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DNA reveals secrets of New Zealand’s big bi -

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HideRobyn Williams: Time. Crazy creatures. Imagine a bird three metres high and an egg twice as big as your head. That's in the laboratory of Mike Bunce at Murdoch University in Perth.

What is that bone here on your lab bench?

Mike Bunce: That is a bone of one species, Euryapteryx, an extinct New Zealand moa.

Robyn Williams: How big was it?

Mike Bunce: That particular one was on the smaller side of moas. They got up to about 250 kilos in weight, about three metres tall. That one was probably about half that.

Robyn Williams: One and a half metres is still taller than a person.

Mike Bunce: It is, yes, they were very large birds.

Robyn Williams: And what particular bone is that?

Mike Bunce: That is a tibia metatarsus, so it's essentially an ankle bone.

Robyn Williams: And how did you get it?

Mike Bunce: We dug it out of a swamp, it's from a swamp called Bell Hill, it's actually a vineyard. They were putting in some vines, digging irrigation trenches and they uncovered it, and I've been involved in a large research project in collaboration with the University of Canterbury.

Robyn Williams: So you bring the bones back, and then what happens?

Mike Bunce: Normally we don't bring all of the bones back. That's a demonstration piece there, that's a real bone, that's about 3,500 years old. We bring them back, we grind a little bit of material off the bone which ends up looking like a little pile of icing sugar, if you like. Then we extract the DNA from that. By that I mean we separate the DNA away from all the other things that are in bone, things like salts, fats, proteins, and so we get a pure preparation of DNA.

Robyn Williams: But the DNA is a very, very big complicated molecule. How do you get something in sufficient states that you can look at a barcode there intact?

Mike Bunce: You're exactly right. In your cells the DNA is in big stretches, wrapped up essentially in chromosomes, but in the post-mortem environment, that's when you die, the DNA starts to break into small little pieces. So that moa bone there has got DNA in it, but what is left there is highly fragmented. So we put together the...sometimes they are thousand-piece jigsaw puzzles, sometimes they are billion-piece jigsaw puzzles, and we try and piece bits of DNA together to get a meaningful picture out of it.

Robyn Williams: And presumably you've got sufficient backgrounds that you can look at a section of this barcode and say, ah, that matches this bit.

Mike Bunce: That's right, we can easily identify the different moa species away from each other, but we are sort of onto more subtle questions than that now, we're looking at relatedness of individuals within the swamp, whether that bone and another bone are distantly related to each other. So we can track their genetic footprints right up to that extinction point about 500 or 600 years ago.

Robyn Williams: Okay, that is very, very recent. Of course the story, as we've said on The Science Show before, is that people came to New Zealand very recently, and very quickly they had an impact. And there's no question they were responsible for killing off most of these rather large creatures. Is that the kind of story that you're tracking?

Mike Bunce: Yes, New Zealand is a fascinating story in that regard. In other parts of the globe there are still quite large debates around whether it's climate, humans, disease, a combination of all three of those, but in New Zealand the evidence is very clear cut. As people arrived, a lot of these moa birds ended up in middens, ovens essentially, and also there were forest fires that swept through large portions of New Zealand as well. In New Zealand, unlike Australia, is not really conducive to large-scale burnings, so the New Zealand ecosystem probably didn't bounce back as quickly as it might have here in Australia. So a combination of fires and hunting led to the demise of these birds, and it happened very rapidly.

Robyn Williams: Over what period?

Mike Bunce: It's really hard to nail that down from carbon dating bones because the eras associated with them are sometimes larger than the periods that we're talking about, but the best estimate reckons they are about 100 to 200 years the moa would have been extinct.

Robyn Williams: Those great big birds, three metres tall as you said, huge creatures, who obviously haven't seen people before, were quite benign; they just stood there and got knocked on the head, that was the end of it. But it's terribly sad, isn't it.

Mike Bunce: It is terribly sad. When you look at New Zealand as a whole, half of its endemic bird species, that's over 100 bird species that were extinct since humans arrived about 700 years ago...New Zealand is a strange place to study evolutionary processes because there are no mammals in New Zealand, apart from a couple of species of terrestrial bats. And so your ideas about how mammals and birds and plants interact, you've got to take that and throw that out the window a little bit when you talking about in New Zealand. It's how the rest of the globe might have evolved really if the mammal lineage hadn't really taken off.

So to give you an example, in ratites, and this is a group of birds that the moa belong to, which is the ostrich, the emu, the cassowary all belong to that same group, sex roles are reversed, so males sit on the eggs. And they tend to sit on these eggs for long periods of time, maybe one or two months, we don't really know with extinct animals, that's half the problem with studying extinct animals is trying to figure out exactly some of their behaviours.

And when we start looking at the archaeological sites we find a large portion of male birds there compared to female when we start to sex the actual bones we find, and we think that's because the early Polynesians were knocking the males on the head when they were nesting and eating the males of course, from their bones, and of course eating a whole lot of eggshell as well, which we find a lot of in these archaeological sites.

Robyn Williams: Which brings me to this gigantic egg on the top of your bench. It is really one of the biggest eggs I've ever seen. Is that moa?

Mike Bunce: No, it's not, it's from the extinct elephant bird, which again is a relative of it. It is a large egg, it's the biggest egg ever, it is larger than a dinosaur egg, and yes, it's a fascinating piece of biology, isn't it.

Robyn Williams: The legend is of course that these elephant bird eggs floated across and they would land up on a beach and that's where you found many of them.

Mike Bunce: Well, the elephant bird we should say is native to Madagascar, and two of them have floated all the way across from Madagascar and landed on West Australian beaches, and there are two of them in the West Australian Museum here. So they are fascinating stories. In Madagascar you can walk on areas of beaches over there which is just loaded with eggshell, and yes, if you are very lucky you can find one of these. If you are even luckier you can sell it because they are worth a lot of money these days. You know, one sold at Sotheby's for about €80,000 recently. We don't have the budget for that.

Robyn Williams: I see there is a packet of bones over here, all in plastic bags, and you've got some test tubes full of round bits. What are they?

Mike Bunce: That's right, these are some of the projects that we're working on in the lab currently. There's been a rapid advance in how DNA has been sequenced in the last five years. You and your listeners may be aware, they hear of all these genomes coming out. You know, they did the Neanderthal genome, there are lots of human genomes, the mammoth genome has been completed. It's referred to as next-generation sequencing, and it's a big thing, it's a big advance. It is the equivalent of if I had a Morse code machine on my desk and I was trying to communicate with you, sure, I could do that. It would be really slow and inefficient. And then somebody comes and replaces it with a computer. That's the kind of technological advance that we've seen in next-generation sequencing. So they've taken away your Morse code machine, they've put a supercomputer on there and are saying communicate more effectively. And you're going, well, sure thing, that's not a problem. So what next-generation sequencing is able to do is sequence small pieces of DNA really, really fast and lots of it.

Robyn Williams: What's in the samples there?

Mike Bunce: These are traditional Chinese medicines that we've been looking at. So we're involved in a study published in PLOS Genetics that's trying to use next-generation DNA sequencing techniques to figure out what is in stuff. So we can say what is in this bag of bones, what is in this traditional Chinese medicine or what is, indeed, in the faecal material, to figure out what an animal actually eats.

Robyn Williams: You've got coprolites, have you?

Mike Bunce: We've got plenty of coprolites, yes, we extract them from caves, and we've got a lot of modern faecal material as well.

Robyn Williams: Ancient poo.

Mike Bunce: Ancient poo, coprolites, that's right, figure out what animals ate in the past.

Robyn Williams: In this lab, finally, what are the main mysteries that might be resolved in the next short period?

Mike Bunce: Okay, if I draw you back to this pile of bones here, we're doing a research program with the Noongar people down in the south-west, and this is an ARC Discovery project, to try and understand archaeological significance of these sites from a molecular perspective and try and understand about the past biodiversity of the area. So you're standing at the moment in one of 34 biodiversity hotspots in the world, a massively significant area in terms of its endemic flora and fauna.

What the unknown question is is how that has changed over time. And we can actually use the DNA preserved in bone material like this to try and figure out what was happening in the past. So this bone material has been extracted from an eight-metre deep hole in the ground that goes back 50,000 years, that's how long the Noongar people have been living in this land for. So what we did in April when we went down and did an excavation is we pulled out tiny, tiny fragments of these bones. This is what archaeologists refer to as the scrapheap because there is not a whole lot of material in here that can be used for bona fide identification purposes because it's just small fragments of bones that they can't tell if that's a...

Robyn Williams: Barely a handful.

Mike Bunce: Yes, barely a handful, but we've pulled out many, many kilos of this. This is accumulated in these archaeological sites over many, many thousands of years. 50,000 years is a long time. When you think the pyramids were built 4,000 years ago, go back 10 times longer than that and that's when the Noongar people were living down here. So there is a huge genetic legacy really that we are trying to uncover.

So what we can do from here with freshly excavated material is we can get DNA out of these bones that goes back 50,000 years. When we collect all of these bones and we grind each of these tiny bone fragments for a few seconds we create a synthetic powder of a pile of bones. We do a single DNA extraction from that powder, and then we use the next-generation DNA sequencing to tell us what all the sequences are in there.

So, for instance, in this bag of bone you might find three species of possum, a Tasmanian devil, a couple of species of rock wallabies, all from one DNA extraction in hundreds of bone fragments. We've found birds, snakes, reptiles within this pile of bones. So what we're trying to do is trying to build a picture of biodiversity through time, how it changed from the Pleistocene into the Holocene when there was some warming going on about 18,000-odd years ago, and understand this biodiversity hotspot more over time.

Robyn Williams: Thank you very much.

Mike Bunce: Cheers.

Robyn Williams: Mike Bunce of Murdoch University in Perth. And do you know they've found in those Chinese medicines remains of Asiatic black bear and other endangered species, like saiga antelope. Dr Bunce is a future fellow at Murdoch.