Talk:DNA barcoding

Balance

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)

Good rewrite. Putting barcoding in context ("...not a new concept...") is good, as is the bold cutting of some stuff previously there that I had left because I didn't want to step on the toes of prior contributors. The references are also good. I'll make some other changes in the next few days when I have time, and hopefully together we can make topnotch page. Arga Warga 01:28, 4 January 2006 (UTC)

Thanks, I was hoping to get a bit of help. I think this is a really interesting topic and I've been looking for an article to contribute heavily too, it would be nice to get it too featured article quality. What do you think about the 'Case Studies' subsection? I wasn't really sure if it was proper Wikipedia style, as this was adapted from an essay I wrote for uni. Mdhowe 08:09, 4 January 2006 (UTC)

For the record, the "not a new concept" line is misleading. DNA barcoding is explictly not based on determining evolutionary relationships; that is, DNA barcoding is not phylogenetics or systematics (although this is a common misconception). The Woese introduction is therefore out of place. The idea of using a standardized gene fragment to identify all animal species (but not to classify them) is a new idea, although you might make the argument that using genetic data to identify "species" is normal practice in bacteria and archaea.

Would it be incorrect to say that DNA barcoding is a tool used in phylogenetics? --Mdhowe 08:14, 22 February 2006 (UTC)

Yes, it would be incorrect. Phylogenetic methods (NJ trees) are used in barcode analysis, but barcoding itself is very clearly stated (by actual barcode researchers) to not be phylogenetics.

Not to confuse methodology with a scientific discipline... ;-) No, of course can't barcoding be phylogenetics, just as cladistics despite being the unchallenged leader in phylogenetics methodology is not phylogenetics. The tool collects (barcoding) or analyzes (cladistics) the data, the discipline interprets it and puts its hypotheses to the test against it. Still, at present, molecular barcoding (which is a tool suitable for phylogenetics just like an apple-picker is a tool for picking arboreal Rosaceae fruit) is not really used much in phylogenetics (which is a scientific discipline) because researchers are somewhat hesistant to make much of the method until it has matured (which of course "the guy in the lab across the hall" should do, thank you very much). There is a rather harsh critique of the A. fulgerator study around, I think in the Zool.J.Linn.Soc. something like one year ago, which would benefit the article if it were discussed. The A. fulgerator case is especially damning since IIRC scientific essentials such as reproducibility were somewhat lacking, according to the critique, and many of the barcoded "species" were apparently just morphs. Have it around somewhere on my HD, but as butterflies are not my #1 topic (bird-food, that's what they are), someone else could try to dig it up; it might be many months until I happen across it again.

To go back to the original question: Currently, yes. In 10 years' time, maybe not anymore. Dysmorodrepanis 09:39, 11 November 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)

Maybe this was the right choice, but you did it in the wrong way. You should have used the "move" button. Now you have destroyed the edit history for this page. You might want to ask an admin to fix this. Onco_p53 20:44, 4 September 2005 (UTC)

I tried. Wasn't allowed to use move feature. There was essentially no history anyway (only minor edits here and there), and it has not been destroyed at all. If you want it, go here: http://en.wikipedia.org/w/index.php?title=DNA_barcode&action=history. Evolver 20:50, 4 September 2005 (UTC)

It's 'destroyed' in the sense that it's no longer associated with the place where everyone will do the editing. If you can't move a page (because the target already exists) you should ask an admin to move it at Wikipedia:Requested moves. --Saforrest 20:41, 28 February 2006 (UTC)

need for more citations for statements made in the text

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)

Here is one that I came across in travels from Bird->Bird nest->Protocalliphora. T.L. Whitworth, R.D. Dawson, H. Magalon, E. Baudry 2007. DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae). Proceedings of the Royal Society B: Biological Sciences 274(1619):1731-1739 [1] Shyamal 08:21, 27 September 2007 (UTC)

Another reference - Will, K. W., B. D. Mishler & Q. D. Wheeler 2005. The Perils of DNA Barcoding and the Need for Integrative Taxonomy Syst. Biol. 54(5):844–851 [2] Shyamal 06:00, 28 September 2007 (UTC) + S.G. Newmaster, A.J. Fazekas, and S. Ragupathy 2006. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can. J. Bol. 84: 335-341 [3]

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). ”

If that's the actual quote, it is actually irrelevant to the section in which it is placed, which refers explicitly to the ability of barcoding to identify species-level taxa. It's simpest to remove it entirely, then. Dyanega 17:56, 28 September 2007 (UTC)

The "Identification of birds" section is especially in need of balance. If you have read the original paper, you'll note that the standard is extremely low. Specimens cannot be traced, location is not taken into account. It is obvious that a Holarctic migratory bird is liable to have more divergent COI barcodes than a restricted-range endemic, while each can be one and only one good species following most all species concepts - namely in a widely-distributed species there may be a high barcoding sequence divergencs AND the population may be contziguous and coherent and reproductively isolated still, with gene flow between subpopulations abundant but on a global level very slow due to the wirde range; the Osprey is a case that comes to mind. Hybridization has not been taken into account.

Basically they apply one of the most uncritical positivist interpretations I've ever seen in a peer-reviewed paper; it actually makes me wonder how this wretched thing passed peer review. Dyanega, you remember the clash we had about the honeybees - you seem rather reserved about these things and I respect your profdessional opinion[*], so can you take a look at the paper (ref 3)? There has not been a published criticism, but the criticism is indeed very fundamental here; I would go as far as to say it barely falls short of glorified bunk science. So rather than waiting til someone has sorted through the large amount of data (which may be never; I get the impression that most avian taxonomists simply don't consider this specific work it worthy of a critique and rather hope it will die quietly) a more fundamental critique of failing good scientific practice would be the way to go. But what to cite here?

[*] Though I still guess you misunderstood me in the honeybee thing - I would not propose the mol-phyl paper to be a study which revised taxonomy, but yet another study which provided yet more evidence which taxonomic approach to prefer. The ecological, behavioral and now also the molecular data support species status for the Himalayan giant honeybees; though they may be morphologically similar to the South Asian ones there seems sufficient evidence of long-standing reproductive isolation - they almost certainly don't mate to any significant degree, making them not just phylospecies but biospecies. I.e. the studies support the taxonomic treatment as proposed by the original describer. Nothing more, nothing less; had species status never been proposed I would never have suggested to adopt it (a remark to the effect "it may well be a distinct species" is in order in such a case, but I try to be careful not to pre-empt proper taxonomic work - though you may not have noticed, since your specialty field is not CJO Harrison's London Clay fossil birds ;-) ) Dysmorodrepanis (talk) 10:59, 5 April 2008 (UTC)

Another thing that entirely goes under in the whole brouhaha - COI barcoding is nothing revolutionary. The sequence is new, but the use of short DNS sequences for taxonomical purposes was extensive in birds in the mid-1990s (though usually for phylogeny in general rather than for species identification). Nobody wants to repreat this these days were it not for barcoding: it has turned out that e.g. 300 bases of cytB are insufficient and too much affected by hybridization to yield reliable data. I have put up a few papers in Testudo (genus) that show how molecular phylogenetics on the species level is done today; multiple sequences and longer sequences and mtDNA as well as nDNA sequences combined with GISing the voucher specimens and optimally also morphometric analyses are considered the "gold standard".

To use a very short stretch of DNA - even considering COI evolves extremely rapidly in parts - may seem expedient, but take away the flashy name and 5 years ago almost anyone in the field would have considered the technique "yesterday's science" and bad science at that. I have seen a lot of quality papers in molecular phylogenetics on the species level, and barcoding papers are not usually among them. And the expanded barcoding protocols are simply molecular phylogeography without the "-geography"; the technique offers (or seems to offer) only a single advantage in keeping the sequencing effort down by smart sequence choice. But with that, it introduces errors.

Especially the belief of some barcoding advocates that phylogeography and thorough analysis of within-population variation is unnecessary is almost farcical. Too many of the supposed "two bird species in one" are based on a sample size of n=2, with no way to tell whether these two specimens were from the same place and time (which would indeed suggest they are two species) or from opposite ends of a large contigous range (which would almost certainly mean that they are not two species but a phylogeographic artefact).

But what to cite? A few of the refs are good in this respect, but most recent critics tend to get involved in mudfighting; to me it seems as if the real issue with barcoding is that as originally proposed it is little more than a rehash of a discarded approach.

It may be that older work like doi:10.1007/s002390010197, doi:10.1007/PL00006481 and doi:10.1016/0169-5347(94)90028-0 could deliver the background needed here (I have not read them). In general, to provide a "deep" critique of barcoding as originally proposed it seems that one has to go back to the mid-late 1990s, when the shortcomings of the "barcoding without the name" approach that was hot in the early-mid 1990s became apparent. Basically, "it must be taken into account that people tried something very similar 10 years before and largely discarded it because the results were too unreliable". I get the impression that the "barcoding battle" is very much a fight about funds and too little a fight about the philosophy of science. But then, I am firmly with Popper on the latter issue and apparently Hébert et al. aren't. Dysmorodrepanis (talk) 10:59, 5 April 2008 (UTC)

doi:10.1071/MF07050 seems another (recent) study that tackles the issue right at the root:

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.

In other words: useful to get additional data, but neither a panacea nor even really new.

It is astounding how few recent papers in the barcoding debate care to discuss the debate of 10 years ago! Dysmorodrepanis (talk) 11:15, 5 April 2008 (UTC)

Also interesting (from 1995): this

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.

This is precisely the crux in the barcoding approach - that you'd want a (short and rapidly evolving) sequence (to make it a superior technique from the view of the field researcher with limited time and ressources) but that this will inevitably introduce a particular kind of error - an error you cannot (with the limited data) recognize. I have also seen a nice study on the Bonefish, showing that this may be anything between 2 (or 3) and 8+ species of Albula, but that if a barcoding approach had been followed the result would have been flawed: the correct evolutionary relationships only resolve with heavy-duty sequencing and analytical effort. I can't find this paper again right now, but eventually I'll do and it'll be a reference at Albula (fish) where it can be picked up. Dysmorodrepanis (talk) 07:19, 9 April 2008 (UTC)

This is a reply to the above (Moore 1995) paper, saying it's even worse in particular lineages. One may well check the examples where standard (mtDNA COI) barcoding doesn't cut, whether they fit this bill: "clades exhibiting female philopatry and male dispersal, or a polygynous mating system". Dysmorodrepanis (talk) 07:23, 9 April 2008 (UTC)

Got the bonefish paper - it's here. If you check out figure 2, you'll note that the least one would have to accept as species is Albula vulpes, A. neoguinaica, and (tentatively) lineage "E". Because the latter cannot be unequivocally placed but appears basal to the A. vulpes clade (including lineages "A" and "C"). But to get to that point, it was necessary to run 4 analyses on "564 bp of mitochondrial DNA (mtDNA) cytochrome b from 174 individuals collected at 26 locations". Whereas e.g. the claim of Hébert et al. that Tringa solitaria is more than one species is based on a "648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI)" with a single (NJ, which is the worst possible method in cladistics as it's essentially sexed-up phenetics) analysis of just 12 specimens from unspecified locations of this taxon from a group that is known to hybridize vigorously. :( Dysmorodrepanis (talk) 07:41, 9 April 2008 (UTC)

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)

You'd be correct if I had discussed tis "as is" in the article, but that's why I did it here. A problem with scientific standards exists it seems, somewhat underrepresented in the current debate (which is more about whether essources are drained from other fields of taxonomy etc), but echoing debates of 10 years ago. And if I am right, this would seem to be article material. BUT: it cannot be article material unless there is citeable sources supporting the conclusions.

So people might want to like to go citation-hunting, and I did all this lengthy write-up to make them aware of what to look for. Sundry results of a Google Scholar search for molecular "proper vouchering" can probably be contrasted by the complete lack thereof in the bird barcoding studies. Studies of within-population variation, hybridization, etc in specific taxa can be contrasted with the conclusions drawn for the selfsame taxa to show that conclusions are premature. For example there is massive COI paraphyly in a calidrid in the follow-up study to the 2004 one... Hybridization in shorebirds anyone? (The Handbook of Avian Hybrids of the World should be able to deliver sources, but I do not have this).

As regards the most controversial issue - and I agree that this is thorny indeed -, namely "quick-and-dirty" COI barcoding being a repeat of outdated "quick-and-dirty" cytB sequence snippet cladistics but with the added problem that some barcoding studies (those that don't use apomorphy vs plesiomorphy analysis but only compare seqence similarity outright) are bordering on phenetics: as I said, there are almost certainly citeable sources, but we'd have to dig deep.

For I know that essentially the same thing that is being toutes as brand new was done 10 years ago with a different gene, and it is not being done anymore these days as it was then, and this is because of the methodological drawbacks.

And I'd guess that there was much discussions about that, "molecular taxonomy" was a controversial issue then.

So in conclusion, there should be good sources to point out that a problem exists, even though nobody at present cares to write about it. Not to say in the article "it's all rubbish", but to say "hey look at that, it seems that we have a knowledge/awareness gap in the current research, so caveat lector". SORA might be a place where literature can be found; most of the journals where the debate is now being held didn't even exist back then.

In any case, see here. Highly recommmended. Note the extensive analysis of within-population variation and the proper vouchering and locality information.

In general, I think Talk pages should be used more often to collect studies and other sources addressing actual or potential issues of articles. This approach was extremely successful when we overhauled passerine systematics - the references listed were collected over the course of many months, evaluated, discussed, until they could finally be incorporated in the article in one stroke. The Polymorphism article benefitted from a similar approach. Dysmorodrepanis (talk) 12:26, 17 May 2008 (UTC)

Tag removed

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?

Merge this article with Consortium for the Barcode of Life? JmCor (talk) 05:26, 20 August 2010 (UTC)

The article at Consortium for the Barcode of Life is short, and most of what is there duplicates what is here. Furthermore, I'm somewhat skeptical of having articles for every scientific consortium; there is, in general, little to say about them apart from the results of their research (which better fits in articles for the subject matter in question, not for the consortium). So I'd be fine with merging that article here (not the other way around, though, given the existence of various barcoding consortiums). Kingdon (talk) 20:59, 7 September 2010 (UTC)

How is it done? Why call it "bar coding"?

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)

Metabarcoding

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)

I'd vote for making it a section on this page. It could be split out later as more variation in methods generates material to make a longer page. Although it is not usual to expect to be able to identify the organisms that the sequences come from, I believe that is the eventual aim of some workers. I doubt that metabarcoding will retain its emphasis on environmental chemistry divorced from taxonomy. Sminthopsis84 (talk) 22:51, 28 November 2015 (UTC)

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"Criticisms" section

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)

OK, I've had a go at this section - placed a historic context on some of the text, removed some inaccurate claims, and added a new paragraph with quote taken from on a comprehensive 2018 review I have found. Hopefully a bit better now - still room for input by others if desired :) Regards Tony Tony 1212 (talk) 22:42, 28 July 2018 (UTC)

Also just added another quote and renamed the section concerned to "Initial criticism and current status" since the last portion now deals with the current status and leaves most of the criticism behind. Tony 1212 (talk) 05:38, 29 July 2018 (UTC)

Ph.D. course in barcoding restructuring page

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)

Just to let you know that actual subpages in Wikipedia are no longer supported, see Wikipedia:Subpages. If you want to suggest creating separate pages for items such as the present 2.1 Barcoding animals / 2.2 Barcoding flowering plants / 2.3 Barcoding fungi / 2.4 Barcoding protists, etc., then you can suggest that, and leave the headings and brief content as they exist in the current article, then under each subhead you can insert e.g.

Main article: DNA barcoding of animals

etc., if you feel that such single topic pages are justified (I have no view on that, and other editors would review such pages and decide whether or not they are justified). If you want to create some test pages for discussion or experimentation purposes without them becoming part of the official, published wikipedia then I believe there is a "sandbox" facility (see Wikipedia:Sandbox) for this, but have not used it.

You might also like to read https://dynamicecology.wordpress.com/2014/05/05/using-wikipedia-in-the-classroom-a-cautionary-tale/ (scroll down for quite a lot of discussion). The following sentence from one commenter may be of relevance:

"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."

I would just say from my own experience that there is quite a learning curve to discover not only what is general "wikipedia style" with citation and formatting of references, etc. (which can be learned to a degree by reverse-engineering existing exemplar articles) as well as deciding what exactly to say - what points to make in what order, clarity of synthesis of existing literature, choice of wording, etc. etc. which may not come naturally to the typical student without good supervision. I guess what I am saying is that a good Wikipedia article is probably somewhat more advanced than a typical class essay, more akin to a mini literature review. If you feel your students are (or can be brought up to) that level, all well and good, however it is still somewhat demanding in my view to write a good article from scratch at the first attempt. If in spite of these warnings you decide to go ahead, good luck! Regards - Tony Tony 1212 (talk) 02:30, 4 October 2018 (UTC)

Actually having just checked out http://dnaqua.net/publications/ I see your group has a lot of expertise in this area, so probably my misgivings are unfounded (it was just the word "students" that raised minor alarm in my mind). If your group bases its updates on appropriately cited new work that has appeared since the most of the original page was written (not by me I would add) there should be no problem... Best - Tony Tony 1212 (talk) 19:28, 4 October 2018 (UTC)

In Sweden, we are since 2014 engaging researchers to contribute to Wikipedia in a scholarly fashion as part of their science outreach. I teach about 200 PhD students every year in how to edit Wikipedia and they are all improving and sometimes creating articles (mostly in en:wp). Typically it works quite fine, but we are aware of that we as researchers have as our main task to deliver correct and up-dated information in the areas we work and that most of us are not Wikipedia gurus. For this particular course, the intent is to have 10-20 PhD students (early career research scientists) to together and under the guidance of professors develop pages such as the ones you mention. I.e. where particular organism groups have their own barcoding pages and in addition, to up-date the whole page as such. We will develop these new pages in sandboxes and I will assist so that the content and new pages as close as possible meet the Wikipedia standards. That being said, we are until the course starts asking for feedback from the community on what to emphasize the writing on (kind of a wish list). Also, and when the course is running we want to get feedback on the new pages being developed. Olle Terenius (UU) (talk) 21:01, 4 October 2018 (UTC)

Sounds good, also if you get no specific feedback here then I would take that as endorsement to go ahead with changes as you see fit (which may of course be subsequently edited or altered by others, but that is the nature of Wikipedia)... Best regards - Tony Tony 1212 (talk) 02:15, 5 October 2018 (UTC)

Tony - we invite you to check our final product of the new DNA barcoding page text and structure before we publish it (i.e. replace the old one with our version). We have so far worked on my sandbox, so please feel free to leave comments in the talk page there. We are of course aware that previous users have done by others earlier, and have used their text where possible. More explanation on my sandbox talk page https://en.wikipedia.org/wiki/User:Maria_Kahlert_(SLU)/sandbox[[4]]

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)

Moving COI specific part toward the COI Wikipedia page

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 Bonnie, actually I would do things the other way around: on the page/section Cytochrome_c_oxidase_subunit_I#Use_in_DNA_barcoding, insert the link

Main article: DNA barcoding

since my intention, in adding the paragraphs above to the present page, was to bring the various threads earlier in the page together and up-to-date and provide something of a summary of the present situation, something I felt was lacking when I looked at this mid-2018. You can of course expand the relevant section on Cytochrome_c_oxidase_subunit_I but I would not remove the quotes from the present page... Just my view of course; however it may help if you think about the wikipedia pages as a bit of a hierarchy: the COI page talks about the chemistry of the protein/gene, then it has various applications of which DNA barcoding is one, which is where the main talk about that application then belongs. Actually it is more of a network since DNA barcoding also employs other genes as well, each of which then has their own page dealing with the chemistry of that one, however the uses in DNA barcoding all live together on this page.

In the section above, others have announced an intention to restructure this page somewhat which might include some re-writing anyway and possible split into sub-pages for animals, plants, etc., so you might also want to seek an update on their plans via this or their own "talk" page - or hopefully they are watching it and may give us one. Regards - Tony Tony 1212 (talk) 18:43, 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)

OK, Thanks Maria... bottom line is that people are free to make changes as they think best for the article (although it is good to seek feedback before making substantial changes, via the talk page as you are doing), while recognising that anything you or I write can get changed as well in the future. I am happy to observe since I have no particular scientific involvement in the topic, I just came to WP to learn a bit more and ended up researching then writing some of it! All the best - Tony Tony 1212 (talk) 10:15, 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)

Congratulations Maria and team on a large task well done! Cheers Tony Rees Tony 1212 (talk) 08:59, 23 May 2019 (UTC)

Possible further work: improving readability

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)

Wiki Education assignment: Seminars in Forensic Science

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)