Robyn Williams: The Science Show on RN, where the big science story of the week was of course the Tasmanian tiger. Kevin Rowe at Museum Victoria.

Kevin Rowe: They have been trying to crack it for quite a while, and so the idea of cracking the complete DNA sequence of an extinct species has been around for a while, and palaeontologist Mike Archer tried to crack that thylacine genome. But the technologies weren't really available, and only recently with new sequencing technologies has it become more tractable because all the thylacine genomes are stored only in museum collections because the species is extinct.

Robyn Williams: In fact Mike Archer from the Australian Museum at the time, and now at the University of New South Wales where he has gone back, was hoping that you could get enough out of the genome to put it into an egg and get a resurrected thylacine.

Kevin Rowe: Yes, that was the pitch, that we could clone a thylacine, because cloning at the time had become possible with Dolly the Sheep, but still, cloning an animal requires having a host egg that is exactly related, or very closely related, and unless you find a thylacine egg lying around its going to be hard to clone.

Robyn Williams: And fairly intact DNA.

Kevin Rowe: You need intact DNA, it needs to be in a chromosomal structure, and so when we are sequencing nowadays it's very short fragments.

Robyn Williams: And so it's from your specimen, is it, and work being done at the University of Melbourne.

Kevin Rowe: Yes, it's a specimen in the Museums Victoria collection that it was actually a pouch young that was fortunately put into alcohol almost 100 years ago and is the best preserved DNA of any thylacine that we know of in any collection, and has helped researchers from the University of Melbourne to be able to sequence the complete genome, so every nucleotide base pair of the DNA, understand what kind of evolutionary history we lost, and also how they are convergent with dogs and similar predators.

Robyn Williams: Talking about similar, you come from the United States…

Kevin Rowe: Yes, I do.

Robyn Williams: Have you got anything remotely like a thylacine? Do you have many marsupials in North America?

Kevin Rowe: We have one species of marsupial in North America, the opossum, which in some ways is like the thylacine. Its skull shape and cranial shape is actually very close to the thylacine. And you should stay tuned for some cutting-edge work via palaeontologists on that front. So in some ways this little garbage-eating opossum that we have could be a lot like the thylacine.

Robyn Williams: Doctor Kevin Rowe from Museum Victoria. And as you may have heard this week, Professor Andrew Pask from the University of Melbourne who was on The Science Show years ago having borrowed a thylacine gene and put it into a mouse, it was he who published the paper on the entire genome this week.

Andrew Pask: I think it was 10 years ago when we resurrected the thylacine gene in the thyla-mouse, and then showed that we could actually get that gene to be expressed and you could actually recapitulate its function in a mouse. So it was the first time anybody had taken extinct DNA and then resurrected its function in a whole living organism.

Robyn Williams: And then what happened?

Andrew Pask: Well, it kind of opened up a can of worms for us in terms of you could actually take extinct genome information and start to functionally analyse it because that had been a huge roadblock before. We could get the blueprint, we could read the sequence code, but then actually seeing how those things functioned and worked we couldn't do. But by taking that gene and putting it into a mouse, we showed that you could actually get that piece of DNA to be functional again, and then actually start to figure out what it did and how it worked.

Robyn Williams: It didn't wreck the mouse though, did it?

Andrew Pask: No, we were just looking at where it was switched on. But you could potentially do that, you could take a thylacine gene and replace it in the mouse genome and then see how it changes development or some aspect of its physiology.

Robyn Williams: Fine. Going back to the paper, just been published this week, why did you want to look at the thylacine genome in the first place?

Andrew Pask: The thylacine I think is one of the most fascinating marsupial species we ever had. It's just this incredible example of what we call convergent evolution, which is when two species evolved to look extremely similar, and that's because they occupy the same ecological niche, so they both have the same sort of role in the environment, and so they get this extraordinarily similar body design. And we see that between the thylacine and with dogs. They have this absolutely unbelievable, unsurpassed level, as we have shown in this paper, of convergence. And that's really interesting because I'm really interested in how the genes in our genome shape our development and shape those sorts of trajectories towards a particular body plan. And so having this amazing example of convergent evolution, we can then look at the genome, which is what we've sequenced for this paper, and then say if we see this striking convergence in body form between dogs and a marsupial, can we also see that reflected in the DNA itself.

Robyn Williams: And therefore if you look at a particular section, for instance…I don't know whether there is one in the barcode, the design of the skull because the skull has got to be used as a hunting, biting device. And would you see similar sorts of things between the dog and the thylacine like that?

Andrew Pask: That's exactly what we predicted. We did a lot of work to show just how similar the thylacine was to the other mammals that are around like the wolf and the red fox. They were the two species that we showed it has the closest form to. Basically you can just take skulls, you can 3-D scan them, and then you can overlay them to see how similar they are. And when we did that we saw that the thylacine was just an unbelievably close example of looking just like a canid or any of the existing dogs, and it didn't look anything like related marsupial species. That was a really fascinating finding, and we could actually quantify that level of convergence. So you can go through and do the maths to see just how much they overlap. And when we did that we saw that it was probably the best example of convergent evolution that has ever been described.

And what's even more fascinating about that is that the dog and the marsupials have not shared a common ancestor since the Jurassic period, so about 160 million years ago. And so it was an extremely deep ancestry that they share. And so yes, the next question then is digging into the genetics of that. Can we find these skull related genes that are really driving that developmental outcome?

So the first thing we looked at was the actual genes in our genome, so they are the things that actually encode proteins, and they make up a very, very small part of our genome. So about 1% or less of our genome is actually protein coding. And we can actually analyse that portion quite easily, and so we compared all the protein coding genes between the thylacine and the dogs to see if we could identify any similarities, and we did, but only in a very, very small number of genes, so nothing like the number you might expect to find if those genes were really super important in driving that body design, and that was quite an unexpected finding for us.

Robyn Williams: Were you surprised, Andrew, by the huge reaction publicly, at least in the press, this week for what you found?

Andrew Pask: Yes, it's been really fantastic that the public…I think they really like the thylacine. It was such an iconic Australian marsupial species and one that was extremely tragic in that we forced them into extinction and they were really persecuted for hunting sheep, which it turns out they probably never did in the first place. And so I think Australians are really quite passionate about the thylacine. And I think anything we can do that gives us more information about the biology of that amazing species…and it's nice because I think it's a really good topic for getting the public engaged in interesting science that we can then do with these genomes to really not just understand more about the thylacine but more about just developmental biology in general.

Robyn Williams: And how different genes, as he said, seemed to lead to the same parallel design. Andrew Pask is an associate professor at the University of Melbourne, and the paper was published this week.