunity in advance for advice, and you can find our conversation above. I am especially grateful to Olle Terenius, who helped us in the wide world of Wikipedia. And thanks so much Tony for the support of course as well! Hopefully, our work is useful for others. Please feel free to add work on the started stubs on missing organisms DNA pages (under "further reading"). best wishes, Maria Maria Kahlert (SLU) ( talk) 07:47, 23 May 2019 (UTC)
I came to this page after seeing a presentation at Wikimania by User:Olle Terenius (UU) about his work with PhD students which I think is an excellent initiative. Just in case there is further work planned with students on this article, I suggest that you work on improving its readability. The value for readability of this article is currently rather low at only 29 (see here: http://www.readabilityofwikipedia.com/check/DNA%20barcoding). The higher the value the better with 100 being the theoretical maximum. Readability is important for the general public but also for future translations of this article. There are great tools out there that can help in improving readability. I really like the App Hemmingway ( http://www.hemingwayapp.com/). Could be a great project for a "science communication" class in future... EMsmile ( talk) 13:05, 2 September 2019 (UTC)
This article was the subject of a Wiki Education Foundation-supported course assignment, between 9 January 2023 and 6 April 2023. Further details are available on the course page. Student editor(s): St030302 ( article contribs).
— Assignment last updated by St030302 ( talk) 19:01, 6 February 2023 (UTC)