environment

Stoat ‘CSI’ possible now genome is mapped

The genetic secrets of New Zealand’s predatory 'lion' have been revealed with the mapping of the stoat genome, and there's hope better, kinder ways of getting rid of the introduced killing machines might be found

A stoat’s spleen, liquid nitrogen, supercomputers, and 18 months of international effort has led to the mapping of the stoat genome.

It’s hoped this new knowledge will help create tools, such as more efficient toxins, to target the introduced predators, and could be used to pinpoint stoat identity and spread.

Manaaki Whenua - Landcare Research vertebrate pest ecologist Dr Andrew Veale led the research. 

He’s spent half his life working with stoats and finds them fascinating and “beautiful” to the point of recently getting a tattoo of them on his arm. 

He describes them as the extreme athletes of New Zealand predators, explaining that rather than waiting and pouncing, they run down their prey.

“In New Zealand, they are the top predator, they are our lions. They shouldn't be here and they do incredible amounts of damage.”

They were first introduced in the 1880s in order to control introduced rabbits. As Veale puts it, “stoats don’t necessarily know what their job is”. They quickly moved from fields to forests.

Capable of surviving in most New Zealand habitats and with the ability to swim up to three-kilometre distances, they’ve turned local fauna into an all-you-can-eat buffet. 

“One stoat swam out to Motuotau Island off Mount Maunganui and in a three-week period killed 93 storm petrels. That was just the number of bodies found.”

Stoats are implicated in the extinction of the South Island subspecies of bush wren, laughing owl and New Zealand thrush.

Dr Andrew Veale's arm tattoo. Photo: Supplied

Coromandel’s Stoaty McStoatface’s immortalised spleen genes

The first step to mapping a genome is getting a decent sample from a fresh stoat whose DNA hasn’t degraded.

“ … most of the time when I receive stoat samples from trappers they are minging,” said Veale.

This work was done thanks to a live-trapped stoat from the Coromandel Ranges. As a male he had an X and Y chromosome making him a perfect candidate for sequencing. Veale said he was humanely euthanised by a vet.

“Within 15 minutes of that I had every organ dissected out and flash frozen in liquid nitrogen.”

The stoat's body has been kept. Veale said it would "probably be preserved at a museum for posterity as the stoat genome individual".

Most of the sequencing was done using the spleen as well as mitochondria, and nuclear DNA. Veale described the nuclear DNA as the “complex interesting stuff” for sequencing. 

From there, it took around 18 months of international effort to get the genome sequenced. 

The super computers capable of doing this cost millions of dollars. The Coromandel Ranges stoat’s organs were sent on dry ice to the United States Rockefeller Institute where the sequencing was done. Funding came from the Predator Free 2050 Limited and Biological Heritage Science Challenge. Collaborators included scientists from the Vertebrate Genome Project and the Wellcome Sanger Institute.

Veale's analogy of pulling everything together to create the final genome sequence is a bit like trying to put together a giant jigsaw puzzle after losing the box lid. 

Four different technologies were used to pull the terabyte of genome data together, some were better at creating big jigsaw puzzle pieces, others at creating small pieces, or giving information about where the puzzle feed fits. 

After checking that what the computer did looks right, it’s then annotated. 

“That's using RNA to then go ‘Well here are the genes’, otherwise, you just have lots of letters, and you don't know what they do. You need to actually say, ‘Okay, this gene is for this purpose’, to make it useful.”

What can you do with a genetic sequence?

As well as using the genome to look for stoat-specific toxins that can be used, there’s the potential of building a 23andMe-style stoat family tree.

Much of Veale’s stoat work is related to understanding how stoats spread across the country. One way would be to catch and collar some, but this is hard, time-consuming, and limited in scope.

Looking at the genes of trapped stoats allows Veale to know who each stoat is related to and map how they spread. 

“Instead of sticking a collar on five individuals and then spending time with a radio transmitter trying to find those five individuals, you could get 300 individuals, and then know exactly all the landscape features that matter. Then you can use that to plan your trapping or your fences or whatever you're doing.”

There’s also the ability for CSI-style forensics. Stoat saliva from bites on a native could be matched to stoats caught in the area. If it’s a match then the culprit has been caught, if there’s no match it means the killer is still at large.

This approach could be used to help solve the recent stoat mystery on a pest-free Motukorea/Browns Island in Auckland, where evidence of a stoat was found, prior to lockdown.

Hours spent trapping and combing the island for the interloper were unsuccessful; However, around the same time a stoat was detected on nearby Motutapu Island. DNA could prove whether the two stoats were in fact one stoat with a penchant for swimming. 

Veale said it’s hard to know all the ways sequencing of the genome will be used.

“We don't know exactly where it will go but now we've got one of the highest quality genomes of any animal in the world. We can look and see what we can do in terms of using that to help control them in humane ways and also just to find out about them because they're really fantastic animals.”

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