some of you know my goal is to photograph every species on the planet and the invertebrates are hard to identify (especially with flatworms and Copepods and Ostracods) and would like to know if something like this exists and i’m out of the loop.
Is there a person or a place i can send species to for DNA and Genetic analysis to identify species?
1 Like
There are a number of different sequencing facilities that can do DNA barcoding, and so it will depend where you are located. However, I have a feeling that it won’t be quite what you are imagining - while sequencing technology has come a long way in the past couple decades, it is still relatively expensive and labour intensive. If you do not have access to lab equipment to isolate the DNA yourself, paying the facility to isolate the DNA for you will quickly become pricey if you’re trying to sequence every species you encounter. If you have access to lab equipment and can isolate the DNA yourself and also amplify the DNA barcode sequence yourself, then Sanger sequencing is not too expensive - it can range around $5-$15 per sample. However, you would likely have to learn how to analyze the results yourself - it is not all that hard, but requires an understanding of genetics to interpret the data. Keep in mind that not every species on Earth has been sequenced yet, so it won’t be possible to identify every species this way. Also keep in mind that sequencing a single gene will not lead to 100% reliable IDs every time (for a variety of reasons, sometimes different species will share identical barcode sequences).
12 Likes
any tools you can send me a link too so i could possibly buy some of the DNA isolating and sequencing myself??
I’m not sure what your background is, but the International Barcode of Life website has some information, and the step-by-step is outlined here: https://ibol.org/site/wp-content/uploads/2021/03/DNA-barcoding-webinar-en.pdf
The equipment involved isn’t really something that can be bought and learned independently as a hobby - the equipment can be quite dangerous without proper training (centrifuge, toxic chemicals, etc). If you decide that this is a skill that you want to pursue, the first step would be to get experience working or volunteering in a molecular biology lab where you would be able to get training in how to safely use the equipment.
The DNA sequencing machines themselves are extremely expensive, so even genetics labs don’t normally have their own - usually a lab will extract DNA from their samples, prepare the DNA for sequencing (for barcodes, this means making many copies of the barcode DNA), and then sending that DNA to a dedicated sequencing facility that will sequence the DNA for a cost.
5 Likes
Wow, very ambitious! How do you plan to get some of the deep-sea species, or those endemic to areas hard to travel to (North Korea, Afghanistan, closed caves).
1 Like
When you consider how many ARE acsessible, those inaccessible ones come out in the rounding. Just to say something like “I’ve observed every species in Florida” would be incredible and maybe doable but would realistically have to exclude things like the hundreds of marine micro snails that are all smaller than a grain of rice. I’ve been digging through sand for years and have only gotten up to 220 mollusk species. Obviously this is just a something I specialize in and any other taxa (especially insects) can be just as bad but my point the problem isn’t that they aren’t accessible, but that you have to specialize in a taxa if you really want to get anything done.
If you find 100 marine mollusks in Florida, I will let you say you found all of them
A quick scroll down this exhaustive list (as far as I can tell) and the comment that I’ve only found 220 of them may make my point more obvious.
http://jaxshells.org/atlantic.htm
This list doesn’t even include bivalves
Imagine what it’s like for beetles or moths!
4 Likes
Very hard i do say!
I got like 65% of all birds in Ohio (BREEDING) and atm my hardest thing to get and find ate mammals
Atm i have 1921 added (about 30 or so more from an Aquarium left to add)
Almost at 300 plants
20 Fungi
2 Lichens
1 Algae
Might end up making a website for these and use that instead of my SD cards
Precisely, one also runs into the issue that earth’s biodiversity is simply insanely vast.
I will say, even taking birds as an example, they can be quite difficult. Peter Kaestner, perhaps the most prolific birder alive, has observed about 10,000 species. That’s a man who has dedicated a significant portion of his life to birding, and he’s 70. There are about 8.7 million known species on earth. Let’s say you were born yesterday, and you live to 100 years. You would have to photograph 238 new species a day, every day, from birth til death.
You’ve photographed about 2000 species so far. I don’t mean to make any assumptions, but for the sake of a thought experiment let’s say you’re 20. If you are, it’ll take you 87,000 years to complete your project at the current pace. If you’re 10, it’ll only take 43,500.
I don’t say this to discourage you, but to give you a sense of scale. I’d encourage you to work on a similar project – it looks like you’re well on your way to observing every bird and mammal in Ohio, and there are lots of good sets to complete (every bear, every big cat, every crocodilian, every great ape). Photographing every species may prove difficult, however.
12 Likes
I’m rewatching the Big Year right now and just keep thinking about this.
I keep typing and deleting things because I don’t want to be negative, but honestly, photographing every species is an impossible goal. So figure out the why for that goal and do the why, not the thing.
And if you haven’t, watch The Big Year. And have more everything.
edit- this movie is making me feel really emotional, and I’m sorry for all of this.
5 Likes
A nanopore MinION + sequencing kit comes in at around $2000 at the moment. That doesn’t include the flongle + flowcells (you really don’t need the fullsized one for much beyond full genome sequencing or a massive amount of samples,) PCR primers, thermocyclers, centrifuge, etc… but it’s doable for a really dedicated hobbyist. That said, even with the smaller flongle, its really not worth the cost unless you’re sampling hundreds of specimans at a time - if you’re not doing that its better just to pay the money to send things off for Sanger sequencing.
For fungi sequencing at least, keep an eye out for mycoblitzes; Mycota labs has an open call for specimans from a few states (https://mycota.com/free-sequencing-opportunities/) and they run period mycoblitzes that cover larger areas of the country.
2 Likes
Oh, that’s not bad! Much more affordable than the $1,000,000+ high-throughput Illumina sequencers haha. I guess someone with a big budget could set themselves up… still, I hope nobody is trying to DIY a genetics laboratory without full safety training! I can’t so much as use a stepstool at work without completing a safety training module, I hope nobody is purchasing a centrifuge without some sort of hands-on training.
Yeah, sequencing tech has come a long way and is actually at the point where it is approachable for people who don’t have access to professional laboratories.
And bonus, nanopore can sequence longer reads than Illumina - so with fungi sequencing, we can easily get the full ITS1 - 5.8s - ITS2 easily for barcoding. I wouldn’t be surprised if someone starts adding on LSU as well, though there is less reference data available currently for regions outside of ITS
EDIT: One more bonus - nanopore works by collating individual reads into a fastq file. Which means you can look at all of the reads and see if there are multiple haplotypes present - I personally just think this is extremely cool (but also, frustrating because there isn’t an IUPAC ambiguity code for nucleotide-or-gap)
I just want to say I whole-heartedly approve of this topic and conversation. Respectfully, of course, @anycade1’s goal to photograph every species on the planet is ridiculous. Just in a technical and mathematical way, mind you - who wouldn’t want to see every species on the planet? I share @anycade1’s goal!
But the practical challenges of DNA/genetic analysis are rarely discussed, and what good nature-lover hasn’t wondered about this sort of thing? Utility of an amateur sending random samples for genetic testing? Cost to DNA sequence every species in the world? How to make my own super-dangerous home DNA lab? I want to know!
Edit: I just want to add - I mean, really, isn’t iNaturalist’s goal the same as @anycade1’s? Let’s do this :-)
5 Likes
https://mycota.com/product/dna-barcoding-with-ont-minion-course/
So mycota offers a nanopore course to help fund their ongoing sequencing efforts; the live zoom class was in March, but it was recorded and still available.
So you know, if you’re interested… That course is focused on fungi, but transferrable to other kingdoms.
EDIT: while I’m thinking about it, this is one lab you can send stuff of to if you want to get things sequenced http://www.alvalab.es/
1 Like
That’s awesome! Is the single sequence usually enough to get the fungi to species? I mostly work in groups where there’s enough gene flow and incomplete lineage sorting among close relatives that often almost no single gene is really diagnostic, at least not 100%.
I’m holding my breath for Pac Bio hifi sequencing to get cheaper, I’ve only worked with short reads and it can be frustrating when an interesting part of the genome just can’t be assembled from the short reads - so close, just out of reach.
1 Like
For most groups, barcoding works pretty well. ITS is the most common barcoding region, though for some groups I believe LSU, TEF1, or RPB1 work better (not comprehensive and I’m certainly not an expert at this, I’m not actually sequencing myself I just do validation for our group.)
There are some cryptic groups, and some groups that need multiple regions to get to species - but the vast majority are pretty easy to figure out, assuming there is good reference data - good meaning either a type sequence, or a consensus in the community on what sequence actually represents what species. Genbank is a bit of a mess sometimes so some groups are a still a little bit up in the area as to which sequence actually represents the strictest sense of the species.
Some groups do have ITS regions that don’t evolve as quickly, so may be difficult to tell apart from just that region - different species occasionally have the same ITS. so some species may have a 1 or 2 BP difference that legitimately belongs to a separate species, meanwhile other groups have almost a 2% difference in similarity but still definitely belong to the same species - though the latter is fairly extreme.
I look at a lot of barcodes. Its a weird, very specific job LMAO
5 Likes
Good to know, thanks! Sounds like a cool job. I work on birds, which come with the luxury of having most of the species-level diversity pretty well described already (beyond some minor details). Fungal diversity seems to have so many question marks in comparison - sounds daunting but exciting.
2 Likes
The difference of understanding between birds and fungi is completely understandable but also wild to me.
Sequencing, I truly think, is going to be huge for getting fungal taxonomy untangled. There’s too many species that were described multiple times, or cryptic complexes that contain multiple species, or even groups where names were applied to mushrooms that clearly differ from the species from the type location. So yeah, it is very exciting! There’s a lot of collaboration amongst sequencing groups, as well - its refreshing to not have things stuck behind a paywall.
3 Likes