Science Friday
Hosted by Flora Lichtman and Ira Flatow
Ancient squirrel poop provides a snapshot of life during the last ice age. And, how different types of laughter originate in the brain.
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Hey, it's Flora and you're listening to Science Friday. Hundreds of thousands of years ago, deep in the mountains of the Yukon, a ground squirrel pooped. And that scat stayed frozen for millennia until very recently, when researchers thought it out and found a real data dump. Scientists analyzed the DNA in the droppings and identified traces of a surprising number of animals and plants, providing this new detailed snapshot of life during the last ice age. Joining me now is the lead author on that study, Dr. Tyler Merchi, who studies ancient DNA at the Hawkeye Institute in British Columbia. Tyler, welcome to Science Friday.
Thanks. It's awesome to be here.
Thank you for being here. Is poop underappreciated in archaeology? Like, is poop the new amber?
I would definitely say so. At the beginning of the field, there is a lot of people who had worked with paleo feces to try to get DNA, but it's always kind of been this undercurrent of the field because people really gravitate towards, you know, the big amazing tusk of the woolly mammoth or these, these super cool bones. The idea of looking at poop, you know, it's not as flashy of a, of a sample type. And so a lot of these have just kind of been in cold storage for some time. And I think this paper and some of our other ongoing work is really highlighting, you can get amazing ancient biomolecules from unsuspecting sources like, you know, old poop.
Yeah. Okay. So tell me a little bit about these specimens. Where did you find them? When were they from?
Yeah. So a lot of this field work is done by folks like Scott Cocker and Dwayne Fraze. And they go out to these areas in the Yukon that are these placer gold mines. And so the miners are there trying to thaw gold out of the permafrost sediments. And so they spray water cannons on the walls. This, this thaws out the gold, it ends up in the river bottoms. But then the thing that they maybe don't expect to find are tons and tons of fossils. And so tens of thousands of remains of, you know, mammoths and steppe isin and all the ice age critters you can imagine, end up exposed. But you also see in these large vertical exposures, a bunch of pockets of ground squirrel burrows.
And these burrows and remains in general age between, you know, thousands of years ago to our oldest samples here are 700,000 years old, which is, you know, really ancient. It's, you know, anatomically modern humans maybe arose about like 300,000 years ago. So twice as old and more than that.
So they're sampling within these burrows?
Yeah. And well, part of the effort is to get up to these burrows and see like, oh, hey, what's all in there? And a lot of them contain, you know, bits of plants. Um, there's unidentified bone, there's seeds and nuts and all this kinds of stuff. And then there's this whole mid in this latrine area that's just full of poop. And there's hundreds of poops all kind of packed together in one spot. This is their pooping area. And we thought, well, what if we looked at the DNA that's inside those? I wonder what all's in there.
Wow. Okay. So you bring it back to the lab and then what's the next step? What exactly are you analyzing?
Yeah. So we're trying to pull the ancient DNA out. And in part that involves taking a small sample and then digesting the organic and inorganic parts of that to release the DNA that ends up in solution. The funny part is that, you know, when you're working with samples, usually there's no smell. But with these samples, it was only once you put them in solution and digested that you and you open the tube to pull out the super date. And then you realize, oh, wow, yeah, this is definitely liquefied poop right now.
The smell holds up. That's kind of amazing. For 700,000 years?
Yeah. Well, it's in part, they've been frozen in permafrost all that time. So it's really spectacular preservation.
Wow.
Yeah. And then so you're trying to get, you get the DNA out and then you have to attach adapters to the ends of the fragments. And this is because when using high throughput sequencing technologies, where we get hundreds of millions or billions of DNA sequences for every sample, you have to be able to identify, okay, which sample's which. And that took quite a lot of effort because there's so many partially degraded organics in poop that make chemically it quite challenging. But then after you do all that, you have to then try to pull out the DNA you're interested in, which is a whole other biochemical effort because, you know, 90% of the sample is just DNA that we don't know what it is. And so that just kind of. Gets put into some other bin and then of the 10% or so that we can identify 99.9% of
that is bacteria and then of the 0.1% that's other stuff is all the other things that are in there and we're really interested in here in case of the plants and animals.
Are you cross referencing with a library or something? I mean, how do you, how do you do that? Is there a simple way to talk about it?
Yeah, so the NCBI Nucleotide Database, people, their genomics is basically just upload all of their DNA data for every organism they've ever discovered and it just goes on this database. We then pull a local copy of this database, which is huge, you know, hundreds of millions, or it must be billions of reference genomes on there now at this point, maybe not full genomes, but sequences anyway. And then we, one by one, every, you know, 30 little base pair sequence of DNA, ancient DNA that we get, we align it to this gigantic database and you have to use high-performance computers to run through, you know, these enormous calculations to figure out what everything is. In this case, it took something like running continuously on four
high-performance servers at four different universities, three to five months or so of continuous and I was hogging the machines for most of that time. So it's a lot of data.
Wow. All right. Well, talk me through some of the highlights of what you found.
Yeah, well, when we first started, I thought, oh, this, it's going to be mostly ground squirrel DNA and their gut microbiome. So the kind of bacteria and stuff that live in their guts. But I really wasn't expecting to find woolly mammoth and step bison and horse and wolves and basically a snapshot of the Ice Age in ground squirrel poop and even more DNA than we typically find even in the sediments in these areas. So it's really this kind of enriched picture of all these different animals and plants and fungi and microbes.
And not only are we getting individual little fragments of these organisms that we're able to identify as, oh, yep, this definitely belongs to, you know, this species of grass or this belongs to like this type of herb. We can actually start reassembling the genomes of these different organisms all at the same time and stitch those back together to then look at how they're related to other things today. And so there's all sorts of applications you can get into.
How did?
And the kind of the
Go ahead. No, go ahead.
Oh, I was just gonna say that the, the big question is, why is this all this DNA in there? Like, why is it not just squirrel DNA?
What did these squirrels get up to?
Yeah, so one of the important parts is that Arctic ground squirrels, they are in hibernation or state of torpor for about eight months of the year. So they really are unconscious most of the time and in their burrows. And so the period of the year that they're actually awake, they need to be out in that landscape, getting everything they can for nutrition. And even when we first started, I kind of just assumed ground squirrels were, you know, mostly eating nuts and seeds and stuff like that. I didn't realize that they are really kind of like little bears almost. So we think there are so many big animals around during the Pleistocene. There's this kind of paradox of productivity, tons of big organisms all over the place, that there is dead carcasses of mammoths around and such.
And we think that they're eating those remains and bringing back bones and bits of tissues to their nests to help make it through, you know, cold winter months during the Ice Age, during extremely cold periods of time.
Hmm. I mean, is there anything about poop in particular that makes it a really good time capsule?
Yeah, that's another great question. I think in part, it's sort of a natural enrichment of the environmental DNA that's on that landscape anyway, you know, like we're shedding DNA all the time. And if that DNA ends up in the sediment and can end up binding to minerals in the sediment and preserving long term, I would think the DNA that passed through the digestive system of a squirrel, you wouldn't think that that would have great preservation. So it's kind of wild to imagine that these coprolites would be that well preserved. And so I don't know if it's just there's so much to begin with that it could make up for the fact that there is natural degradation from those microbes. Or maybe there's some other sort of microbiome effect where the bacteria in the poop are
protecting it from the kind of other environmental bacteria that might break down that DNA. So that's definitely an area that we want to get more into. I'm sure there's some chemistry involved for why the DNA is preserving so well.
Did any of your findings challenge any assumptions of sort of Ice Age ecosystems?
Yeah, well, one of them that's kind of a tentative call in our in our assignments is we had hits to Puma, which is Cougar, but there weren't Cougars, as far as we know, in northern Yukon at that time. They really came from South America. But when we look at the the hits to Puma, they also match to American Cheetah. But there wasn't an American Cheetah genome available on the reference database at the time. So it hit the next closest ancestor, which was Cougar. I suspect these are actually Cheetah reeds, American Cheetah, which is actually, it's kind of a little bit of misnomer. They're not that closely related to cheetahs in Africa. But I think they initially thought
they were. And so this is sort of a little bit of a challenge of, well, were either Cougars present here and much deeper in the past? Or was it this other organism? There's some more investigations needed there. But then when we get into the squirrels, that's a whole other can of worms in that there was maybe several additional species that have just kind of been assumed to all be the same thing. In part because people aren't as interested in squirrels. So there hasn't been as much effort into their like own taxonomic, you know, evolutionary history. So we've definitely the one at 700,000 years old seems like a totally different thing. And then the ones that are even there today are probably actually several species that have been grouped together into one thing.
When you walk down the street and you see like scat on the ground, are you like, ah, there's so much in it?
I feel like definitely now I realize, oh, yeah. Well, and especially from an environmental DNA perspective, just realizing, you know, we're shedding millions of skin cells every day. There's just so much DNA being released. And yeah, poop is full of DNA, but also we're just kind of like, you know, the character Pigpen from Charlie Brown, just releasing information, all these like, you know, incredibly small molecules of DNA all the time. So there's just, there's kind of gold mines all over the place and all these unsuspecting locations.
Dr. Tyler Merchi is a biomolecular archaeologist at the Hocke Institute in British Columbia. Tyler, thank you so much.
Thanks for, thanks for chatting. This was great.
We have to take a quick break, but if you liked these poop buns, stick around. More on that beat. The neuroscience of laughter is after the break.
Support for Science Friday comes from the Heising Simons Foundation. Unlocking knowledge, opportunity, and possibilities. More at hsfoundation.org.
Hey there, it's Ira. I want you to think about the last time you had a big old laugh. You know, the kind where you're running out of breath, clutching your stomach, your eyes are tearing up, and you just can't seem to stop. You know, there's a fancy phrase for this. It's called spontaneous or involuntary laughter. Now, this feels like a very different kind of laugh than, let's say, how you might laugh making small talk with your neighbors, or chuckling at Flora's and my jokes. This is called voluntary laughter. And not only do these two types of laughs feel very different, but a new study found that they originate in different parts of the brain. Joining me is study author Dr.
Sophie Scott at University College London. Dr. Scott studies how our brains process and produce speech. Welcome to Science Friday.
Thank you so much.
Nice to have you. Okay, Sophie, what did you find? Where do these different laughs come from?
So there's basically, in the human brain, two different ways that control how sounds are made. And one is called the volitional motor system, and it's associated with brain areas you actually only find in humans. And they are recruited when you are talking, when you are singing, when you're using your voice in a volitional way. And by volitional, I don't mean you're kind of paying attention to exactly how you make every single speech sound, but you are, it's a voluntary act. You could stop at any time. And we also have an evolutionarily older system that's running down the midline of the brain, and that is the one that we share with all other mammals. And it's associated with much more involuntary, reactive, emotional sound.
So if you were really frightened by something, you'd be much more likely to start screaming than to just say, "I am frightened." And that's very different from that volitional motor network. And it seems to be consistent with that spontaneous, helpless laughter.
Has a very different profile. As I said, once you've started, you can't stop doing it. Whereas that volitional laughter, which is actually, most of the laughter you encounter is more like that. And that happens in conversations. And there, in conversations, people time the laughter really, really precisely. So everyone laughs together at the end of a sentence, and then they carry on. And they start and stop at the same time. So that kind of motor control, that's not possible with spontaneous laughter.
Is that just a fake laughter then? I mean?
Well, it would, it's probably like a world of laughter, actually, because as I say, most laughter actually fits in that more kind of volitional way. So if you look at people, well, there was a fantastic American psychologist called Robert Provin, and he pointed out that though we think laughter is about jokes and comedy, most laughter happens for social reasons. And of course, conversations, what we're doing now, that's how humans around the world maintain social interactions. So that laughter sort of is natural home is in those conversations. And in those conversations, sometimes people are laughing because something's funny, that does happen. But also, they're laughing because they might just catch a laugh from somebody else, they're laughing contagiously, or they're laughing to show agreement or understanding. And people will use laughter
to cover up other, you know, embarrassment or other emotions, or they'll use laughter to deal with stress. So it's like a hall of mirrors. And most of that, I've just described, would fit probably under that volitional network.
Was the discovery that there are two kinds of laughter and that they originate in two different parts of your brain, was that a surprising discovery? How did you figure that out?
I'd been, I'd been thinking about the fact that it had to relate in some way to these different motor networks. But we didn't have good evidence for this. And what was really nice about getting to work on this paper with Fausto Caruana is that he does really detailed mapping studies of what happens when you stimulate different brain areas. And he'd become interested in laughter, because sometimes when you stimulate brain areas, you do get laughter. It's what is called pre-surgical mapping. You are looking to see, identify brain areas which are involved in epilepsy. We've been using these data to study laughter because what it lets us do is actually relate in a really precise way which brain areas people are stimulating when they record examples of people laughing.
So it gives us much greater precision and the ability to actually record while people are laughing because a lot of other techniques like functional magnetic resonance imaging, they really can't cope with the fact that people move a lot when they're laughing. So this really does give us both precision and also it makes it actually possible.
So you basically zap their brain and they start laughing?
Yeah. And sometimes the laughter just seems to happen and the people go and it's sort of mirthless. And other times the laughter happens and people feel a sense that something was funny.
Well, knowing all of this, do you think about your own laugh differently, I guess is how I would put it?
I do. I, um, many years ago, I'm talking about like 1998, my father was desperately unwell and dying in a French hospital and he lives at the end of the story, don't worry. But we were all sitting around and waiting for doctors to do something and he suddenly said, oh, we've, we've laughed a lot, haven't we? And I said, yes, Dad, you know, we have, we really have laughed a lot. And I wasn't, well, I didn't work on laughter at the time. I didn't, I was sort of thought about it, it stayed in my mind. And then I started working on laughter and I thought, oh, he's right, you know? The times in your day when you're laughing with people, it can feel trivial and silly, like it's just, you know, frivolous, time wasting, you know, you're not achieving anything there. But it's actually probably the most important points in your day in terms of the making
and maintaining the bonds you have with other people and, and feeling better together.
Well, we can certainly use a lot more of that laughter, Dr. Scott. Thank you for taking the time to be with us today.
Thank you.
Dr. Sophie Scott is a professor of cognitive neuroscience at University College London. This episode was produced by Rasha Aridi. I'm Ira Flatow. We'll catch you next time.
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