Geneticists Studying Ancient DNA Discovered A Girl Whose Parents Were Two Different Species

At a laboratory in Leipzig, Germany, a researcher is puzzling over a piece of ancient bone. Surely it can’t be true? According to DNA tests, this relic represents something that paleontologists thought they would never find: a hybrid between two of humanity’s early relatives. It’s no surprise that the expert first suspects an error has been made. But there’s no mistake here. Astonishingly, these remains come from a girl whose parents were from two entirely different species. And this breakthrough could well revolutionize what we know about our ancestors.

Although scientists have long suspected that interbreeding between ancient humans took place, the chances of uncovering proof of first-generation offspring were considered slim. Then researchers in a cave in Siberia stumbled upon a tiny fragment of bone. And while, initially, the team didn’t even realize that this came from a hominin – a term that just means “all the species regarded as human” – an incredible story soon began to unfold.

After its 2012 discovery, the bone languished in obscurity for years, with nobody deciphering its true importance. But one intrepid researcher, the Max Planck Institute for Evolutionary Anthropology’s Viviane Slon, decided to begin extracting DNA from the artifact. And what she found has turned decades of research on its head, revealing exciting new truths about how ancient humans made their way in the world.

Ever since Neanderthal remains were first identified in Germany in the 1850s, scientists have been battling to understand more about our ancient ancestors. And thanks to their efforts, we now know that a number of different species walked the Earth both before and even alongside modern humans. But this particular discovery, whose findings were first reported in August 2018, marked the first time that a direct hybrid had been unearthed. It was history in the making, and it’s no wonder that researchers reacted to the news with delight.

So, what is the story behind this fragment of bone and the girl to whom it once belonged? Well, as it turns out, her tale is intricately intertwined with that of the human race. Today, all people belong to the same species, Homo sapiens, which first emerged approximately 200,000 to 300,000 years ago. But that hasn’t always been the case.

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The earliest-known human ancestors were actually the Australopithecines – a number of different species that were capable of both climbing and walking on two legs. According to research, these distant relatives of Homo sapiens first emerged in Africa more than four million years ago. And, of course, they would have looked very different from how we appear today.

Next, scientists believe, the various species of Homo began to emerge. At first, they evolved longer legs that were better suited to running and walking. Then their brains began to grow. And these adaptations may have signaled a change in behavior, as these early humans began to hunt and take on a more carnivorous diet.

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Then, about 700,000 years ago, the species known as Homo heidelbergensis emerged in Africa and Eurasia. And experts have suggested that these hominins were much more like modern people in their appearance, laying the groundwork for how their descendants would evolve. They acted pretty differently from their predecessors, too.

Apparently, Homo heidelbergensis was likely more intelligent than those who had come before. Members used advanced tools and honed their hunting techniques, for example. Some even believe that individuals may have teamed up to bring down larger animals, which indicates a degree of social cohesion. But despite Homo heidelbergensis’ many strengths, the species still died out.

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You should know, though, that Homo heidelbergensis didn’t disappear from the Earth without leaving a trace. Far from it, in fact. An estimated 390,000 years ago, in the Middle Pleistocene era, a number of different species began to split off from this common ancestor. And from these branches, modern humans would ultimately emerge.

Of course, the story of mankind is one of rich and varied evolutionary history, with many species of hominin thought to have coexisted alongside one another over the millennia. And they didn’t just tolerate one another’s presence. For years, researchers have known that a degree of interbreeding took place between these different groups of early humans. Until the German discovery, however, no one could prove this for sure.

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And, yes, although it’s often said that members of different species cannot successfully interbreed, this is far from an established fact. As Forbes’ Michael Marshall pointed out in a 2018 article, while a mule born from a donkey and a horse is always infertile, the outcome of other inter-species pairings could vary from animal to animal.

Apparently, it’s all to do with DNA. You see, a mule is the product of a horse, which has 64 chromosomes, mating with a donkey, which has 62. So, the offspring of the two animals ends up with 63 chromosomes – an odd number. And, naturally, this has consequences. As the mechanics of sexual reproduction require an egg and a sperm to each contain 50 percent of an animal’s chromosomes, this non-even number means the creature has a “defective” genetic code – one that prevents it from reproducing further.

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But some primate species, such as gorillas and orangutans, share identical numbers of chromosomes. Some researchers have theorized, then, that it could be easier for them to produce healthy offspring. There’s even evidence that bonobos and chimpanzees have interbred at various points throughout their history.

Interestingly, this theory could also explain why some big cats are able to successfully interbreed. The much-touted liger never actually occurs in nature, as lions and tigers’ natural habitats are typically too far apart for mating to occur. But several zoos around the world now house examples of this large creature, which, as an adult, is usually bigger than either of its parents. Ligers can also go on to produce their own offspring.

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And, crucially, early humans are also thought to have shared the same number of chromosomes. That meant the different species were able to interbreed. Experts believe that Homo sapiens began mating with Homo neanderthal not long after migrating from Africa and spreading out around the world.

That’s why most modern humans from Asia and Europe have about 2 percent Neanderthal DNA. Perhaps you noticed this in your own genetic test? But Homo sapiens wasn’t just coupling with Homo neanderthal. Apparently, members of the species also mated with those from another branch of the human family tree. They’re known as the Denisovans.

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The Denisovans are a fairly recent discovery in the field of evolutionary studies. In fact, definite evidence of their existence has only come to light in the 21st century. In 2010 a team of scientists, also from the Max Planck Institute, announced the results of their latest research. After having analyzed a tooth and a finger bone found in the Altai Mountains in Siberia, they had found evidence of a new species of early human.

Pleased with their monumental breakthrough, the researchers dubbed the species Denisova in honor of the cave in which the specimens were found. But aside from what could be interpreted from DNA, little was known about this human ancestor. Then, in 2012, research at the same site in Siberia turned up another small fragment of bone.

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At first, researchers lumped the unremarkable fragment in with the countless animal fossils that were also retrieved from the cave. And it wasn’t until years later, when the University of Oxford’s Samantha Brown took a closer look, that its true nature was revealed. Tasked with cataloging the artifacts, Brown analyzed the proteins inside this bone – and realized that it had come from an ancient human.

After that, the bone passed to Slon, a paleogeneticist. And in order to learn more about this mystery hominin, she, too, began to investigate the DNA contained within the fragment. But in the end, she found more than anyone was expecting.

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At first, it seems, the bone did not appear to be anything particularly remarkable. Just one inch in length, it is believed to have come from a teenage girl who was probably around 13 years of age. It’s thought that she died approximately 90,000 years ago, when the Denisovans populated this small corner of the Altai Mountains.

But when Slon analyzed the DNA present in the bone’s mitochondria, she was in for a big surprise. As anyone with a keen interest in genetics knows, this type of cellular structure contains material that a child inherits only from their mother. And in this case, it indicated that the teenager was descended from a female Neanderthal.

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“This was already very exciting,” Slon told National Geographic in 2018. “It only got more exciting when we started looking at the nuclear DNA.” Our knowledge of genetics tells us that this material is passed down through both the male and female lines, and it allowed scientists to learn more about the father of this ancient teenager.

“That’s when we realized there was something a bit funky about this bone,” Slon continued. In fact, the results were so shocking that she was initially convinced she had made a mistake. Had she somehow skewed the data without realizing it? Or had the sample perhaps been corrupted in the laboratory?

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Eventually, though, Slon realized that there was no mistake. Although the teenager’s mother had Neanderthal DNA, her father, according to the analysis, had been a Denisovan. And that wasn’t all. While analyzing the bone fragment, the paleogeneticist also discovered that the girl’s genetic makeup was remarkably varied as a whole.

But what does that mean in layman’s terms? Well, it’s all to do with a concept known as heterozygosity. Essentially, if your parents were closely related – let’s say, second cousins, for example – the amount of heterozygosity present in your genes would be relatively meager. If you were the result of inter-species breeding, on the other hand, those levels would be sky-high. Make sense?

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And with the bone found in Denisova Cave, it was definitely a case of the latter. Speaking to National Geographic, computational biologist Richard E. Green explained of the ancient DNA, “It’s heterozygous out the wazoo. That’s really what nails it.” Amazingly, Slon had discovered one of the holy grails of human evolution: a first-generation child born of interbreeding between species.

“We knew from previous studies that Neanderthals and Denisovans must have occasionally had children together,” Slon told London newspaper the Evening Standard in 2018. “But I never thought we would be so lucky as to find an actual offspring of the two groups.” And at Harvard University, geneticist David Reich agreed.

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“It’s amazing to be able to find something like this,” Reich said to National Geographic. “It seemed unlikely that we would be able to catch it happening in the act – an individual that’s really the product of a first-generation hybrid.” The discovery was so fortuitous, in fact, that it has raised questions about how common such interbreeding really was.

“It is striking that we find this Denisovan/Neanderthal child among the handful of ancient individuals whose genomes have been sequenced,” the Max Planck Institute’s Svante Pääbo told the Evening Standard. “Neanderthals and Denisovans may not have had many opportunities to meet. But when they did, they must have mated frequently – much more so than we previously thought.”

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Although it’s possible that the discovery was little more than a lucky break, researchers are considering other explanations. One of these is that the two species of hominin actually interacted – and interbred – with each other on a regular basis. And if this theory is true, it would turn our previous understanding of the ancient world on its head.

But the bone of the teenager – who has been dubbed Denny – isn’t the only evidence that lends support to this hypothesis. Up to 2018, scientists had only conducted genetic research on a relatively small number of ancient humans – 23, to be precise. Still, even within this tiny sample, there were at least two specimens that showed evidence of interbreeding between species.

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Take the individual known as Oase 1, for instance. Identified by their lower jaw, this member of Homo sapiens is believed to have walked the planet about 37,000 years ago. But despite their relatively recent place on the human family tree, they were found to be carrying Neanderthal DNA.

And we’re not talking about the very distant past, either. According to a report published in the journal Nature in 2015, Oase 1’s Neanderthal forebears may have been alive only four to six generations previously. If interbreeding between species had only occurred sporadically, Pääbo reasoned, discoveries such as this should be few and far between.

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On top of that, the study from the Max Planck Institute noticed something else about Denny. Apparently, the teenager’s father also had Neanderthal DNA combined with his Denisovan genes. And that’s incredibly revealing. According to Pääbo, “It suggests that these groups, when they met, mixed quite freely with each other.”

Previously, most researchers assumed that interactions between these different groups had happened only infrequently. So, how do these latest developments alter our view of ancient humans and their evolving society? Speaking to National Geographic, Reich explained, “[It]… qualitatively transforms and changes our understanding of the world. And that’s really exciting.”

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Of course, there could be other explanations as to why a first-generation hybrid has already appeared in such a limited sample size. In Green’s opinion, caves such as the one in the Altai Mountains could simply have been popular meeting points for ancient humans, bringing sampling bias into the equation. Or, as the specialist neatly put it in an interview with National Geographic, “They’re the singles bars of the Pleistocene Eurasia.”

But was it simply proximity that inspired the Denisovans and the Neanderthals to interbreed? Or was something else at play? Well, according to the University of Tübingen’s Katerina Harvati-Papatheodorou, such cross-species interactions could have formed a vital part of survival. Speaking to New Scientist, the German academic explained, “Human groups were very small and vulnerable to drastic mortality.”

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And as more information emerges, scientists hope to solve some of the mysteries that have long puzzled those who study human evolution. Did the Denisovans and Neanderthals quickly die out as Homo sapiens began to thrive? Or were they simply assimilated into the dominant species? In an interview with New Scientist, Princeton University’s Joshua Akey admitted that Denny’s DNA points to the second of those assumptions, although we are a long way from a definitive answer.

But even something as small as a tooth can shed light on human evolutionary history. It’s not the look of the remnant that answers scientists’ questions, however. Instead, the experts have developed a process to analyze the enamel of this 800,000-year-old chomper. And the results will clarify the standing of an ancient, meat-eating ancestor that we only discovered as recently as 1994.

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Experts have long known that the closest living relatives to humans are chimpanzees and that the two species split apart approximately 7 million years ago. But the evolutionary changes between primates and humans aren’t clear-cut. And as such, researchers and scientists have spent years exploring the possibilities of how we got from point A to B.

Now, there are some definite plot points along the way. One of the most famous fossil finds of all was Lucy – a partial skeleton discovered in Ethiopia and estimated to be 3.2 million years old. Lucy had had long arms and a chimpanzee-sized brain, but experts could tell that she’d walked on two legs – unlike a primate.

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In finding Lucy, experts happened upon a partial skeleton of one of our ancestors, the Australopithecus. In the case of this more recent development, though, all they had to work with was a tooth. And as such, it would take years of careful analysis to yield fruitful results.

But the tooth had just enough genetic information to help scientists learn more about a particular species. And while studying this sole dental record, they realized that another space was needed on the human family tree. Indeed, from chimpanzees to Lucy and all the way through to modern-day man and woman, a new piece of this vast jigsaw had popped up.

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So scientists have long known that Neanderthals and their sister species, the Denisovans, shared a common ancestor with modern humans. But the placement of the species Homo antecessor never quite fit into the mix. In fact, fossils of the latter species were only discovered in 1994 at an ancient site in Spain.

Neanderthals, for one, roamed the Eurasian continent up until about 40,000 years ago. The Denisovans lived only in Asia, and some of them may have survived until 30,000 to 15,000 years ago. The Homo antecessor lived long before either, though – estimates have them in Western Europe from 1.2 million to 800,000 years ago.

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Now, Paleoanthropologists first uncovered remnants of the Homo antecessor during a dig in Spain’s Sierra de Atapuerca region. Specifically, the team – made up of José María Bermúdez de Castro, Eudald Carbonell and Juan Luis Arsuaga – excavated a massive cavern on-site called the Gran Dolina.

And Gran Dolina has 11 different layers of rock in the ground, most of which feature fossil remnants of either animal or human inhabitants. On the sixth layer, Bermúdez de Castro, Carbonell and Arsuaga found remains from the latter category. Furthermore, they dated the ancient remains to approximately 780,000 years ago, which qualified them as the oldest human fossils found in Europe.

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This particular species became known as Homo antecessor. Of course, “homo” means “human,” while “antecessor” is Latin for “early settler,” “pioneer” or “explorer.” The name fit, considering the remnants were Europe’s oldest. So far, they are the continent’s first-known human population, making them trailblazers. And, with further analysis, they surprised experts in more ways than one.

You see, the Homo antecessor didn’t have a particular physical feature that separated it from other early human species. However, it did have a unique combination of details – particularly in the teeth, cranium and lower jaw – that made it unlike other ancient people. In fact, some of their traits appeared more closely linked to modern humans.

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For instance, the Homo antecessor had a brain approximately 1,000 cubic centimeters in size, compared to a modern human’s, which measures in at 1,350cc. Their frame was likely “similar to modern humans, but more robust,” according to the Australian Museum’s website. And men belonging to this ancient species had rather short stature, typically measuring in at five foot two to five foot nine.

What’s more, the face of the Homo antecessor looked relatively modern, too, especially in the middle part of its visage. They also had noses that projected outward and cheekbones that appeared hollowed, just like today’s humans. But that’s where the similarities end, and more ancient-looking characteristics start making their way in.

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For example, the Homo antecessor had a short forehead, as well as a brow ridge with double markings – a trait mirrored in Neanderthals, as well as in the Chinese Homo erectus. Also, the oldest European fossils indicated that the species had robust teeth, with long incisors shaped like shovels on the top half of their jaws.

Mind you, the Gran Dolina site provided clues as to how the Homo antecessor lived during their day, too. Archaeologists dug up the skeletons of multiple large animals, all of which would’ve been carried to the site intact. This indicated that the species didn’t operate with an every-man-for-himself mentality. Instead, they worked together to survive, and they ate together, too.

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Specifically, it seemed that the Homo antecessor would go out in groups to hunt, then carry back their successful kills. This showed that they had some sort of social structure, dividing up labor and sharing their food amongst each other. And experts could see that they ate species such as wild boar, mammoth, wolves, bear, hyena and deer.

But in contrast, the remains at Gran Dolina appeared to show that Homo antecessor had a brutal side to its nature, too. Yes, some of the remains of the species had cut marks and evidence of crushing and burning. This evidence seemed to show that they had cannibalistic tendencies.

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Of course, the Homo antecessor’s cannibalism could have been an extreme measure in a life-or-death situation. There’s certainly no indication that it was performed in rituals. And even so, other ancient species also exhibited this type of behavior. Neanderthals, for instance, partook in routine cannibalism, it’s believed, and sometimes ritual defleshing of bodies, as indicated by cut marks on their uncovered skeletons.

As such, the paleoanthropologists who found the Homo antecessor fossils did some initial dating of the species. And they figured that it stood as the final link between humans and Neanderthals before they split into their own respective species. You see, the similarities between Homo antecessor and Neanderthal bones couldn’t be ignored.

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But the conversation didn’t end there. Instead, anthropologists embarked on a protracted debate as to where Homo antecessor fit into the human family tree. And the conversation progressed as newer studies revealed the facial similarities between modern humans and the ancient species – and the dissimilarities between them and Neanderthals.

So, a new set of scientists from the University of Copenhagen and the Spain-based team at the National Research Center on Human Evolution took a fresh look at the Homo antecessor’s fossilized remains. This time, they didn’t compare fossil shapes or outward appearances – they utilized protein contained within a single preserved tooth.

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Specifically, the experts relied on a technique called palaeoproteomics or mass spectrometry, which the University of Copenhagen had developed themselves. This allowed them to pull even the tiniest piece of molecular evidence from the 800,000-year-old tooth, which could, in turn, link or unlink the known species of ancient humans.

In this case, experts plucked proteins left behind in the Homo antecessor’s tooth. Then, they rebuilt the amino acid sequences found in these strands. In turn, they did the same with the amino acids found within proteins from modern humans, Neanderthals and Homo heidelbergensis, a species that lived from 700,000 to 300,000 years ago.

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For modern humans, though, the researchers didn’t have to pull the proteins from enamel – they already had full DNA sequencing to work with. Ideally, it would have been easier to do the same with the Homo antecessor’s genetic code, too, but such information did not stand the test of time as the enamel-bound protein did.

Comparing ancient and modern proteins in their respective sequences would answer some lingering questions for researchers. Namely, they would be able to place Homo antecessor in the line-up – were they a sister species to the human race, or did they fit in elsewhere? Knowing this would also bring clarity to the debate which has rumbled on for years since the 1994 discovery in Spain.

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As previously mentioned, experts have known for a while that humans and chimpanzees evolved from a common ancestor – who split into two species roughly nine to seven million years ago. Beyond that, they have known frustratingly little about how the species developed to become their modern selves – and how many other iterations of humans and primates lived and died in the process.

Indeed, the study’s leading author and associate professor of the University of Copenhagen’s Globe Institute, Enrico Cappellini, spoke to Science Daily about previous limits to the research. He said, “Much of what we know so far is based either on the results of ancient DNA analysis, or on observations of the shape and the physical structure of fossils.”

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Before their experiment with the Homo antecessor’s 800,000-year-old tooth, experts hadn’t been able to look back that far into history. Cappellini further explained, “Because of the chemical degradation of DNA over time, the oldest human DNA retrieved so far is dated at no more than approximately 400,000 years.”

Luckily, though, the updated methodology would reveal sequencing that stretched back further in time than ever before. Cappellini said, “Now, the analysis of ancient proteins with mass spectrometry, an approach commonly known as palaeoproteomics, allow us to overcome these limits.” And in this case, a sample of enamel had become a perfect opportunity.

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Still, it took a decade for the project to come to fruition. Paper co-author Jesper Velgaard Olsen collaborated with Cappellini as they carefully extracted the material they needed from the ancient tooth. Olsen put it simply, saying, “This study is an exciting milestone in palaeoproteomics.”

As Olsen went on to explain, “Using state of the art mass spectrometry, we determine the sequence of amino acids within protein remains from Homo antecessor dental enamel. We can then compare the ancient protein sequences we ‘read’ to those of other hominins, for example Neanderthals and Homo sapiens, to determine how they are genetically related.”

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As such, palaeoproteomics finally explained where Homo antecessor fell into the lineup of ancient humans all the way to modern times. Study co-author and post-doctoral research fellow at the University of Copenhagen Frido Welker told Science Daily, “Ancient protein analysis provides evidence for a close relationship between Homo antecessor, us [Homo sapiens], Neanderthals and Denisovans.”

And Welker said that the protein analysis helped to clarify that relationship. He said, “Our results support the idea that Homo antecessor was a sister group to the group containing Homo sapiens [us], Neanderthals, and Denisovans.” So you see, this differed from the original conclusion that Homo antecessor was the final shared ancestor between Neanderthals and modern-day humans.

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Bermúdez de Castro – one of the original paleoanthropologists to find the first remnants of the Homo antecessor – served as the paper’s co-corresponding author. He said, “I am happy that the protein study provides evidence that the Homo antecessor species may be closely related to the last common ancestor of Homo sapiens, Neanderthals, and Denisovans.”

It was particularly exciting, considering the Homo antecessor appeared so much earlier than the Neanderthals and Denisovans. Bermúdez de Castro went on to say, “The features shared by Homo antecessor with these hominins clearly appeared much earlier than previously thought. Homo antecessor would therefore be a basal species of the emerging humanity formed by Neanderthals, Denisovans and modern humans.”

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Of course, for the researchers behind this milestone project the eye-opening results were just the beginning. You see, the University of Copenhagen team said afterward that they want to develop their protein-extracting method further so that they can re-evaluate other fossils and bones. Because perhaps those remains have more information to share after all.

Furthermore, Cappellini told Science News that the bone-centric research “would be extremely interesting.” It could potentially link even more ancient humans together, from the Neanderthals to the Homo antecessor to the 3.2-million-year-old Lucy skeleton and beyond. You see, it’s all about harnessing as good a protein sample as possible.

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That’s right, and Cappellini explained this further. He said, “The more proteins we can extract from the fossils, the more we can say about the prehistoric humans, and the more easily we can construct our own family tree for the time since we diverged from the chimpanzees between seven and nine million years ago.”

Indeed, Homo antecessor was just scraping the surface, as far as research into human history could go. And Cappellini hoped to one day analyze proteins from the two-million-year-old Homo erectus to the Australopithecus (Australopiths), a species of hominins that roamed Africa from four to 1.9 million years ago. As we mentioned earlier, Lucy was one of them.

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According to Science Daily, the University of Copenhagen had the funding to continue its protein-centric research. Perhaps its team would uncover many more connections between modern humans and the species that brought us here today. Cappellini, for one, was excited. He concluded, “I really look forward to seeing what palaeoproteomics will reveal in the future.”

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