The hunt for the oldest human genetics

For years, scientists have been trying to find ever older ancient DNA to fill in more and more pieces of our evolutionary tree. As of recording, I believe the oldest human genetic material came from these four teeth. They were excavated in Swartkrans, South Africa, one of the most important sites for the study of human evolution, the kind of place where time just melts away and you come face to face with humans that lived well over a million years ago. These teeth come from the oldest layer of the cave. Their owners lived between 1.8 and 2.2 million years ago. It's here I must confess that I have misled you slightly. Whether the owners of these teeth are human or not, it kind of depends on your perspective. The teeth belong to a group of hominins we call Paranthropus Robustus. Our distant cousins for sure, but still upright walking hominins like us. Does that fit your definition of human? I don't know. I don't know. It's definitely human-like. And the genetic material as well, it didn't come from their genome. It actually came from proteins. This is the science of paleoproteomics, not genetics. The study of trapped ancient proteins is our best attempt, our best opportunity to look at the genes of extremely, extremely ancient hominins. If you follow this subject at all, you know proteins have been appearing in big study after big study, most famously recently tying a skull to the denisimans, the enigmatic denisimans. I got to speak to three members of the team behind that paper about those four teeth. I wanted to know how do proteins help scientists untangle our evolution? What are the advantages? What are the limitations? And yeah, what does it tell us about our strangest cousin, one of our strangest cousins, Paranthropus Robustus? Yeah, ancient proteins. Let's get into it. This small pile of bones here, you can see at the bottom jaw, half of a face, this was the first Paranthropus Robustus remains ever found back in 1938 in South Africa. Paranthropus means besides man, alongside man, and Robustus means chunky. They're alongside us and chunky, okay? Chunky and with us but chunky. They were upright hominins like us for sure. We found, you know, lots of remains from them that, you know, we know that is the case but they were probably a distant cousin of ours, probably not a direct ancestor. Although with the amount, although, you know, with hominins admixing here and there who knows if they did contribute a small amount to our ancestry but not a major branch of our ancestry, that would be quite unlikely. Cousin of ours. Paranthropus lived between maybe 2.3 and 1 million years ago. To put that into context, modern humans evolved roughly 300,000 years ago, so a long time before us indeed but they did live alongside earlier forms of human, like Homo erectus. Whether you think of them as human is subjective. They were very short, the chaps maybe 1.3 meters, the ladies 1 meter, probably quite hairy, more sort of what you think an ape looks like. I know we're apes but probably a real archaic form to be honest. Does that qualify as human? You tell me. What they lack in stature though, they make up for in teeth. What's very unique and distinct about Paranthropus is that its dentition was, it had huge dentition, so I think the terminology that they use is mega dentition and this a lot of researchers assume that it had like very strong biting force. You can kind of see here the the difference in jaw sizes. This female Paranthropus robustus, male Homo sapiens, adult male, they kind of have bigger palate, bigger teeth and yet they're like half the size of us. Whoops. So big teeth people. The males also had this big sagittal crest running along the middle of their skull to help hold chewing muscles but also when there's a big difference between males and females, what we call sexual dimorphism, it probably suggests there's some pretty intense competition for the ladies going down. Even if you're like twice as tall as Paranthropus, I probably wouldn't get in the way of a chap and his lady. You might be in for a bad time there. Their big jaws, thick broad teeth were almost certainly used to chew a pretty tough diet, fibrous diet, grasses, leaves, sedges, things like that. So they really were on a different evolutionary path to us but that doesn't mean they weren't successful. They lived for over a million years and they also might have had some really really human tendencies. This is dnh155, one of the best preserved Paranthropus, robustest craniums ever found. Their cranial capacity was about 450 milliliters which is towards the lower end of the range of Paranthropus and about half the size of contemporary Homo erectus, contemporary humans. But despite their smaller brain sizes, it seems that they were, you know, producing tools. Bone tools found at Dremel in South Africa suggest that they were often digging for termites. It's also possible that they produced stone tools as those have also been found at Dremelin but could it have been early Homo there too? Could be. But there's no reason to think that some like really close relatives of ours couldn't produce tools. They're much closer relative to us than the chimpanzee and chimpanzees use tools all the time so they were no doubt using tools. For Claire, Yanis and Palesa though, they were trying to answer a different question. They were trying to use proteins to learn something else about Paranthropus. What is unique about the one that is found in South Africa, so the Paranthropus robustus, is that it has a very high morphological variation. So there's multiple fossils that are found within South Africa and they're found from different sides and it seems like there's differences within the group of Paranthropus robustus. So it's extremely varied and that makes it very interesting for studying variation in the past. This is one of the constant challenges in paleoanthropology and the study of human evolution. You have these diverse fossils, all these different ancestors knocking about. How do we untangle the relationships between them? Are they just a highly diverse group? Are they multiple species? Are they the same species just separated by like a lot of time? These are the kinds of questions the team were trying to answer using proteins. But the fossil record also tells us something else. You know, throughout Earth's history, extinction is common. Many species that were once alive are now gone. But the difference today is that we're driving that mass extinction. We're not just passive observers. That's why I joined and partnered with Planet Wild. They're a community-based nature protection organization. Think of it as crowdfunding, but for nature. Every month their 20,000 members, including myself, fund a new carefully selected mission to help bring back endangered species, protect our oceans, or restore forests. It's fully transparent. They document everything on their YouTube channel, so we can really see how our contribution helped. I said this last time, but really truly, especially since I've had kids, they just love nature so much, man. I have such a newfound appreciation of nature through my kids, and I want them to live in a world that's just thriving. Paranthropus lived across eastern and southern Africa, and one of Planet Wild's missions has been to restore forests in this area. Using a unique method involving underground forests, their support is going to help restore 3,000 hectares of degraded land there. Any amount will help, just the price of a coffee, and you can join this growing community protecting nature. It's honestly great to feel like you're doing something to not feel so powerless. The first 100 people to sign up using my code STEFAN22 will get their first month paid by me. Just scan the QR code or click on the link in the description. And the best part, you'll immediately see the impact you're having in less than 30 days here on YouTube. And there's no catch, you can cancel any time. If you want to see them in action, check out their video on this underground forest down below. Thanks to Planet Wild. So how can proteins help us untangle a diverse fossil record? I have to be honest man, whenever I make a video, whenever I do an interview, I'm always the dumbest in the room. Always. But in this particular situation, I felt that especially so. It's gonna make me sound like such a simple person, but when I think of proteins, I basically just think of the food that I eat. You know, are these the same proteins that you study? I mean, to be honest, I don't fully even know what a protein is. Yeah, I've actually had the discussions with friends who was like asking me, we're talking about proteins. And I've talked to him a couple of times. He was like into like working out a lot. This is why he was interested in proteins. It was like completely random. I was like, okay, but when you biologists say proteins, you mean something else than what we mean. This is not true. We're talking about the same thing, but like your skin or your hair or your muscles or your bones are essentially proteins. Bones and teeth are proteins fused with minerals like calcium. They form your bones and teeth. I just did not realize how many proteins there are in our bodies. They're just chocked full of them doing all sorts of different things. Like just looking at a protein sequence, there would be more than 20,000 proteins in the human body. For this study that's trying to understand and trying to use proteins to understand hominins that lived at least 1.8 million years ago, though, it's the proteins in the teeth that they were after. This is the magic of proteins. This is why they're so important. Usually after 2 million years, right, DNA fully degraded, especially in Africa, under the hot sun, there's no DNA left in a hominin fossil, really, or at least none that we currently can access with our technology. It's just broken down. But the proteins fuse with minerals to create your bones and teeth. They fuse with things like calcium, and that sort of being embedded with those minerals basically preserves them. This is why they can help us where DNA can't. Now, I know you're thinking, and I was thinking this too, okay, great, you found a protein. How does that help us understand evolution? It's because the chains of amino acids in the proteins reflect the DNA that created them. This whole process is essentially the translation of information that is on the genome. Parts of the genome are genes. In biology, we usually call them protein coding genes because they have the information on how to create the structure of a protein, initially a long string of amino acids that eventually folds into a 3D space and takes a form in 3D space and does functional things in your body. So the amino acid sequence of a protein essentially mirrors the DNA sequence that created it. You have a pretty good idea of what the DNA sequence that created the protein looks like, and you can use that information to do other things. The specific amino acids can be measured using science called mass spectrometry. This is really way above my head, to be honest with you, but basically it tells sort of different elements apart, different things apart based on their mass to charge ratio. To me, it's magic. You're going to have to go to another channel to explain how mass spectrometry works. I can barely even say it, let alone understand it. But fundamentally, fundamentally, what me and you as the layman need to know is that these amino acids, these long chains of amino acids within the proteins reflect the genomes that created them. If there's a change in the amino acids, that's because there's a change in the gene that made them. Okay, that's basically how these proteins help us untangle evolution. They reflect the genes that made them. Sounds simple when I say it like that, but of course, there's always loads of challenges. First challenge is always like, contamination. How do you know your results are truly from what you're trying to study? It's a huge challenge in ancient DNA. Huge, huge challenge. But in paleoproteomics, it's a little bit less of a challenge. And not only that, the fact that we're studying proteins also kind of acts like a proof, acts as like a test, a failsafe in the studies. Then most of those proteins are actually tissue specific. And that's quite important in paleoproteomics. Because, for example, the proteins that we would get in dental enamel are extremely specific to dental enamel. So we know that those proteins are actually coming from the sample. So it's sort of like a test to make sure it's not contaminated in a way, because hopefully your teeth proteins are not in the sample. Yeah, there's very limited risk of contamination from like modern dental enamel, actually. Yes, yeah. You have to be careful not to do this study around any like seven year old children, I suppose, with wobbly, wobbly teeth. Second major challenge, getting samples to study. This is a really new field of science. Very, very new. Especially trying to study fossils that are like potentially over two million years old. It's very new. If you look at the four teeth that they chose for the study, you can see they're really beaten up, cracked, chipped, snapped in half. These are not museum grade pristine samples, okay? This was really important to help push this study forward, to help advance this science, there's not infinite hominin teeth around to study. Even though now scientists are so good at being minimally destructive, there's just a finite number of things that we can test. And so the team really had to go through this huge process of proving the study had a chance of working, proving the science, finding appropriate samples, samples that are not going to be missed in a museum. It took years. It took literally years for them to do this work. Final major challenge from my understanding, information loss. Even though these proteins are preserved because they're bound to minerals, they're still degrading. They're still degrading a little bit. Nothing is preserved perfectly for two million years. The magnitude of the information reduction is pretty crazy if you think about it. Because from the whole genome, it's just like 2% in humans that is actually gene coding regions. And from that, these are, let's say, 20,000 proteins, we get 10. So imagine how much little information. And even those 10, they go through degradation that Alessa explained. It's ridiculously far less information than having a whole genome. And yet it's still incredible that we can use it to learn something. The first thing they were able to identify is the male and female paranthropus specimens from those four teeth. And that's because thanks to a quirk of evolution, there are six specific amino acids in dental proteins. So amylogenin exists in two isoforms. So there's the chromosomally linked, so they're linked to our sex chromosomes. So that means that there are two versions that exist. There's the one that is linked to the X chromosomes. And for male individuals, there's the X chromosome version and the Y chromosome version of amylogenin. I think these two teeth were male. These two teeth were female. This is obviously important because paranthropus, very sexually dimorphic. Clearly, we need a way to tell male and female, even from very, very fragmentary remains. Hopefully that will help us learn a lot about their society. The other thing, this is a little bit more complex, but they were kind of able to tease apart some population variation within these paranthropus remains. Initially, the team tested the three out of the four teeth. And we could see there were two sites, like two individual amino acids, that they differed. From all the amino acids that we covered, it was just two of them that differed from paranthropus to modern humans, which was also kind of surprising. We weren't really sure what to expect, like how different it would be, or how similar. But essentially, we had this one site, what we covered in all three individuals, that we could see was different from all the humans. Modern humans had an arginine, and paranthropus robustus, the three samples, had a glutamine. So the team thought that this specific point, these specific amino acids, could be characteristic of paranthropus robustus. That in future studies, they can use this spot to try and identify these paranthropus remains. However, when they tested the fourth tooth, that's not what they found. The fourth tooth had that human version of the amino acid. And we did panic when we saw that. Yeah, we were like, okay, we probably did something wrong. We thought we had done something wrong. There was panic. When they dug further into their data, they also found that one of the other three teeth initially tested was producing both forms of amino acids. This was a bit of a surprise because proteins are way more conservative than genes. They change a lot less than our genes. So the that they were able to detect any population variation at all is quite remarkable. Is there just a high degree of variation within paranthropus? Or is that actually a sign that maybe there are two species of paranthropus, another species of paranthropus, that has been identified by these protein studies? That's something that's going to have to be worked out in future studies. Now I do hear some of you thinking kind of like, ah, these are kind of humble results, Stefan. You know, what's the point? Maybe if you feel that way, you've stopped watching the video already, who knows? Even though these results may admittedly seem humble, you know, it's not the same as identifying the face of a long lost human cousin. We have to remember these four teeth are over two million years old, potentially. The fact that we can find any information out about paranthropus from them at all is incredible. It's remarkable. And it's really opening the door for this paleoproteomics to really kind of peer into human evolution way deeper than any sort of ancient DNA we've ever found in any fossil before. The team are hopefully going to expand this to look into the australopithecines, you know, like famous australopithecines like Lucy. How do they relate to paranthropus? How do they relate to early homo? At the minute, we have no idea how all these fossils relate to each other, but in the future, this is all entirely possible. Especially, especially in like, if you have fossils that are even more recent in time than this more recent than 2 million years, we have opportunity to learn lots more stuff. We only have access to the enamel proteome, the only thing that concerns in like 2 million years ago. But if you look at samples are 100,000 or like 300,000, their protein preservation is much better, you can actually have access to other parts of the skeleton, like the actual bones or other parts of the tooth, that have much higher complexity in proteins. Like there's far more proteins in there naturally, and also they preserve better so you can actually recover them. And there you have much more information and you can actually start getting a bit lower in depth in terms of like within species or between the different subpopulations of a species. For example, like recently there were a couple of Denisovan publications that say, you know, this sample matches a Denisovan. Oh, this other sample matches a Denisovan. And this is because they have access to much higher like quality of proteome, so they can more comfortably assign it to a subpopulation or like a different population within like the Homo family. You know, the area where this might be most helpful is these tropical regions, these hot regions. At the minute, it's just been hard to get DNA from places like Indonesia, where there are incredible fossil records of Homo erectus, Homo floresiensis. We believe the Denisovans were down there too, but at the minute we haven't identified any of their remains, or if we do have them we don't know. Because of the hot climate that these fossils have been in for so so long, there's just almost no DNA left in them. At least we've never been successful in getting DNA out of any of these really hot tropical fossil specimens. But if enough of these proteins survive, bound to the minerals in our bodies, we really might be able to place some of the most interesting fossils in their position in our human evolutionary tree. It's crazy, it's crazy. All from some ancient proteins stuck to the calcium and four very very very very old teeth. It's highly cool, highly cool. Thank you for watching. Thank you for watching, and thanks again to Planet Wild. If you want to make a difference, if you want to support real conservation work, do check them out. You'll really make an impact, and you can see the results here on YouTube. Why not go see that video on restoring those underground forests? Do it.