The future of DNA barcoding, and its use in citizen science

To me this has been one of the huge contributions of iNaturalist and similar sites. I have learned so much more about field ID of the plants of interest to me since I’ve been helping with identification on iNaturalist. And I had been doing field botany for 30 years before that!

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I’m not sure that is a balanced view of the situation, but rather an inadvertent case of something like “cherry picking” (no botanical pun intended!) on your part. You can always actively find examples to illustrate the importance of vouchering in such cases. My view is that such examples are in the minority of cases, so photo observations will be fine in the vast majority of cases where we think we have the taxonomy sorted out already. Those old Phragmites observations aren’t now “useless”, I suggest. The genus is still correct and they point us to sites where it may be worth having another look (assuming the plant is still present there, and if it isn’t, then it sort of doesn’t matter much any more anyway!)

In botany, “field identification” depends a lot on phenology. How many monocots can you field ID if they are sterile? In entomology, it is actually standard to not be able to field ID certain groups at all. But, one big advantage here of the iNat approach is that it is not limited to photos in the field. There is nothing to stop someone (and I do this a lot), uploading a series of diagnostic photos taken in the lab (including of dissections). Then if the ID is clear from the photos, I discard the specimen rather than waste resources on trying to keep the specimen safe in perpetuity, when it has already given me all the useful info I am likely to get from it!

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Although I can’t speak for much of the hard science, I think a balance does have to be made, because at no point is the boundary between one species, subspecies and another consistent and clear-cut. Speciation as we know it does not fit very well into evolution, because species concepts rely on a taxonomic unit that is stable and relatively consistent. The consequence is cases like Phragmites australis, where the plant is clearly in a state of flux and we are seeing populations that are starting to diverge, and we have no idea what to do with it. Besides split it up into a large number of “microtaxa” that attempt to classify what it is becoming.

I still think taxonomy needs to work together with field ecology and biology – besides following the “most correct taxonomy”, what does breaking up a species into hardly separable cryptic taxa really accomplish? For any practical field work, it seems like it is only harmful, leaving more and more organisms that you can’t quantify to a classifiable level. Rubus fruticosus had this problem and the cryptic microspecies require every life stage of the plant for ID – that is just not feasible in many cases.

I think at times many people mistake “most correct taxonomy” for “perfect taxonomy”, and claim this as inspiration or justification for cryptic taxonomy work. And in some cases, this is justified! But, I have doubts sometimes. Although I admire the intention of “correct taxonomy”, there has to be a point where we just leave a species as “genotypically variable”, right?

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Let’s face it, part of the problem is that taxonomy is a human activity and therefore subject to “politics” in some broad sense. Add economics (i.e. “funding”) into the mix, and taxonomy is being pushed and pulled in several different directions at once! Everybody has slightly different ideas on what is or isn’t “important”, and the fact that the organisms themselves aren’t simply “black and white” provides plenty of scope for argument!

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Someone made the comment recently, that poor Hypoblemum must be suffering an identity crisis! If they could have an identity crisis, then they are equally likely to be highly amused at our ridiculous efforts to put square organisms in round taxa!

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Is DNA barcoding to the point that it is useful for a hobbyist? That LifeScanner website makes it look like for about $15 a sample I could credibly barcode aphids that I collect. That isn’t great compared to the perhaps $1 I am spending on a microscope slide, but it isn’t outrageous either.

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$15 a sample, but there is a huge upfront setup cost

My understanding is that with the Lifescanner kits you just collect the organism and mail it to them?

Here is a review I found in an iNaturalist journal and its comments: https://www.inaturalist.org/journal/dhobern/4253-lifescanner-dna-barcoding-for-all

I found this related project but it is way more expensive: https://news.uoguelph.ca/2018/05/u-g-supports-biodiversity-moving-dna-barcoding-lab-real-world/

I just read about this project today: https://conservationxlabs.com/dna-barcode-scanner
https://conservationx.com/project/id/4
From this article: https://www.nature.com/articles/d41586-019-01678-6
Doesn’t look like it’s out yet though.

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Just shouting out a current podcast that may interest some here

https://www.theguardian.com/science/series/science

" In part two of The Age of Extinction takeover of Science Weekly, Patrick Greenfield and Phoebe Weston explore a relatively new and controversial technology called DNA barcoding that is helping scientists to differentiate between species – including fungi, which we heard about in part one. As the catastrophic loss of biodiversity around the world continues, could DNA barcoding at least allow us to accurately record the species that are perishing?"

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I didn’t have time to read the whole thread, but as I see it, this will face the same obstacle that most citizen science faces: gatekeeping. Just try getting access to laboratory equipment, or collecting permits, if you are not affiliated with a university or research institute. Google Scholar will not even validate my profile – with my list of publications – because I do not have an institutional email address separate from my personal one.

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Just wanted to chime in on this thread to boost the Citizen DNA Barcoding Network: https://dnalc.cshl.edu/programs/citizen.html

Come on over to the iNaturalist Discord Server (https://discord.gg/uskv2yx) if you’d like to get involved in an effort to barcode previously unbarcoded ants, beetles and mosquitos.

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Here’s a similar project looking for caddisfly specimens: https://caddisflycollective.com/

https://onlinelibrary.wiley.com/doi/10.1111/syen.12538
besides, I noticed that vandalism in herpetology was mentioned in the conclusions. I googled “vandalism in taxonomy” and am dismayed. Barcods create new opportunities in this “field”.

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