Ancient Bone Proteins May Offer Insight On Megafauna Extinction

FLORA LICHTMAN: This is Science Friday. I’m Flora Lichtman. If you think about Australia, one thing that probably comes to mind are the animals that live there, from koalas to kangaroos to a surprisingly large selection of creatures that can kill you. But once upon a time, the Australian landscape had some even weirder fauna, like a marsupial with immense claws and a small trunk, or a slow-moving kangaroo-like creature that walked on all fours, a wombat the size of a hippo. They’re all extinct now, and researchers are trying to figure out why.

Writing this week in the journal Frontiers in Mammal Science, researchers described one tool they’re using to hunt for clues. It’s called ZooMS, and it uses samples of ancient protein, not DNA, to identify what animal a bone came from. Joining me now to talk about it is Dr. Carlie Peters. She worked on this project at the Max Planck Institute of Geoanthropology in Jena, Germany, and is now a postdoctoral researcher at the Interdisciplinary Center for Archaeology and the Evolution of Human Behavior at the University of Algarve in Faro, Portugal. Welcome to Science Friday.

CARLI PETERS: Thank you so much for having me. It’s great to talk to you more about what we’ve been doing.

FLORA LICHTMAN: Well, you had me at giant wombats, obviously. Tell me a little bit about them.

CARLI PETERS: So basically, the animals that we studied are all extinct now. And they’re all giant versions of what you could still find in Australia today. So you would have the giant wombat or a giant kangaroo. And you also have creatures that don’t really have anything similar today, like the Palorchestes, the creature with the giant claws that you were talking about. There’s not really any closely related animal alive anymore today.

FLORA LICHTMAN: When you say giant wombat or giant kangaroo, how giant are we talking?

CARLI PETERS: We generally put the term “megafauna” on any animals that are larger than 45 kilograms. What we’re talking about here, for example, the giant wombat, you can kind of think like hippo-sized, so a lot bigger than your average wombat today.

FLORA LICHTMAN: And the kangaroo? I must know.

CARLI PETERS: I believe it’s about 2 to 3 meters tall. Really big. You wouldn’t want to run into it.

FLORA LICHTMAN: That’s almost 10 feet tall.

CARLI PETERS: [LAUGHS]

FLORA LICHTMAN: Yeah, you’re right. I don’t think I’d want to run into it. When did they live?

CARLI PETERS: So many of these animals went extinct during the late quaternary, which is the period before the one we live in now. So basically, they went extinct around 50,000 years ago. And they lived for hundreds of thousands of years before that, obviously, multiple different species of the same type of animal. But they ultimately went extinct about 50,000 years ago.

FLORA LICHTMAN: I think when listeners hear “giant wombat,” the burning question on everybody’s mind is, obviously, would a giant wombat have giant cube-shaped poop?

CARLI PETERS: This is something I’ve wondered myself as well, and unfortunately, I don’t have a good answer to that. We haven’t found any of their coprolites, which are fossilized poop.

FLORA LICHTMAN: Ugh. Let’s keep hoping.

CARLI PETERS: Yeah, it would be really cool to get the answer to it, though.

FLORA LICHTMAN: What are the other big questions about these animals?

CARLI PETERS: So there is a big debate mostly about, first of all, their exact timing that they all went extinct. But the other burning question is what actually caused their extinction. About 50,000 years ago is also around the same time period that humans first entered Australia.

So there are people who argue that human colonization of Australia caused the extinction of these animals. But there was also climate change at around the same time. So that could have also been a factor. There’s people who argue that it’s a little bit of both. But really, we don’t know why they went extinct.

FLORA LICHTMAN: And how does your technique, ZooMS, help with figuring that out?

CARLI PETERS: One of the major issues that we have when we try to look at why these animals went extinct is that we don’t really have a lot of data for them. So for example, Diprotodon, which is another one of these extinct marsupials, they’re best represented in the fossil record.

And there’s about 12, 13 well-dated fossil remains for them all over Australia. So that’s not really enough data points to get to a good theory testing of why they went extinct. So now that we have the collagen peptide markers that we developed for our study, we can use them to find more of these animals in fragmented fossil remains.

FLORA LICHTMAN: So your method is a way of identifying bones, what animal they come from. And it uses collagen, not DNA. Is that right?

CARLI PETERS: Yes, that’s correct.

FLORA LICHTMAN: Why not use DNA? What does collagen offer that DNA doesn’t have?

CARLI PETERS: There’s two main things. The first one is that proteins– and that includes collagen, but also other proteins- they tend to preserve better in the fossil record. So for example, the oldest DNA that’s been recovered at the moment is from a permafrost of about a million years old, if I’m correct.

But proteins can preserve for a lot longer. The oldest preserved proteins so far are up to 4-million-year-old eggshells. And they also preserve better in harsher environments. So for DNA, you often have to look at really cold regions of the world. But obviously, Australia is not very cold, so that doesn’t really help you there.

And the other reason is that this technique is a lot cheaper to do. So with this technique, you can analyze thousands of bones for a fraction of the cost of what you would get if you would do DNA analysis on them.

FLORA LICHTMAN: That’s fascinating, because I think I would have assumed– when I think of collagen, I think of my skin. I think of it in my cartilage, like stuff I assume breaks down actually more easily.

CARLI PETERS: Yeah.

FLORA LICHTMAN: So this is surprising to me.

CARLI PETERS: Yeah, you are correct. Collagen is the main protein component in skin and in cartilage, but it’s also actually the main protein in your bones. It’s what keeps your bones flexible. And because it’s in this mineral environment of the bone, it preserves well over time.

FLORA LICHTMAN: And is one animal’s collagen different from another’s?

CARLI PETERS: It depends a bit on how evolutionarily distant they are. So, for example, you wouldn’t be able to tell apart a wolf from a dog. They’re too similar. But you can tell apart a horse and a donkey or a sheep and goat. So it depends a bit. It’s variable.

FLORA LICHTMAN: What about ancient humans? Can you tell the difference between a Neanderthal and a modern human using this?

CARLI PETERS: No. Unfortunately, we can’t. But we can identify that it’s a human or closely related to a human. So then you could still send it for DNA afterwards, once you’ve identified it as a human. That’s what people tend to do, so to then get more detailed data on it.

FLORA LICHTMAN: So is this technique that you’re using, is it made possible by new technology? Or was it a new idea? What advance led us to this technique?

CARLI PETERS: So the technique itself was first developed in 2009, and it was mostly brought on by developments in mass spectrometry, which allowed people to actually study in more detail the protein sequences and mass from a lot of different materials. And because of all of these developments, people on the brink between archaeology and chemistry were looking into whether we could use it in archaeology as well. And that’s why it was first developed, mostly for European animals.

FLORA LICHTMAN: Hmm. Are there other proteins that you could use in this way to figure out what animal a remain is from?

CARLI PETERS: Yes, you can. You can use keratin, which is obviously in your hair and nails. And people use it sometimes to look at old textiles to see from which animals the textiles were made from. You could also do a similar thing with eggshell. So you have specific proteins in eggshell, and then you can tell from which species a specific shell is from. So for example, if you want to look at which birds were exploited by people in the past, you can look at eggshell remains from archaeological sites in that way.

FLORA LICHTMAN: So here’s the thing I don’t understand. I mean, I understand you’re making a reference library. So you can say, OK, this bone is from this animal. And so then I can map the signature of this protein that corresponds to this animal. But what if you encounter an animal you’ve never seen before?

CARLI PETERS: Yes, I’ve had this in my research in the past. Sometimes you can tell what broader taxonomic group it’s in. So for example, in Australia, sometimes, I’ve had where I can tell it’s a marsupial, but I just can’t really say which one because it’s not– we don’t have the reference data available for it. But sometimes you really can’t tell, and then it’s just a question mark still.

FLORA LICHTMAN: Are there huge protein databases the way that there’s DNA databases– a reference library, basically?

CARLI PETERS: Yeah, there is some stuff, but it’s still very much in its infancy. It also very much depends on whether a specific animal is interesting for modern clinical trials as well. So the databases are lacking a lot. And at the moment, if you want to specifically do this type of work that I do, you’re best off if you want to focus on European medium-sized mammals. That’s the best–

FLORA LICHTMAN: They’re the best represented in the library.

CARLI PETERS: Yeah. Yeah, that’s where it started, and it’s still best represented.

FLORA LICHTMAN: OK, so how do you apply this? Is it you go in the field and you dig stuff up, and you use this method? Or are you going back to museum collections? What’s the use case?

CARLI PETERS: So for what I’ve done, I’ve mostly worked with museum collections. And so basically, an archaeologist or a paleontological team would work at a site. They dig up everything they find that remains. And then first, a paleontologist or a zoo archaeologist, which is someone who looks at the animal remains at archaeological sites, that they would look at the material, and based on specific elements or features of a bone, they would be able to tell which bone it is and from which animal.

But then there are a lot of remaining fragments that are too tiny to see what they are from. So they normally, they get bagged up, and they get put in either a museum storage or university storage. They’ll be saved, but they’ll never really be looked at again.

FLORA LICHTMAN: They’re like the scraps, the bone scraps.

CARLI PETERS: Yeah. That’s normally what I call it, too, the bone scraps. And then what I’ve done is I’ve gone through these museum collections to select from these bone scraps material to sample and to then identify later on.

FLORA LICHTMAN: That’s so cool. So you’re using all of these parts of the collection that would have just maybe collected dust and not told us anything.

CARLI PETERS: Exactly. That’s also what I find very fascinating about it. And of course, in museums and universities all over the world, there are so many of these bags of bone scraps that no one really has looked at since. So there’s still a lot of work to do.

FLORA LICHTMAN: Is there a bag of bone scraps you’re dying to test?

CARLI PETERS: I know. It’s difficult to tell because you don’t what you’ll find, right? At the moment, I’m working at a new institute, working on new projects. And it’s really cool to see hopefully some ancient human remains or from these extinct animals, where we don’t really get much data from them. I don’t know. There are so many interesting things that you could, in theory, find. I don’t know. There’s so many cool sites. I’m an archaeologist. I love all the sites.

FLORA LICHTMAN: Thanks so much for joining us today.

CARLI PETERS: Yeah, thank you so much for having me.

FLORA LICHTMAN: And good luck. Good luck with the scraps.

CARLI PETERS: [LAUGHS] I will. There are so many waiting for me.

FLORA LICHTMAN: Dr. Carli Peters, postdoctoral researcher at the Interdisciplinary Center for Archaeology and the Evolution of Human Behavior at the University of Algarve in Faro, Portugal. Before we go, some good news– or news that sounds good, anyway– our galaxy may not be heading for a smash-up with neighboring galaxy Andromeda after all.

Andromeda is hurtling at us at over 100 kilometers per second, and it was long thought that we were in for a collision, but new calculations suggest that’s not a sure thing. Joining me now to talk about it is Dr. Till Sawala, astrophysicist at the University of Helsinki. He recently wrote about this in the journal Nature Astronomy. Welcome to the show.

TILL SAWALA: Thank you very much for having me.

FLORA LICHTMAN: This is a thing that I didn’t have on my worry list, and now I feel like I just get to write it down and cross it off.

TILL SAWALA: I guess, it’s possible to answer this question in several ways. So the merger, even if it happens as was previously predicted, would still take about 4.5 billion years. So I don’t think that’s something any of us have to worry about. But we do find, indeed, that even this merger in the far future is not certain. We find, in fact, only about a 50% chance that there’s any merger in the next 10 billion years. And for a merger in less than 5 billion years, we now see only about a 2% chance.

FLORA LICHTMAN: Was this a surprise?

TILL SAWALA: The short answer is yes. I was initially interested in a completely different question related to the future evolution of the Milky Way and Andromeda. I wanted to understand how the cosmic environment might influence this. But as a starting point, I thought I would revisit this prediction. I had expected that we’d basically be able to confirm this prediction.

But we found that, in fact, when we included all the observational uncertainties and also when we considered a more complete system, including the effect of the Milky Way’s most massive satellite galaxy, yeah, we only found a 50/50 chance. And that was a big surprise.

FLORA LICHTMAN: So it sounds like the old calculations weren’t wrong. You just have now more data to work with.

TILL SAWALA: Yeah, exactly. In the past, people have considered the effect of the next most massive galaxy in the local group, the Triangulum Galaxy, or M33. But we find that, actually, we need to go one step further and also include the effect of the Large Magellanic Cloud, which is a dwarf galaxy, a satellite galaxy of the Milky Way. It’s important to stress that the old calculations were not wrong. We just explored a bigger space of possibilities. And what was predicted in the past is definitely one of the possible outcomes. It’s just not the only possible outcome.

FLORA LICHTMAN: Well, what are we missing out on if we don’t collide with Andromeda?

TILL SAWALA: What would happen precisely depends a lot on when that merger will happen, what the energy of the orbit will be at that time, what the relative inclination of the two galaxies will be at that time. So how precisely the merger will play out, I would say, it’s too early to say that.

We currently have two large disk galaxies in the Milky Way and Andromeda. And the most likely outcome of such a merger is that they would essentially be destroyed and constitute a new elliptical galaxy that would form after some time.

For a brief period, there would be an intense period of star formation, a so-called starburst. But that would produce a lot of young stars, which would result in intense radiation. The two supermassive black holes in the center would also find each other and merge. That would create even more radiation, which would eventually shut off star formation.

So the long-term result of that merger would be basically that the two large disk galaxies that currently constitute the local group, including our own galaxy, the Milky Way, and Andromeda, they would cease to exist. And in its place, after some billions of years, would be an elliptical galaxy that would not have much new star formation and would basically slowly, slowly fade. So that would be the long-term future. And yeah, it’s important to say that’s still very much one possible scenario.

FLORA LICHTMAN: This is a thing that may or may not happen in the next 10 billion years. Why do you care about this?

TILL SAWALA: I think it’s a really good question. So I mean, on one level, we know for certain that the sun will explode in about 8 billion years. Even before that, it will make Earth uninhabitable. The calculations are about maybe 1 billion years. So this is all beyond human lifetimes. I think it’s just something that I’m curious about because it affects my own galaxy, even though I might not be around when that merger will happen. I think it’s just part of human curiosity that we like to know.

And what actually fascinates me is the question of why we are interested and why we might even prefer one outcome over another. At least personally, I can say I prefer the Milky Way to continue to live, even if there’s no impact on my life or human lifetimes, I think. And but why that is, I think, is more a question for maybe psychologists compared to astrophysicists.

FLORA LICHTMAN: Thank you so much, Till.

TILL SAWALA: OK.

FLORA LICHTMAN: Dr. Till Sawala, astrophysicist at the University of Helsinki.

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