Get Regular Updates!
Search
|Preventing the aquokkalypse: How DNA could save a species

Earth

image|

Getty Images

Preventing the aquokkalypse: How DNA could save a species

Preventing the aquokkalypse: How DNA could save a species

What can you do with a quokka genome? And why are scientists releasing it for free?

Preventing the aquokkalypse: How DNA could save a species

Earlier this month, researchers from UWA produced a complete genome for arguably WA’s most famous marsupial. Then they uploaded it to the internet, for anyone to access, as part of an international project called the DNA Zoo.

Here’s why that’s a big deal – and it’s not for the reasons you might think.

But first – how?

Extracting DNA is easy. You can do it with a blender in your kitchen. The hard part is reading it. DNA lives in tightly packed structures called chromosomes, so to read it, you kind of need to break it first.

Rather than smashing the whole structure, like earlier techniques, the DNA Zoo approach tries to keep related parts of the chromosome together.

“Basically, we photograph the DNA in three dimensions, and we do it using 1% formaldehyde,” says  Parwinder Kaur, Associate Professor at the Faculty of Science at UWA and Director of DNA Zoo Australia.

Then, when the time comes to put it back together into a sequence, that extra information helps reassemble the sequenced pieces in a computer.

“We learned this from Facebook in a way. Sometimes when you post a lot of photos on Facebook, Facebook comes back and starts suggesting relationships. You post a lot of photos with this person, you guys must be related. So it’s the same approach for DNA,” says Parwinder.

Particle - The science story accelerator
Image|Parwinder Kaur
Parwinder in the lab
"It’s just a very clever way of looking at the DNA, unpacking it and then putting it all together.

That makes it faster, easier and way, way cheaper – a species’ complete genome can be sequenced for $1000.

“If it was $2 million or even $1 million, I’d have to write I don’t know how many grants to get the quokka genome. All I need now is just to go ask for samples,” Parwinder says.

(Those samples, by the way, come from vets and other researchers who already work with the animal population. No quokkas were harmed in the making of this genome.)

View Larger
Image|DNA Zoo
It may not look like much, but this is a complete snapshot of the quokka genome.

Once all that’s done, the DNA Zoo team releases the whole lot online, free for anyone to use. But what exactly are people going to use it for?

Welcome to Quokka Park

Let’s start with the obvious question: does this mean we can clone the quokka? Should the unthinkable happen and quokkas go the way of the dinosaurs, does this mean we can restore the species from their freshly uploaded cloud backup?

“With the technological advancements, probably in the next 5 to 10 years you will be able to do it, yes,” says Parwinder.

“But I ask you a question back for this one. Would you spend all your resources cloning something back which you’ve already lost? Or would you spend your resources to save what you are going to lose?

“You can probably bring back the Tasmanian tiger. But can you let your devil go? Can you let your quokka go? Can you let your koala go?”

Image|Jurassic Park
Except this time they actually did.

The point of projects like DNA Zoo isn’t to bring species back – it’s to stop them going extinct in the first place.

Macropod Matchmaking

To understand how, we need to look at what DNA data is actually useful for.

There are two quokka populations – one on Rottnest and one on the mainland. Quokkas may be abundant on Rotto (and on Insta), but that doesn’t mean they’re not threatened.

“There were about 500 quokkas which were living on the mainland, and in 2015, the wildfires wiped them out. So from 500, we got down to 39,” Parwinder says.

Small populations in a small area are much more at risk of extinction.

“Just one wildfire and you lose them all,” says Parwinder.

Unfortunately, it also makes the solution harder. Fewer quokkas means fewer copies of the DNA out in the wild. That means there’s a much larger chance of weak or damaged genes being passed on to future generations. Breeding programs can work around that – but it helps if you know what you’re looking for.

View Larger
Image|Getty Images
A reference genome means quokka breeding programs aren’t working blind.

“Because we’ve got a reference genome, we will be able to exactly map what level of genetic diversity is left on the mainland and then which are the best bets in terms of breeding,” says Parwinder.

Marsupial superpowers

The genome also helps us better understand what unique adaptations a species might have. That’s not so we can build a human-quokka hybrid, but so we can understand how they might deal with an increasingly uncertain future.

“There is no DNA code available for a lot of species which are already gone from the planet,” says Parwinder. “There’s things that we’re not gonna know about them and all the superpowers they had, all those little adaptations.”

Genes can determine how well a species deals with disease, new habitats, new food sources and even climate change. Knowing what genes the quokka has lets us know where they might need help and how we might help similar species too.

View Larger
Image|Danny Lam
Yes, they’re cute, but no, you still shouldn’t pat them.

Genetic data can also help us understand diseases spreading the other way, from animals to humans. That transfer is called zoonosis, and it’s an understandably hot topic right now. It’s also why you really shouldn’t pat the quokkas, even though they’re really cute.

If you love something, do it for free

So a genome isn’t a backup of a species for future scientists to restore. It isn’t about building superheroes. It’s about helping quokkas make the most of the superpowers they already have so that mammoth effort of de-extinction isn’t needed.

That’s information, Parwinder says, that researchers and conservation bodies could be using straight away.

“It may take me two years to put a good publication together, which will appear in a nice decent journal.”

“Who knows what could happen in those two years.”

 

The entire DNA Zoo team at their home lab in Houston
Image|DNA Zoo
The entire DNA Zoo team at their home lab in Houston
“So it’s all publicly accessible, and anybody who’s good at coding, who’s good at wildlife knowledge, can join in. And we would love to have more and more people join to share it and help us.”

Particle Puns

Republish

Creative Commons Logo

Republishing our content

We want our stories to be shared and seen by as many people as possible.

Therefore, unless it says otherwise, copyright on the stories on Particle belongs to Scitech and they are published under a Creative Commons Attribution-NoDerivatives 4.0 International License.

This allows you to republish our articles online or in print for free. You just need to credit us and link to us, and you can’t edit our material or sell it separately.

Using the ‘republish’ button on our website is the easiest way to meet our guidelines.

Guidelines

You cannot edit the article.

When republishing, you have to credit our authors, ideally in the byline. You have to credit Particle with a link back to the original publication on Particle.

If you’re republishing online, you must use our pageview counter, link to us and include links from our story. Our page view counter is a small pixel-ping (invisible to the eye) that allows us to know when our content is republished. It’s a condition of our guidelines that you include our counter. If you use the ‘republish’ then you’ll capture our page counter.

If you’re republishing in print, please email us to let us so we know about it (we get very proud to see our work republished) and you must include the Particle logo next to the credits. Download logo here.

If you wish to republish all our stories, please contact us directly to discuss this opportunity.

Images

Most of the images used on Particle are copyright of the photographer who made them.

It is your responsibility to confirm that you’re licensed to republish images in our articles.

Video

All Particle videos can be accessed through YouTube under the Standard YouTube Licence.

The Standard YouTube licence

  1. This licence is ‘All Rights Reserved’, granting provisions for YouTube to display the content, and YouTube’s visitors to stream the content. This means that the content may be streamed from YouTube but specifically forbids downloading, adaptation, and redistribution, except where otherwise licensed. When uploading your content to YouTube it will automatically use the Standard YouTube licence. You can check this by clicking on Advanced Settings and looking at the dropdown box ‘License and rights ownership’.
  2. When a user is uploading a video he has license options that he can choose from. The first option is “standard YouTube License” which means that you grant the broadcasting rights to YouTube. This essentially means that your video can only be accessed from YouTube for watching purpose and cannot be reproduced or distributed in any other form without your consent.

Contact

For more information about using our content, email us: particle@scitech.org.au

Copy this HTML into your CMS
Press Ctrl+C to copy

We've got chemistry. Want something physical?