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

#1

Ask me what I want to be invented in my life time, and my answer is usually consistent. Remember Star Trek’s tricorder? Ever played a video game where you, as the player, could “scan” organisms in the world and know immediately what they are?

One thing citizen science has revealed, more than ever, is how much we don’t know. Almost every insect sighting is a new data point. There are new and undescribed species all around us, even flourishing in our backyards. But at the same time, the world is rapidly changing, and species are disappearing, some which we may have not even known about. If LA disappears, people may lament the lost bird colonies, and mammals, but what about the tens of thousands of still unknown flies, wasps, beetles, and micro-life? Ordinarily we would wait for specialists to rise up, say in crickets, to compare specimens and work out the species, where they are found, and their biology. But there are still many groups without specialists, and even those with specialists are often slow progressing. The research in Stenopelmatus has taken more than a decade, and the researchers are still not nearly done!

For citizen scientists to really go all-out, we’d be collecting specimens and DNA on what we find. At the moment most of us can only really do “sight records”, which only works for species that can be confirmed visually. For many groups, or even ages (e.g. plants with no flowers), this is not possible. But DNA barcoding is very expensive, requires taking a specimen out of its environment, and not feasible for even some seasoned researchers.

What we need is a handheld device, that lets us identify DNA, and barcode it. At the least, it will let us see what species is in front of us. At the most, it can store that DNA barcode and add it to a database of barcodes, which are extremely important for taxonomy and classification. Visual sightings have already helped researchers and scientists enough – what if we could provide DNA data as well?

I thought this was just an optimistic dream for a while but recently I was shown this tech, apparently first worked on in 2012: https://nanoporetech.com/products/minion

It describes a device that is able to barcode DNA within a much more feasible time. A start, but we need something more efficient I suppose. What does everyone think about this? Having a handheld DNA scanner?

The only downsides seem to be psychological – A. it would “ruin” the fun of identifying species manually or B. it would make life “too easy”. But I think at this point you have to consider that right now, we are probably in the most rapidly changing environment the world has seen in modern human history. We can’t afford to be ignoring new species, or even known species, at the tip of a hat. Plus, if you can identify things quicker, now you can spend more time looking for more neat stuff!

Cheers to iNat having a “upload DNA barcode” feature in the (hopefully near) future…

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#2

Wow, I was just talking with one of my undergrads last week about this potential capability coming soon- and it’s already here, accessible at least for certain affluent citizens or groups!?

Ten years from now the price will probably be way down and the capability increased. But by then some species may be harder to document, so I hope a few early adopters will give it a try!

#3

So true. I hope we get this too. It may make parts of my job outdated, but that’s true for so many tech things and so many jobs anyhow. In any event, I agree that we just need to understand and using tools is not ‘cheating’… no one says using a hand lens to ID a plant is cheating.

My biggest concern would be that it would be an even bigger barrier separating some disadvantaged groups from nature, unless it was really cheap and easy, which won’t happen right away even if it does later.

#4

After coming across this observation, I looked the LifeScanner kit up to see if I could do the same thing and was disappointed to find that it costs $50 and can only be used 4 times.

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#5

This has been the dream of Costa Rican biologist Dan Janzen for many years. Sadly, it appears that Nature is more complex than we thought and that the use of a single segment (596 bp) of mitochondrial DNA is not always enough to identify species. Lepidopterists are finding that additional DNA sequence information from nuclear genes is sometimes needed. Still, I would love to have a hand-held device that would provide some DNA sequence information easily and cheaply!

#6

I use the “DNA Barcode COI” Observation field for now:
https://www.inaturalist.org/observations/478367
https://www.inaturalist.org/observations/478475
https://www.inaturalist.org/observations/478466
https://www.inaturalist.org/observations/478418
etc.

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#7

It’s 50 Canadian dollars though! (Roughly USD$37.) That’s less than $10 per sequence. Not bad really.

#8

The big flaw in your “vision” is that the taxonomy has to be done before barcodes have any meaning. Individual organisms are typically not clones, so their barcodes differ. Without first doing the taxonomy, you cannot (1) assess in any meaningful way whether two individuals belong to the same species or not; or (2) associate a species with a scientific name. In theory, you could potentially discard scientific names in favour of something like just the barcodes themselves (though there is still problem (1) above), but that would be “throwing the baby out with the bath water” and creating a hole new raft of problems and I, for one, will simply walk away if that ever happens!

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#9

Interesting Stephen. I’ve already seen a number of cases where specimens have been “DNA matched” through databases such as BOLD and that used as justification for ID. I made an assumption, perhaps an incorrect one, that DNA barcoding was a reliable alternative form of ID.

So is it not really possible to quantify species into those categories without the taxonomy? I am sure I have seen papers where barcoding was used to categorize currently named species, and determine which populations needed further review as potential new species. It took specimens from each species and formed them on a chart, with obvious “clusters” that marked records of the same species.

At the least, such a “vision” would still help record data on otherwise indistinguishable invertebrates that are currently taxonomically stable.

#10

Looking at the genes is just another way of looking at an organism, same as counting anthers or measuring sepals. "doing taxonomy first’ based on phenology is basically a big part of why they are redoing everything. Which I don’t like, but that’s a whole other post i’ve already made. I think what you are trying to say is we need to get a lot of data. in theory iNat would allow both phenotypic (photos) and genotypic (samples) which along with sampling herbarium records, insect collections, etc, could be the grounds for expanding that sample size. And… we may very well find that evolutionary convergence works on a molecular scale as well as a phenotypic one, and that the genetics aren’t as good a tool as people think. But it’s worth looking.

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#11

Well said @stephen_thorpe.

To put it in (maybe) more relatable terms, what is the human barcode? It is the common denominators of 7+ billion individual genomes that we decide belong to the species Homo sapiens. Thanks to the commercial human genetics industry, that sample size continues to grow, but it will always remain an incomplete sample.

Sample sizes for most other organisms will remain infinitesimally small by comparison. One can match a new unknown sample by similarity values to existing sample sets, but they will rarely be exact matches, and will never be able to rule out the possibility of the sample being from an undescribed or previously unsampled species without further taxonomic scrutiny.

Note in the preceding paragraph that there was no mention of DNA. The statement holds true equally for DNA, phenotype, or any other kind of taxonomic evidence.

#12

This document scopes some of this topic quite well, especially the first of the “Year is 2028” scenarios on page XII:

https://royalsociety.org.nz/assets/Uploads/Discovering-Biodiversity-decadal-plan.pdf

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#13

At least at present, BOLD is littered with misidentifications and so incomplete that it is not funny. I’m not being funny when I say that I have been involved in a funded project which used BOLD to try to ID terrestrial inverts in a malaise trap sample from NZ, and some alleged matches were to tropical reef corals and other such random absurdities!

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#14

By “phenology”, I assume you mean morphology?! I think that for most groups, (alpha) taxonomy based on morphology is perfectly fine and that adding in genetics just muddies the previously clear waters (in the worst cases leading to alleged “sympatric cryptic species”!) For some groups however, genetics might help to resolve unclear morphology, but genetics really isn’t the “one size fits all” answer to all our taxonomic problems!

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#15

i don’t entirely disagree but it appears pretty much all taxonomists do.

I also didn’t say phenology anywhere so I don’t know where you got that from.

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#16

This is inevitable (since the tech already exists) and will possibly be a change like the invention of the internet or the rise of social media. Not only naturalists want it. Anyone who is interested in genealogy wants it. People who want to know what genetic diseases they and their family may be at risk of want it. Doctors want to instantly know what medication you will react positively or negatively to. People into breeding pedigreed pets want it and so do the people who buy the animals. Farmers could use it to determine which animals to breed with and nursery people would do the same with plants.

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#17

Cheers to iNat having a “upload DNA barcode” feature in the (hopefully near) future…

That would duplicate resources that are already available, like GenBank and BOLD. If there was a way to link an iNaturalist observation to a GenBank or BOLD accession, that would be preferable.

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#18

So all things now considered Stephen, what do you think is the best step forward?

Is DNA barcoding still useful, even if current data is lacking? What is the alternative? 3D scanning genitalia and external features? Is there some way we can “replace” specimen vouchering in the traditional sense, so that citizen scientists are still able to collect data on cryptic groups? Maybe we don’t ever want to replace specimen vouchering, but specimens don’t last forever.

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#19

Yeah, I look at projects like iNaturalist as very valuable supplements to the primary specimen data (and certainly also as having much additional value outside the arena of taxonomy!). But otherwise, the entire taxonomic framework upon which these projects (and all the rest of the biological sciences, including DNA barcode interpretation) are based literally would not and could not exist without current and ongoing specimen vouchering, and all of the primary and secondary data derived therefrom.

Much as I hope things like iNaturalist, GenBank, etc., last forever, there are specimens out there with a 300+ year head start. Wars, natural disasters, and misguided funding decisions have been their main enemies during that time.

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#20

I got it from what you said!

"doing taxonomy first’ based on phenology is basically a big part of why they are redoing everything

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