Tag Archives: Denisovan

People in the Philippines are the most Denisovan in the world

Genetic analysis has found clear traces that humans and Denisovans interbred in the past. The Philippine ethnic group known as the Ayta Magbukon has the highest level of Denisovan ancestry in the world.

The Negritos group in the Philippines comprises some 25 different ethnic groups, scattered throughout the Andaman archipelago in South-East Asia. They were once considered to be a single population, but the more researchers looked into it, the more they found that Negritos are actually very diverse.

In the new study, Maximilian Larena of Uppsala University and colleagues set out to establish the demographic history of the Philippines. Their project involved indigenous cultural communities, local universities, as well as official and non-governmental organizations from the area. With everyone working together, they were able to analyze 2.3 million genotypes from 118 ethnic groups in the Philippines — including the diverse Negrito populations.

The results were particularly intriguing for a population called the Ayta Magbukon, which still occupy vast swaths of their ancestral land and continue to coexist with the lowland population surrounding them. The Ayta Magbukon seem to possess the highest level of Denisovan ancestry in the world.

“We made this observation despite the fact that Philippine Negritos were recently admixed with East Asian-related groups—who carry little Denisovan ancestry, and which consequently diluted their levels of Denisovan ancestry,” said Larena “If we account for and masked away the East Asian-related ancestry in Philippine Negritos, their Denisovan ancestry can be up to 46 percent greater than that of Australians and Papuans.”

This finding, along with the recent discovery of a small-bodied hominin called Homo luzonensis, suggests that multiple hominin species inhabited the Philippines prior to the arrival of modern humans — and these groups likely interbred multiple times.

The Denisovans are a mysterious group of hominins identified in 2010 based on mitochondrial DNA (mtDNA) extracted from a juvenile female finger bone from the Siberian Denisova Cave. Although researchers haven’t found numerous traces of DNA, they’ve discovered traces of their DNA in modern populations. Apparently, this group in the Philippines has the highest percentage of Denisovan DNA in the world — at least that we’ve found so far.

“This admixture led to variable levels of Denisovan ancestry in the genomes of Philippine Negritos and Papuans,” co-author Mattias Jakobsson said. “In Island Southeast Asia, Philippine Negritos later admixed with East Asian migrants who possess little Denisovan ancestry, which subsequently diluted their archaic ancestry. Some groups, though, such as the Ayta Magbukon, minimally admixed with the more recent incoming migrants. For this reason, the Ayta Magbukon retained most of their inherited archaic tracts and were left with the highest level of Denisovan ancestry in the world.”

Researchers hope to sequence more genomes and better understand “how the inherited archaic tracts influenced our biology and how it contributed to our adaptation as a species,” Larena concludes.

Journal Reference: “Philippine Ayta possess the highest level of Denisovan ancestry in the world” 

Just how “human” are we? At most, 7% of your DNA is uniquely human, study finds

A landmark study found that only 1.5% to 7% of the human genome contains uniquely (modern) human DNA. The rest is shared with relatives such as Neanderthals and Denisovans.

However, the DNA that is unique to us is pretty important, as it’s related to brain development and function.

Image in public domain.

Researchers used DNA from fossils of our close relatives (Neanderthals and Denisovans) dating from around 40,000-50,000 years ago and compared them with the genome of 279 modern people from around the world. They used a new computational method that allowed them to disentangle the similarities and differences between different DNA with greater detail.

Many people around the world (all non-African populations) still contain genes from Neanderthals, a testament to past interbreeding between the two species. But the importance of this interbreeding may have been understated. The new study found that just 1.5% of humans’ genome is both unique and shared among all people living now, and up to 7% of the human genome is more closely related to that of humans than to that of Neanderthals or Denisovans.

This doesn’t mean that we’re 93% Neanderthal. In fact, just 20% of Neanderthal DNA survives in modern humans, and non-African humans contain just around 1.5-2% Neanderthal DNA. But if you look at different people, they have bits of Neanderthal DNA in different places. So if you add all the parts where someone has Neanderthal DNA, that ends up covering most of the human genome, although it’s not the same for everyone. This 1.5% to 7% uniquely human DNA refers to human-specific tweaks to DNA that are not present in any other species and are strictly unique to Homo sapiens.

In addition, this doesn’t take into account the places where humans gained or lost DNA through other means such as duplication, which could have also played an important role in helping us evolve the way we are today.

What makes us human

The research team was surprised to see just how little DNA is ours and ours alone. But those small areas that make us unique may be crucial.

“We can tell those regions of the genome are highly enriched for genes that have to do with neural development and brain function,” University of California, Santa Cruz computational biologist Richard Green, a co-author of the paper, told AP.

The exact biological function of those bits of DNA remains a major problem to disentangle. Our cells are filled with “junk DNA“, which we don’t really use (or we just don’t understand how our bodies use it yet) — but we still seem to need it. We’re not even sure what the the non-junk DNA bits do. Understanding the full instructions and role that genes have is another massive challenge that’s not yet solved.

What this study seems to suggest is that interbreeding played a much bigger role in our evolutionary history than we thought. Previous archaeological studies also suggest this: humans interbred with Neanderthals, Denisovans, and at least one other mysterious species we haven’t discovered yet (but we carry its DNA). Researchers are finding more and more evidence that these interbreeding events weren’t necessarily isolated exceptions but could have happened multiple times and over a longer period than initially thought. It’s up for future studies to reconcile the archaeological and anthropological evidence with the genetic one.

The study also found that the human-specific mutations seemed to emerge in two distinct bursts: 600,000 years ago and 200,000 years ago, respectively. It’s not clear what triggered these bursts; it could have been an environmental challenge or some other event, which at this point is unknown.

Researchers say that studying this 1.5-7% of our genome could help us better understand Neanderthals and other ancient populations, but it could also help us understand what truly makes us human. For instance, you could set up a laboratory dish experiment where you’d edit out the human-specific genes and revert them back to their Neanderthal function, and compare the molecular results of this change. It wouldn’t exactly be like bringing back a Neanderthal, but it could help us deduct how Neanderthals would have been different from modern humans — or, in counterpart, what makes humans stand out from our closest relatives.

The study “An ancestral recombination graph of human, Neanderthal, and Denisovan genomes” has been published in Science.

Here’s what the Denisovans might have looked like

Researchers have used patterns of methylation in ancient Denisovan DNA to predict their anatomical features.

This image shows a preliminary portrait of a young female Denisovan based on a skeletal profile reconstructed from ancient DNA methylation maps. Image credits: Maayan Harel.

The entire collection of Denisovan fossils features a pinky bone, three teeth, and a lower jaw — that’s it. From all that, we not only know that they were a distinct species, but we can also figure out some intriguing aspects about them.

Denisovans are a group of archaic humans in the genus Homo, alongside ourselves and the Neanderthals. A decade ago, we didn’t even know about their existence, until small fragments were discovered in the Denisova cave in Siberia (hence the name Denisovans). Since then, we’ve learned quite a bit about them, although in the grand scheme of things, they still remain a mysterious group.

They lived alongside humans and Neanderthals, interbreeding with both groups, even breeding with the ancestors of some modern groups. For instance, it’s estimated that three to five percent of the DNA of Melanesians and Aboriginal Australians comes from Denisovans.

However, we still have very little idea as to what they looked like.

To shed new light on that issue, researchers used a technique called DNA methylation, which has been used before to suggest anatomical features (and the evolution of such features) in groups of humans.

Quite human. Another predicted portrait of a Denisovan. Image credits:Maayan Harel

Essentially, DNA methylation is a process by which methyl groups are added to the DNA molecule. This changes the activity of the DNA strand without actually changing its structure. From that shifting gene activity, epigenetic patterns can be inferred, and these patterns are then traced back to anatomical features. Using this approach, researchers were able to identify 56 anatomical features in which Denisovans differed from modern humans and/or Neanderthals — in other words, 56 features unique to the Denisovans.

For instance, their skull appears to be wider than that of both humans and Neanderthals, and they also had a longer dental arch.

“We provide the first reconstruction of the skeletal anatomy of Denisovans,” says author Liran Carmel of the Hebrew University of Jerusalem. “In many ways, Denisovans resembled Neanderthals, but in some traits, they resembled us, and in others they were unique.”

“By doing so, we can get a prediction as to what skeletal parts are affected by differential regulation of each gene and in what direction that skeletal part would change–for example, a longer or shorter femur,” added first author David Gokhman.

Image credits: Maayan Harel.

While the method isn’t exactly a perfect predictor, it’s a pretty good approximation. In order to check their findings, the team first compared traits of Neanderthals with those of chimpanzees. They found that roughly 85% of the trait reconstructions were accurate in predicting which traits diverged and in which direction they diverged. Furthermore, while the research paper was in review, another study came out describing a Denisovan mandible — and it fit the prediction.

But while this is helping us make the first steps in truly understanding the ancient group, it may also teach us a bit about ourselves. We only have a general idea about where the Denisovans lived, and little information about what their lifestyle was actually like. The environmental pressure and their reactive adaptations could show us what made us a species survive when our closest relatives didn’t.

“Studying Denisovan anatomy can teach us about human adaptation, evolutionary constraints, development, gene-environment interactions, and disease dynamics,” Carmel says. “At a more general level, this work is a step towards being able to infer an individual’s anatomy based on their DNA.”

Journal Reference: Cell, Gokhman et al.: “Reconstructing Denisovan Anatomy Using DNA Methylation Maps” https://www.cell.com/cell/fulltext/S0092-8674(19)30954-7

Humans and Neanderthals diverged at least 800,000 years ago, new teeth study shows

The origin of humans and our closest cousins, the Neanderthals, has been hotly debated. Now, a new study suggests that the two lineages diverged much earlier than anticipated — and the key might lie in modern-looking teeth.

Hominin teeth. Image credits: Aida Gómez-Robles.

The Atapuerca Mountains in north-eastern Spain might not look like much. They feature gentle slopes and a rather dry landscape, interrupted from place to place by forests and the occasional river. But these mountains hold a karstic environment that is key to understanding how humans came to be, and what life was for our early ancestors.

The most important site is a cave called Sima de los Huesos (Pit of Bones). Anthropologists have recovered over 5,500 human remains which are at least 350,000 years old. The remains belong to 28 individuals of Homo heidelbergensis, an archaic hominin that lived from approximately 700,000 years to 300,000 years ago. Researchers also found fossils of cave bears and some remarkable tools and structures developed by these ancient humans.

In 2016, nuclear DNA analysis showed that remains from some individuals belong to Neanderthals, also suggesting that the divergence between Neanderthals and Denisovans (more enigmatic cousins of ours) happened at least 430,000 years ago. Now, Aida Gómez-Robles, an anthropologist at University College London, believes the cave might also have some clues as to when Neanderthals split from humans.

Gómez-Robles studies what makes humans distinct from other primate species, despite our genetic similarities. She also looks at teeth, in particular, using dental variations to assess the evolutionary relationships of fossil hominins. She believes that the Neanderthal teeth found in the cave look more modern than they should, which offers two possibilities: either the teeth evolved unusually quickly (and there’s no reason to believe that that might be the case) or, as she believes, the teeth had more time to evolve. If the latter is true, then this would mean that Neanderthals split up from our own lineage earlier than expected: some 800,000 years ago.

“There are different factors that could potentially explain these results, including strong selection to change the teeth of these hominins or their isolation from other Neanderthals found in mainland Europe. However, the simplest explanation is that the divergence between Neanderthals and modern humans was older than 800,000 years. This would make the evolutionary rates of the early Neanderthals from Sima de los Huesos roughly comparable to those found in other species.”

Previously, DNA analyses have generally indicated that the lineages diverged around 300,000 to 500,000 years ago. This was very important for anthropological context since researchers took it as a temporal anchor for interpreting other findings. However, anatomical evidence (such as the teeth in the Pit of Bones) seems to contradict this timeline. All the evidence we have seems to suggest that dental shape has evolved at very similar rates across all hominin species, so there’s not much reason to believe Neanderthals would be an exception. It’s a strong argument and a plausible scenario.

“The Sima people’s teeth are very different from those that we would expect to find in their last common ancestral species with modern humans, suggesting that they evolved separately over a long period of time to develop such stark differences,” Gómez-Robles adds.

However, not everyone is convinced. Paleoanthropologist Rick Potts, director of the Smithsonian’s Human Origins Program says that it’s an interesting find, but there’s not enough evidence to counterbalance the previous molecular and DNA results. It’s also unclear why only teeth seem to be heavily evolved — the rest is in accordance with the 300,000-500,000 timeline.

There’s also another complication: hybridization. Neanderthals have been found to interbreed with humans and Denisovans, and during this period, with populations being separated from each other, adapting to a particular environment, and then being re-united and starting breeding again — we don’t really know what the effect of that might have on tooth evolution.

Without additional evidence, the jury is still out regarding the early evolution of these hominin species, but this new study goes to show just how complex our evolutionary history is, and how difficult it is to uncover the intricacies that led to the development of humans and our cousins.

The study was published in Science Advances.

First Denisovan fossil found outside of Siberia — our ancient “cousins” spread far and wide

When the first Denisovan fossil was found in 2010, it was hailed as a stunning discovery. Here was another species related to humans, clearly distinct from the Neanderthals and Homo sapiens. However, fossil evidence of this species had only been found in the Denisova Cave in Siberia, from which the Denisovans were named.

Now, a new fossil discovered in Tibet shows that the Denisovans weren’t nearly as localized as some thought. They spread far and wide, being capable of living at impressive altitudes.

Virtual reconstruction of the jawbone. Image credits: Jean-Jacques Hublin, MPI-EVA, Leipzig.

High Denisovans

Back in 1980, a Tibetan monk found a rather unusual fossil: a seemingly human jawbone. The monk passed it on to Lanzhou University, but the fragment was ignored until the 2010s when archaeologist Dongju Zhang and her colleagues began studying the bone. A recent study has now confirmed that the jawbone belonged to a Denisovan, a group of humanoids that lived alongside humans and Neanderthals, interbreeding with them several times across history.

Although genetic analysis has shown that the Denisovans were a unique group, remains from them have been sparse, and until now, limited only to the Denisova Cave. Of course, it’s not plausible that a humanoid group inhabited a single cave, so the hunt was on for other fossils. Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, wondered if they could find such remains in the Tibetan plateau, and turned to the jawbone from Lanzhou University.

Denisovans split from humans about 550,00–765,000 years ago, but we still carry some of their genetic legacies. Previous studies have suggested that Denisovans were well adapted to living in cold environments and at high altitudes, but the fact that they could survive in Tibet is remarkable.

The altitude of the new Denisovan’s home is 3,280 meters ( 10,700 feet) above sea level, an altitude at which you need special adaptations to be able to survive. This also changes the anthropological history of Tibet and the Himalayas, as previous research claimed that the area was first populated by humans around 40,000 years ago. This new finding pushes that date back by 100,000 years.

The fossil was found in this type of Tibetan landscape. Image credits: Dongju Zhang, Lanzhou University.

It’s not completely surprising, however — actually, this finding might help solve one pressing riddle about the genetic history of the Tibetan people: Tibetans and other populations in the region have a gene inherited from Denisovans that helps them live at high altitudes, but how they got this gene from the Denisovans in the first place is a mystery. The fact that Denisovans developed it in the first place was just as puzzling, considering that their only remains had been found in a low-lying area.

“Frankly speaking, until today, nobody ever imagined that archaic humans could be able to dwell in such an environment,” said Jean-Jacques Hublin, a co-author and paleoanthropologist at the Max Planck Institute for Evolutionary Anthropology. “It’s a big surprise because most people thought that challenging environments like the high altitudes were colonized only by modern humans like us less than 40,000 years ago.”

No DNA

Identifying what species the jawbone came from is no easy feat. The fragment is at least 160,000 years old, and DNA tends to disintegrate much quicker than that. So instead, researchers looked at a specific set of proteins, which is much more durable than DNA. Essentially, the strings of amino acids found in some protein can be a tell-tale sign of a particular species.

“Just like DNA, the amino acids in these proteins are ordered in a particular way,” said co-author Frido Welker, a researcher at the Max Planck Institute for Evolutionary Anthropology. “And we can actually sequence these proteins, so we can read the order of those amino acids.”

Of course, DNA analysis would still be much better. This type of protein analysis is still a nascent field, with a low sample size. But for the lack of a better approach, it offers much-needed information. Researchers also hope that these patterns could help determine other bones that they discovered. Researchers working in China have found several such fossils which are still unidentified.

“In China there are a number of specimens that are not Homo erectus, that are not modern humans, and that are good candidates for being Chinese Denisovans,” Hublin said. “But this has been impossible to prove today because in these fossils there is no ancient DNA preserved.”

“I predict that most of the Chinese hominin fossil record younger than 350,000 years and older than 50,000 is made of Denisovans,” he adds.

Identifying these remains could offer some valuable puzzle pieces as to who the Denisovans were, what they looked like, and how they passed on their genes. Also, if Hublin is right, this might help settle the debate over whether our ancestors evolved solely in Africa, or whether Asia played an important role too.

The study was published in the journal Nature.

Archaeologists uncover timeline of Denisova Cave occupation

The Denisovans were, anthropologically speaking, our cousins. They shared a common origin with Neanderthals and ranged from Siberia to Southeast Asia. They lived along with humans, interbreeding with them on multiple occasions. However, we’ve only found direct evidence of their existence in a cave called Denisova. Now, researchers have detailed the timeline of that cave’s occupation.

Natalia Belousova (Russian Academy of Sciences) and Tom Higham taking samples from the Main Chamber at Denisova Cave
Image credits: Sergey Zelinski, Russian Academy of Sciences

In the lush but cold forests of the Altai Mountains in Siberia, there lies a unique cave. You might not think too much of it seeing it from the outside, but its inside hosts some of the greatest anthropological finds of all time.

The Denisovans were a hominin species whose fossils are known only from a few fragments of bone and teeth unearthed in the Denisova Cave. The excavations and subsequent studies have already provided many insights into this population, but the complex and intricate cave has made it difficult to map the entire timeline of the occupation.

Now, two new papers published in Nature analyze that timeline and provide us with a general picture of the cave’s history.

“Denisova Cave, uniquely, contains stratified deposits that preserve skeletal and genetic evidence of both hominins, artefacts made from stone and other materials, and a range of animal and plant remains,” write Zenobia Jacobs, Richard Roberts, and colleagues, who authored the first paper. “Here, we describe the stratigraphic sequences in Denisova Cave, establish a chronology for the Pleistocene deposits and associated remains from optical dating of the cave sediments, and reconstruct the environmental context of hominin occupation of the site from around 300,000 to 20,000 years ago,” they continue.

Laser beam used for optical dating at the University of Wollongong, Australia.
Image Credits: Erich Fisher.

The optical dating they refer to works by estimating how much time has passed since specific mineral grains (most notably quartz) were last exposed to light. This would correspond to the period when the minerals were brought into the cave. Overall, the authors analyzed the remains of 27 species of large vertebrate, 100 species of small vertebrate (such as mammals and fishes) and 72 species of plant.

Using this method, they found that Denisovans occupied the cave approximately 287,000 to 55,000 years ago. They also confirmed that the cave housed not only Denisovans, but also Neanderthals, who were in the cave from 193,000 to 97,000 years ago. This means that there’s a long period of time where both Denisovans and Neanderthals occupied the cave.

Bone points and pierced teeth from the early Upper Palaeolithic layers of Denisova Cave sampled for radiocarbon dating Image credits: Katerina Douka.

In an accompanying News&Views article also published in Nature, prehistoric archaeologist Robin Dennell, who was not involved in the study, comments:

“Although there might still be some uncertainty about the detailed ages of the remains — given the nature and complexity of the deposits and the dating methods used — the general picture is now clear. Deposition of sediment deposits at Denisova was episodic but [..] the site was occupied by Denisovans and by Neanderthals in both cold and warm periods from approximately 200,000 to 50,000 years ago.”

In a separate paper, Oxford’s Katerina Douka and colleagues present three new fossil fragments, as well as new radiocarbon dates of Denisovan bone, and artifacts also made from bone. Based on the distribution and dating of Denisovan fossils, they conclude that the population inhabited the cave since at least 195,000 years ago. Notably, carbon dating of bone points and tooth pendants indicate an age of 43-49,000 years old, which would make them the oldest artifacts ever unearthed in northern Eurasia. Although this is sti uncear, there’s also a good chance that these artifacts were crafted by the Denisovans.

We are just scratching the surface of who the Denisovans were, researchers emphasize.

“There is still much to learn from Denisova. The work by Douka, Jacobs and their respective colleagues creates an important foundation for such efforts by providing a rigorous and compelling timeline for the cave sediments and its contents,” Donnell concludes.

Journal Reference:

  1. Jacobs et al. “Timing of archaic hominin occupation of Denisova Cave in southern Siberia.” Nature, DOI: 10.1038/s41586-018-0843-2.
  2. Douka et al. “Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave.” Nature, DOI: 10.1038/s41586-018-0870-z.

Archaeologists find 50,000 year-old tiara, made from wooly mammoth ivory

To make things even better — it wasn’t built by humans, but rather by an extinct species of hominins called Denisovans.

This is perhaps the oldest tiara in the world. Image credits: Novosibirsk Institute of Archeology and Ethnography.

 

In the 18th century, a Russian hermit named Denis lived in a remote cave in the Altai Mountains, near the border of Russia, China, and Mongolia. Little did Denis know that he would lend his name not only to the cave but also to a new subspecies of humans — for in the 1970s, archaeologists discovered evidence of ancient hominins inhabiting the cave, from 100,000 to about 30,000 years ago.

Not that much is known about the Denisovans, especially compared to modern humans or Neanderthals, but we do know that they interbred with humans and Neanderthals and had at least a comparable level of development to these groups. Now, a new archaeological dig has uncovered an extremely unusual artifact: a tiara.

The tiara was built from wooly mammoth ivory and judging by its size, it was probably designed for a man.

There is a hole in the rounded end of the tiara, where presumably, a cord was threaded to tie the tiara at the back of the head. This finding suggests that Denisovans produced and wore tiaras for thousands of years, says Alexander Fedorchenko, from Novosibirsk Institute of Archeology and Ethnography.

“Finding one of the most ancient tiaras is very rare not just for the Denisova cave, but for the world. Ancient people used mammoth ivory to make beads, bracelets and pendants, as well as needles and arrow heads”, said Fedorchenko. “The fragment we discovered is quite big, and judging by how thick the (strip) is, and by its large diameter, the headband was made for a big-headed man.”

Archaeologists note the exact position where the tiara was found. Image credits: Novosibirsk Institute of Archeology and Ethnography.

Scientists discovered the remarkable object during the summer, and it’s not the first ivory object found in the cave. Overall, some 30 pieces have been uncovered, including various types of beads, three rings, parts of bracelets and arrowheads. However, the tiara is an extremely rare find, and the technique required to produce it was quite complex.

“Mammoth ivory plates were first thoroughly soaked in water to become more ductile and not crack during processing, and then they were bent under a right angle,” Fedorchenko explains.

“Any bent object tends to return to their original shape over time. This is the so-called memory of the shape effect. We must remember this while trying to judge the size of the head of the tiara’s owner by its diameter.”

Even after all these years and wear and tear, the tiara still retains a distinct and raw beauty. It’s unclear exactly what its purpose was, though archaeologists speculate that it could have been used to keep the wearer’s hair out of the eyes or to denote status and act as a ‘noble’ passport.

Human hybrid — Ancient human relatives interbred with each other

Ancient human species interbred, new evidence suggests.

Digging in and analyzing in the Denisova Cave. Image credits: Bence Viola/Max Planck Institute for Evolutionary Anthropology.

A rather small and inconspicuous cave in the Altai mountains, Siberia, has revolutionized our understanding of ancient humans. The Denisova cave has yielded some of the most fascinating ancient artifacts and remains, including a new species of hominins — the Denisovans, named so after the cave itself.

The Denisovans were distinct but related to the Neanderthals. Since Neanderthal remains were also found in the cave, this led to speculation that the two groups were living and breeding together, but there was no direct proof — until now.

In a new study, a team of anthropologists describe a small piece of bone belonging to a child whose mother was a Neanderthal and father was a Denisovan. Not only is this an extremely important piece of evidence, but it’s also very unexpected — a needle in a haystack, anthropologically speaking.

“To find a first-generation person of mixed ancestry from these groups is absolutely extraordinary,” says population geneticist Pontus Skoglund at the Francis Crick Institute in London. “It’s really great science coupled with a little bit of luck.”

The new study was led by Viviane Slon and Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Along with their colleagues, they carried out a genetic analysis of the piece of bone, finding that 40% of DNA fragments from the specimen matched Neanderthal DNA, while another 40% matched Denisovan DNA. When they sequenced the sample’s mitochondrial DNA, they found that it comes from the Neanderthal lineage. Since mitochondrial DNA is only inherited from the mother, it means that the mother was Neanderthal, which means that the father was a Denisovan.

But there is another possibility: what if both parents were hybrids themselves?

Denisova Cave.

To figure out which of the two options were more likely, researchers looked at which sections matched which type of DNA. Again, the results aligned surprisingly well, clearly indicating that Denny — as the ancient human was unofficially named — was the direct offspring of two distinct humans, not hybrids. Denny is a first-generation hybrid, and the results, Skoglund told Nature, need to go directly into the history books.

It’s not clear how common interbreeding was, but it seems plausible that both Neanderthals and Denisovans would have jumped at the possibility of breeding with each other. So why haven’t we found more evidence for it, then?

There are a few reasons, starting with the fact that they come from different geographical ranges. In other words, Denisovans and Neanderthals might have simply not met all that often. Also, there’s a chance that hybrids wouldn’t have been fertile, preventing the two groups from truly merging.

Until some 40,000 years ago, Europe was home to both groups. The more well-known Neanderthals were more present in the West, while the elusive Denisovans retreated to the East.

The study was published in Nature.

No bones needed — researchers use DNA in soil to tell if humans were around

Archaeologists might have just come across a game changer after a new study reports a new way of seeing if humans have been around or not.

The average annual temperature of the Denisova cave remains at 0 °C (32 °F), which helped protect the DNA. Image credits: Демин Алексей Барнаул.

For archaeologists, knowing where to look is extremely important. There’s no telling how many sites and even settlements we’ve yet to discover, and what mysteries those might hold. The problem is, it can be really hard to identify these places, and it gets even worse with ancient archaeology when there are almost no structures and no obvious tells.

To a great extent, paleolithic archaeologists rely on human bones to understand the context of a site. Just take the Denisova Cave in Siberia, famous for giving its name to the Denisovans, a species of humans largely similar to Neanderthals. There are plenty of tools there created by some human species, but what species was it? Was it Denisovans, Neanderthals, Homo sapiens… something else? We don’t know. Many believed they were created by Denisovans, because Denisovan bones were abundant in the cave, but the new study claims this is not the case. Even though no Neanderthals bones were found in the area, the paper’s authors confirmed their presence by studying the DNA in the soil.

“This is a game changer for researchers studying our hominin past,” says Christian Hoggard, an archaeologist at Aarhus University who wasn’t involved with the story. His words are echoed by myriad researchers excitedly tweeting the paper: “This is pretty damn incredible,” says Rob Scott, an evolutionary anthropologist at Rutgers. Tom Higham, an Oxford professor who specializes in dating bones, called the discovery a “new era in Paleolithic archaeology.”

The rarity of bones is a major problem for researchers. It’s not extremely rare for scientists to find man-made tools but no bones nearby. The fact that DNA from soil can be analyzed is a big difference.

“Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site,” the study reads. “Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered.”

Viviane Slon, a researcher at the Max Planck Institute for Evolutionary Anthropology, coordinated a large team of multidisciplinary researchers. After extracting genetic material from sediment samples across four caves in Europe, they carried out an analysis focusing on mitochondrial DNA, only a small portion of the DNA in a eukaryotic cell. Basically, you take the soil sample (not much, less than a teaspoon), use chemical agents to release the genetic material, and then put it in a sequencing machine. However, it’s not really as easy as that. Slon and her team used a clever innovation which relies on the geometrical arrangement of DNA, which is kind of like a jigsaw zipper tightly entwined in a double helix structure. What they did is synthesize a half of it, “baiting” and extracting the other half of the sequence from the solution it was placed in.

The structure of DNA showing with detail showing the structure of the four bases, adenine, cytosine, guanine and thymine. Image credits: Zephyris.

It’s not just human DNA that works with this, they found the DNA of ancient mammals like woolly mammoths and woolly rhinos, before ultimately finding the DNA of Neanderthals, confirming their finds using existing archaeological record. After confirming the results of their method, they move onto the unknown, ultimately concluding that Neanderthals and not Denisovans had created the tools from the Denisova cave. They also confirmed the existence of Neanderthal DNA in Trou Al’Wesse in Belgium, where tools and animal bones have suggested Neanderthal presence, but no Neanderthal bones have ever been found.

There are limits to what this method can do, as the oldest DNA ever analyzed was around 700,000 years old, but in most cases, DNA analysis can’t go that much into the past. Furthermore, you might get some DNA contamination which might be very confusing. Archaeologists analyze things in layers, but there’s no guarantee that DNA found in a layer originated in that layer — it may have migrated from a different layer. Still, the possibilities and potential of this method are extremely exciting.

Journal Reference: Viviane Slon et al — Neandertal and Denisovan DNA from Pleistocene sediments. DOI: 10.1126/science.aam9695.

Peculiar ancient skulls have both human and Neanderthal features. Could belong to a new hominid species

Chinese researchers uncovered two partial skulls which might have belonged to a new species of archaic human. In this image, colored in yellow are the fragments found by the researchers which were put together with their mirror-image pieces (purple). Credit: AAAS

Two partial skulls recovered from eastern China have perplexed scientists with their intriguing mix of both Neanderthal and Homo sapiens features. These people weren’t modern human nor Neanderthals but some other species. So far, the likeliest candidate seems to be the Denisovans, an extinct group of ice age people first discovered in 2010 — but until a DNA analysis of the fragments is performed we can’t know for sure. Some speculate we might have come across a new species of archaic humans from the genus Homo. 

Part human, part Neanderthal, with a distinctively Asian flavor

The skulls were unearthed after one fateful day in 2007 archaeologist Zhan-Yang Li spotted quartz tools eroding out of the sediments at a site near the town of Lingjing, in China’s Henan province. Li, who works at the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing, ordered the extension of the field study for a couple more days in light of these findings. He was inspired because the digs eventually surfaced a yellow piece of skull cap protruding from the muddy floor.

After digs made during six seasons, the archaeologists retrieved 45 fossil fragments which came together to form two skulls. The fossils were found in the same sediment layer as the quartz tools and have been dated to 105,000 to 125,000 years ago.

The Pleistocene-era skulls lack jaws and face bones but what remains clearly shows the individuals weren’t human. The brow ridges and skull mass resembled early modern humans of the Old World but the ear canals and large, back section of the skull clearly resemble those of Neanderthals. One of the skulls has a brain volume of 1800 cubic centimeters, which is higher than average for both modern humans and Neanderthals, as reported in the journal Science.

Not Neanderthal nor Homo sapiens, that’s for sure. Nor did the skulls belong to some other archaic humans as Homo erectus or Homo heidelbergensis since the skulls are too light and the brains far too big.

Xiu-Jie Wu, a paleoanthropologist at IVPP, thinks the skulls belonged to a new archaic human that survived in East Asia up until 100,000 years ago. He cites compelling evidence such as another early human skull retrieved from China’s Nihewan Ba­sin 850 kilometers to the north of Lingjing which shares similar features like the broad cranial base and low, flat plateau along the top of the skull.

A mosaic of features

Based on similarities with other Asian fossils dated 600,000 to 100,000 years ago, Wu and colleagues suggest the new crania belonged to members of a regional population from eastern Asia who passed local traits down from generation to generation. In other words, a distinct population of archaic humans who passed their genes in a form of regional continuity. The population must not have been isolated, though, judging from the resemblances to both Neanderthals and modern humans which suggest racial mixing, at least in low levels.

Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology, however, thinks we’re dealing with Denisovans. It is at Hublin’s lab that one day in 2010 researchers identified a new Homo species, the Denisovans in question, after sequencing DNA From a 40,000-year-old adult tooth and an exquisitely preserved fossilized pinkie bone that had belonged to a young girl who was between five and seven years old when she died. When Homo sapiens left Africa, they were not alone — they were joined by both Neanderthals and these elusive Denisovans which traveled deep into Asia.

A molar that belonged to an ancient Denisovan. Credit: Max Planck Institute for Evolutionary Anthropology.

A molar that belonged to an ancient Denisovan. Credit: Max Planck Institute for Evolutionary Anthropology.

Studies show the girl was closely related to Neanderthals, yet distinct enough to merit classification as a new species of archaic humans. But other than these two lone samples, a tooth and a pinkie bone retrieved from the Denisova cave in southern Siberia, we don’t have any other fossils to pin to Denisovans. These two crania could have belonged to some Denisovans, though, or so Hublin believes.

“This is exactly what the DNA tells us when one tries to make sense of the Denisova discoveries,” he said. “These Chinese fossils are in the right place at the right time, with the right features.”

“This would be the combination that one would expect based on the ancient DNA analysis of Denisovans, who were closely related to Neanderthals,” Neanderthal expert Katerina Harvati from the University of Tübingen in German told The Washington Post.

The only way to get to the bottom of things is to have DNA sequenced from these skull fragments. It might prove tricky, but if scientists manage to isolate enough workable samples, a monumental discovery might be in the working. Even if the skulls turn out not to belong to a new species, if these used to be Denisovans than we’ll at least learn much more about our cousins with which we shared this planet not that long ago. This is some very exciting work.

“The biological nature of the immediate predecessors of modern humans in eastern Eurasia has been poorly known from the human fossil record,” said Erik Trinkaus, a corresponding author for the study and professor of anthropology at Washington University in St. Louis. “The discovery of these skulls of late archaic humans, from Xuchang, substantially increases our knowledge of these people.”

More importantly, he noted: “The features of these fossils reinforce a pattern of regional population continuity in eastern Eurasia, combined with shared long-terms trends in human biology and populational connections across Eurasia. They reinforce the unity and dynamic nature of human evolution leading up to modern human emergence.”

400,000-year-old fossils from Spain provide earliest genetic evidence of Neandertals

Researchers working in Spain have made a surprising finding: Neanderthals emerged much earlier than previously believed, perhaps as far as half a million years ago. This comes after previous research suggested that Neanderthals intermingled with humans and other hominins over 100,000 years ago.

via Youtube.

We’re starting to understand that Neanderthals themselves were a much more complex race than we previously thought. For some time now, we’ve known for sure that Neanderthals and humans cross-bred. This is evidenced by the fact that non-African people alive today have about 2% Neanderthal DNA, while sub-Saharan Africans (those whose ancestors were never to Europe) share 0% Neanderthal DNA. But previous analyses of the hominins from Sima de los Huesos in 2013 showed that their DNA is related to that of Denisovans, an extinct species of humans. Until now, the 400,000-year old skeletons were of unknown origin, and some thought they were perhaps a common ancestor of Neanderthals and denisovans. However, using DNA analysis, researchers from Leipzig confirmed that the skeletons are Neanderthals, anchoring them much better in a human timeline.

“Sima de los Huesos is currently the only non-permafrost site that allow us to study DNA sequences from the Middle Pleistocene, the time period preceding 125,000 years ago”, says Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology, lead author of an article that was published in Nature today. “The recovery of a small part of the nuclear genome from the Sima de los Huesos hominins is not just the result of our continuous efforts in pushing for more sensitive sample isolation and genome sequencing technologies”, Meyer adds. “This work would have been much more difficult without the special care that was taken during excavation.”

These findings are consistent with modern humans diverging from ancient timelines 550,000 to 750,000 years ago. Interestingly, while it has been confirmed that they are Neanderthals, their DNA is still extremely close to Denisovans, raising even more questions about how the Denisovans emerged, and interacted with other humans.

It’s a great time to be alive, when modern, advanced techniques can shed light on ancient fossils:

“We have hoped for many years that advances in molecular analysis techniques would one day aid our investigation of this unique assembly of fossils”, explains Juan-Luis Arsuaga of the Complutense University in Madrid, Spain, who has led the excavations at Sima de los Huesos for three decades. “We have thus removed some of the specimens with clean instruments and left them embedded in clay to minimize alterations of the material that might take place after excavation.” The nuclear DNA sequences recovered from two specimens secured in this way show that they belong to the Neandertal evolutionary lineage and are more closely related to Neandertals than to Denisovans. This finding indicates that the population divergence between Denisovans and Neandertals had already occurred by 430,000 years ago when the Sima de los Huesos hominins lived.

A comparison with the genome of a Neanderthal from the same cave revealed significant local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, while evidence was also detected of interbreeding with an as yet unidentified ancient human lineage.

Journal Reference: Matthias Meyer et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins, Nature (2016). DOI: 10.1038/nature17405

Red hair and fair skin are also thought to have been inherited from Neanderthals. [Image Source: BBC News

Interbreeding with Neanderthals gave humans an immunity boost, but also allergies

Some 50,000 years ago Homo sapiens, Neanderthals and Denisovans co-existed, mingled and interbred. While only the human lineage exists today, these inter-species  third degree meetings left a permanent mark on our genome. For instance, an ancient human who lived in what is today Romania had 9% Neanderthal DNA. Today, most Europeans and Asians have between 1 to 4 percent Neanderthal DNA. Indigenous sub-Saharan Africans have no Neanderthal DNA because their ancestors did not migrate through Eurasia. Some of these genes were rendered useless by countless generations of adaption to new environmental cues, once the last Ice Age was over, agricultural and livestock tendering was introduced and other important episodes that changed forever how humans lived. Some subsisted, though. Two studies investigated the functional value of genes inherited from Neanderthals and Denisovans. The researchers found interbreeding lent genes still use today by the immune system. As pesky byproduct was that it also rendered humans more prone to allergies.

Red hair and fair skin are also thought to have been inherited from Neanderthals. [Image Source: BBC News

Red hair and fair skin are also thought to have been inherited from Neanderthals.
[Image Source: BBC News

A team at the  Institut Pasteur and the CNRS in Paris went through the vast swaths of data from the  1000 Genomes Project. Their focus was on 1,500 genes known to play a role in the innate immune system, which they examined for patterns of genetic variation and evolutionary change with an unprecedented level of detail. They were able to estimate the time it took for these variations to take place and the  extent of Neanderthalian contribution.

Apparently, Neanderthals greatly influenced the Toll-like receptor (TLR) genes TLR1, TLR6, and TLR10, which help detect and respond to components of bacteria, fungi, and parasites.

Elsewhere, a team from the Max Planck Institute for Evolutionary Anthropology in Leipzig came to similar conclusions. The fact that they weren’t actually actively looking for immune system genes strengthens those findings made by the French researchers.

What they were interested in was studying the functional importance of genes inherited from archaic humans more broadly. First, they screened modern humans’ genomes for regions which were highly similar to the Neanderthal and Denisovan genomes.  Those analyses led them to the same three TLR genes. Two of those gene variants are most similar to the Neanderthal genome, whereas the third is most similar to the Denisovan genome.

This world map shows the frequencies of Neandertal-like TLR DNA in a 1000 Genomes dataset. The size of each pie is proportional to the number of individuals within a population. Credit: Dannemann et al./American Journal of Human Genetics 2016 .

This world map shows the frequencies of Neandertal-like TLR DNA in a 1000 Genomes dataset. The size of each pie is proportional to the number of individuals within a population. Credit: Dannemann et al./American Journal of Human Genetics 2016 .

These variants increase the activity of the  TLR genes, helping us today fight pathogens better. On the flipside, it also increased the susceptibility of modern-day people to allergies.

“We found that interbreeding with archaic humans—the Neanderthals and Denisovans—has influenced the genetic diversity in present-day genomes at three innate immunity genes belonging to the human Toll-like-receptor family,” says Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

“These, and other, innate immunity genes present higher levels of Neanderthal ancestry than the remainder of the coding genome,” adds Lluis Quintana-Murci of the Institut Pasteur and the CNRS in Paris. “This highlights how important introgression events [the movement of genes across species] may have been in the evolution of the innate immunity system in humans.”

All of this makes absolute sens. Before humans arrived in Europe, Neanderthals had lived there for hundreds of thousands of years. As such, they were better adapted and had a higher chance to survive, and by interbreeding with them we humans became stronger.

Ref:

1 )American Journal of Human Genetics, Deschamps et al.: “Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes” dx.doi.org/10.1016/j.ajhg.2015.11.014
2) American Journal of Human Genetics, Dannemann et al.: “Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors” dx.doi.org/10.1016/j.ajhg.2015.11.015

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Human face diversity may have evolved to make us look unique

face_two

Human face traits are so diverse because of evolutionary pressure, according to a new study published in Nature Communications. Photo: Lynolive, Venice Carnival.

While you might find people sometimes resemble each other, if you look close enough you’ll soon find unique features and facial characteristics that sets them apart. It’s remarkable how diverse human faces are across the billions alive today and the countless billions that used to live in this world. Scientists at University of Berkeley now believe they understand why this is the case: humans have evolved facial variety to make each of us look unique and easily recognizable.

“Humans are phenomenally good at recognizing faces; there is a part of the brain specialized for that,” said  Michael J. Sheehan, a postdoctoral fellow in UC Berkeley’s Museum of Vertebrate Zoology. “Our study now shows that humans have been selected to be unique and easily recognizable. It is clearly beneficial for me to recognize others, but also beneficial for me to be recognizable. Otherwise, we would all look more similar.”

“The idea that social interaction may have facilitated or led to selection for us to be individually recognizable implies that human social structure has driven the evolution of how we look,” said coauthor Michael Nachman, a population geneticist, professor of integrative biology and director of the UC Berkeley Museum of Vertebrate Zoology.

A face like no other

The premise started from a fundamental question: is the widely recognized variance in facial features, like the distance between the eyes or width of the nose, dictated purely by chance or has there been evolutionary selection for these to become more variable than they would be otherwise. To answer this question, the team of researchers first mined a 1988 U.S. Army database that compiled male and female body measurements, then made a  statistical comparison of facial traits: forehead-chin distance, ear height, nose width and distance between pupils. Comparisons in other parts were also made, like forearm length, height at waist, etc.

The researchers found that  facial traits are much more variable than other bodily traits, such as the length of the hand, and that facial traits are independent of other facial traits, unlike most body measures. People with longer arms, for example, typically have longer legs, while people with wider noses or widely spaced eyes don’t have longer noses. Both findings suggest that facial variation has been enhanced through evolution.

[ALSO READ] DNA alone could be used to visually recreate a person’s face

This significant physical difference between facial trait variance and the degree of variation of all other body parts was then put to the test by accessing genetic logs. The researchers turned to the  data collected by the 1000 Genome project, which has sequenced more than 1,000 human genomes since 2008 and catalogued nearly 40 million genetic variations among humans worldwide. Looking at regions of the human genome that have been identified as determining the shape of the face, they found a much higher number of variants than for traits, such as height, not involving the face.

“All three predictions were met: facial traits are more variable and less correlated than other traits, and the genes that underlie them show higher levels of variation,” Nachman said. “Lots of regions of the genome contribute to facial features, so you would expect the genetic variation to be subtle, and it is. But it is consistent and statistically significant.”

Of course, since it has proven to be so productive for humans to be social, cooperate and work together with their peers it seems natural for evolution to facilitate a species grow even further employing the same mechanisms. Other animals, however, which don’t rely that much on vision to distinguish individuals from the same species, seem to look more like each other. With this in mind, what about our hominid ancestors? Were individuals then also geared towards facial uniqueness? It’s yet to early to speak about ancestors who lived hundreds of thousands or even millions of years ago, but the more recent Neanderthals and Denisovans are a different matter. The researchers compared  human genomes with those sequenced from Neanderthals and Denisovans  and found similar genetic variation, which indicates that the facial variation in modern humans must have originated prior to the split between these different lineages.

“Clearly, we recognize people by many traits – for example their height or their gait – but our findings argue that the face is the predominant way we recognize people,” Sheehan said.

Findings appeared in the journal Nature Communications.

Tibetans acquired a unique gene by interbreeding with a now-extinct human species. Photo: easytourchina.com

Unique gene passed by extinct human species makes Tibetans superhuman

Tibetans acquired a unique gene by interbreeding with a now-extinct human species. Photo: easytourchina.com

Tibetans acquired a unique gene by interbreeding with a now-extinct human species. Photo: easytourchina.com

Advancements in genetic sequencing has allowed genomic research to flourish. DNA sequencing is now much faster, cheaper and accurate than ever before, and we’re only now beginning to reap the rewards. It’s the first step to a complete understanding of our bodies. The Human Genome Project, once finally completed, mapped and identified all the genes of the human genome. This helps us get an idea of where are, but to understand how we got here, we also need to peek into ancient DNA. For instance, a recent study found that Tibetans share at least one gene with the ancient Denisovans, an ancient human species that interbred with the Tibetan homo sapiens ancestors. Ironically, the Denisovans’ extinctions was pushed by the homo sapiens presence.

A unique gene that makes the Tibetans genuine supermen (atop the Himalayas of course)

The gene in question is called EPAS1 and helps the Tibetans adapt to extreme altitudes of 15,000 feet or more. In a way, Tibetans are superhuman mountain people, since they are able to survive in conditions that could normally kill a non-Tibetan.

“We have very clear evidence that this version of the gene came from Denisovans,” said principal author Rasmus Nielsen, a Berkeley professor of integrative biology, in a press release.

The Denisovans are a group of ancient humans that have only recently come to our knowledge. In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia – a cave which was also inhabited by humans and Neanderthals. Nobody knows what Denisovans looked like because there are so few fossils. But geneticists have managed to sequence their entire genome to a high degree of accuracy.

An artist's interpretation of how a Denisovan might have looked like. Artwork:  Joe McNally / NGS

An artist’s interpretation of how a Denisovan might have looked like. Artwork: Joe McNally / NGS

The present study is of great significance, because it not only proves without reason of a doubt that homo sapiens interbred with the Denisovan hominids, but is also the first study of its kind that shows a gene from another species of human was used to help modern humans adapt to their environment.

A breakthrough discovery

Particularly, the gene only activates a high-altitudes or atmospheres with low-oxygen content. It’s during this time that a normal homo sapiens gets in trouble, because the low-oxygen atmosphere triggers a rush of hemoglobin, which is the red-colored protein responsible for transporting oxygen in blood. But it’s too much of a good thing causing blood thickening, which can result in heart attacks and death. When the EPAS1 gene activates, however, only a slight increase of hemoglobin is triggered – just enough to compensate for the oxygen reduction.

“We found part of the EPAS1 gene in Tibetans is almost identical to the gene in Denisovans and very different from all other humans,” Nielsen said. “We can do a statistical analysis to show that this must have come from Denisovans. There is no other way of explaining the data.”

The gene can also be found in certain members of the Han Chinese population, which had the gene passed down by the Tibetans. Interestingly enough, natives to the island of Melanesia – an indigenous group which shares up to 5% of its DNA with Denisovans – don’t have this gene. Clearly, because they interbred, the Melanesians also had the gene at one time, but because they never had to use it, the gene came off.

So, how much of us is homo sapiens? The short answer is we don’t know yet. Not too long ago, the community thought modern homo sapiens never interbred with other hominids. Later it was shown that homo sapiens indeed interbred with both Neanderthals and Denisovans, with which we share DNA, and possibly other groups of yet unknown hominids as well. A more refined understanding of the human genome and future remarkable findings will definitely shed further light onto this.

“There might be many other species from which we also got DNA, but we don’t know because we don’t have the genomes,” Nielsen said. “The only reason we can say that this bit of DNA is Denisovan is because of this lucky accident of sequencing DNA from a little bone found in a cave in Siberia. We found the Denisovan species at the DNA level, but how many other species are out there that we haven’t sequenced?”

The results appeared in the journal Nature.

Oldest human DNA ever found – 400.000 years old

The recent discovery of DNA of a 400,000-year-old human thigh bone could provide valuable insight into the evolution of humans; researchers explain this is easily the oldest human genetic material ever found.

When it comes to being a mountain, the Atapuerca Mountains in Spain don’t really have much going for them. It’s an ancient karstic region of Spain comprising mostly of limestone, looking really craggy and run down. But even though they may not impress geologists, the situation is very different with archaeologists. The area is home to a treasure trove of buried archaeological riches: fossils and tools belonging to the earliest known species of ancient humans. The most famous site is called Sima de los Huesos — “The Pit of Bones”, and this is where this femur also came from.

The remains of at least 28 people are there, and archaeologists have so far discovered over 5.500 bones. Now, working in the area, Matthias Meyer, a lead researcher at the Max Planck Institute for Evolutionary Anthropology, and a team of colleagues have recovered and analyzed the earliest known human DNA.

Everything about this discovery is special. First of all, archaeologists had to crawl for hundreds of metres through narrow cave tunnels; then, they had to go down, in the dark, while hanging on to a rope, Indiana Jones style. They believe that the bones (probably bodies at the time) were deposited in inaccessible areas. After they recovered the bones, they carefully drilled into them, obtained about two grams worth of bone, then isolated the DNA using a recently discovered method (in 2013) that employs silica to make the process more efficient.

“Years ago, geneticists said they wouldn’t be able to find DNA that was older than 60,000 years old,” said co-author Jose Bermudez de Castro, from the National Research Centre for Human Evolution (CENIEH), a member of the team that excavated the fossils.

They focused on mitochondrial DNA (the cells’ energy factories), for two reasons:
mitochondrial DNA contains way fewer genes than does nuclear DNA
– because mitochondrial DNA is passed on exclusively from mothers, there are usually no changes from parent to offspring – which makes it a very useful tool for tracking down ancestry.

After sequencing 98% of the mitochondrial DNA genome, Meyer and his team estimated the age of the sample using the length of the DNA branch as a proxy. They estimated the age to be around 400.000 years, which would put it in the Middle Pleistocene and make it by far the oldest human DNA sample ever found. The previous record was a 100.000 year old Neanderthal sample.

The sample comes from Homo heidelbergensis, a group of extinct humans related in many ways to Neanderthals. However, genetic analysis showed that the owner did not share a common ancestor with Neanderthals, but instead with the Denisovans, a mysterious subspecies discovered only in 2008 that last shared an ancestor with Neanderthals and Homo sapiens about one million years ago. This is even more interesting because the Denisovans were initially found in Siberia, which is, needless to say, quite a long way from Spain. Meyer presented three possibilities:

“First, the Sima de los Huesos hominins may be closely related to the ancestors of Denisovans.”

“Second, it is possible that the Sima de los Huesos hominins represent a group distinct from both Neanderthals and Denisovans that later perhaps contributed the mtDNA to Denisovans.”

“Third, the Sima de los Huesos hominins may be related to the population ancestral to both Neanderthals and Denisovans.”

The skeleton of an ancient caveman dubbed Brana 1 yielded the oldest DNA found in a modern human. CREDIT: Alberto Tapia

Earliest modern human genome partially sequenced

The skeleton of an ancient caveman dubbed Brana 1 yielded the oldest DNA found in a modern human. CREDIT: Alberto Tapia

The skeleton of an ancient caveman dubbed Brana 1 yielded the oldest DNA found in a modern human. CREDIT: Alberto Tapia

Researchers have analyzed the DNA from  7,000-year-old bones of two cavemen unearthed in Spain, and have managed to sequence fragments of their genomes, making them the oldest modern human specimens ever found thus far. Ironically, the researchers found that the cavemen bear little genetic resemblance to people living in the region today, instead sharing ancestry with current populations of northern Europe.

The skeletons of two young adult males were discovered by chance in 2006 by cave explorers in a cavern high in the Cantabrian mountain range, northern Spain, at an altitude of about 1,500 meters. This made the region particularly cold, especially during that period of time, but which ultimately helped preserve the DNA in the bones. Judging by the ornament that one was found with of red-deer canines embroidered onto a cloth, also remarkably preserved, the cavemen were hunter-gatherers of the Mesolithic period, before agriculture spread to the Iberian Peninsula with Neolithic settlers from the Middle East.

“These are the oldest partial genomes from modern human prehistory,” said researcher Carles Lalueza-Fox, a paleogeneticist at the Spanish National Research Council.

The team of scientists were able to rescue the complete mitochondrial DNA, the genetic information housed in sub-cellular structures called mitochondria, from  “Braña1,” one of the two skeletons.

“Despite their geographical distance, individuals from the regions corresponding to the current England, Germany, Lithuania, Poland and Spain shared the same mitochondrial lineage,” said Lalueza-Fox in a statement. “These hunters-gatherers shared nomadic habits and had a common origin.

Previously, researchers have managed to sequence the complete genomes of our closest extinct relatives, the Neanderthals and the Denisovans. For the present study, the scientists recovered 1.34 percent and 0.5 percent, respectively, of the human genomes from the bones of these two cave men.

“There are many works that claim the Basques [of the Iberian Peninsula] could be descendants from Mesolithics that became isolated in the Basque country,” Lalueza-Fox said. “We found the modern Basques are genetically not related to these two individuals.”

The researchers now aim to complete the genomes of both cavemen. Such data could help “explore genes that have been modified with the arrival of the Neolithic in the European populations,” Lalueza-Fox said.

Findings were presented in the journal Current Biology; via LiveScience.

A skull from a specimen, recovered from Longlin cave in China, belonging to the Red Deer Cave people - possibly a new species of human. (c) Darren Curnoe

Mysterious hominid fossils found in China hint towards a new human species

A skull from a specimen, recovered from Longlin cave in China, belonging to the Red Deer Cave people - possibly a new species of human. (c) Darren Curnoe

A skull from a specimen, recovered from Longlin cave in China, belonging to the Red Deer Cave people - possibly a new species of human. (c) Darren Curnoe

An incredible find was publicized just earlier  – fossils remains from stone age people were unearthed from two caves in China. Upon further inspection it was found that the bone features, particularly skulls, were unlike any other human or early ancestor remains ever found, suggesting that the researchers may have actually found a new species of human.

Bones, including partial skulls, have been unearthed from at least four individuals, which were estimated to have lived some 14,300 to 11,500 years ago. Presenting anatomical features which mix both archaic and modern human complexion, the Red Deer Cave people, as they’ve been called after the name of the location they’ve been found in, have simply stunned researchers.

“They could be a new evolutionary line or a previously unknown modern human population that arrived early from Africa and failed to contribute genetically to living east Asians,” said Darren Curnoe, who led the research team at the University of New South Wales in Australia.

“While finely balanced, I think the evidence is slightly weighted towards the Red Deer Cave people representing a new evolutionary line. First, their skulls are anatomically unique. They look very different to all modern humans, whether alive today or in Africa 150,000 years ago,” Curnoe told the Guardian.

“Second, the very fact they persisted until almost 11,000 years ago, when we know that very modern looking people lived at the same time immediately to the east and south, suggests they must have been isolated from them. We might infer from this isolation that they either didn’t interbreed or did so in a limited way.”

The fossils were retrieved from two cave sites in China, Maludong, or Red Deer Cave, near the city of Mengzi in Yunnan province, and Longlin cave,  in southwest China. Curiously enough, the fossils were initially found encased in blocks of rock, which hid their features and thus lead them to be ignored. The Red Deer Cave remains were found 1989, while the Longlin cave remains were found in 1979, however they remained unstudied until 2008. Were it not for the inherent curiosity of the researchers involved in the project to study these fossils, they simply would’ve remained to this day in some warehouse, gathering dust as they did for millennias.

“In 2009, when I was in China working with co-author Professor Ji Xueping, he showed me the block of rock that contained the skull,” Curnoe recalled. “After picking my own jaw up from the floor, we decided we had to make the remains a priority of our research.”

Quite possibly a new species of human. How were they different?

Artist impression of what the Red Cave People might have looked like between 11,500 and 14,500 years ago. (c) Peter Schouten

Artist impression of what the Red Cave People might have looked like between 11,500 and 14,500 years ago. (c) Peter Schouten

The individuals have, in some respects, unique features to humans. For instance, strongly curved forehead bone, a very broad nose and eye sockets, large molar teeth, prominent brows, thick skulls and flat faces, which flare widely on the side making wide for very strong chewing muscles. Their brains were average sized by ice age standards, and they used to cook their meals, judging from the number of mammal skeletons found nearby the remains, all of them species still around today, with the exception of the giant red deer.

The Red Deer People are the earliest population found so far, which does not adhere to modern human anatomical conformity. In fact, they’re unique in respect to any other species in the human evolutionary tree. Fact most curious, when considering that their location was surrounded by modern human populations, as attested by fossil evidence from the same period. The researchers suggest that they either stayed extremely isolated or kept interbreeding off-grounds.

This is the latest, although not yet confirmed as a new species, of a wave of new identified human species found only in these recent past years. Homo floresiensis or the “hobbit”, which lived on the island of Flores, Indonesia, until as recently as 17,000 years ago, was first discovered in 2007. The Denisovans lived around 30,000 years ago and the first and only trace of them so far was found in the Denisovan Caves of Siberia in 2010. All of them found in Asia, along with past Neanderthal sites and this latest one in China.

Curnoe and colleagues have a couple of possible scenarios concerning the existence of these Red Deer Cave people. One is that they’re part of very early migration of a primitive-looking Homo sapiens that lived separately from other forms in Asia before dying out, while another assumes that they were indeed a distinct hominid species, which evolved in Asia and lived near modern human populace. The last hypothesis is the most interesting, as well – they were hybrids.

“It’s possible these were modern humans who inter-mixed or bred with archaic humans that were around at the time,” explained Dr Isabelle De Groote, a palaeoanthropologist from London’s Natural History Museum.

“The other option is that they evolved these more primitive features independently because of genetic drift or isolation, or in a response to an environmental pressure such as climate

The findings were reported on March 14 in the journal PLoS ONE.

Ancestors of homo sapiens breeding

High-resolution genome sequence of ancient human ancestor released online

Last year, researchers at the Max Planck Institute for Evolutionary Anthropology, produced a draft of the Denisova genome, in order study in what proportion they relate to homo sapiens sapiens. The  Denisovans, are a new group of hominids, discovered just two years ago, which is believed to have lived around 30,000 years ago, alongside Neanderthals and early homo sapiens ancestors. Since they first released their draft, the researchers from Germany have now produced a highly refined version of the Denisovan genome, sequenced 30 times, which they also publicaly released on the web to help other scientists with their study.

The idea came after Max Planck paleogeneticist Svante Pääbo was at a meeting in Sweden, and noticed there that his fellow colleagues were working and studying based on year-old sequence data, and that the all the other labs in the world were probably using the same outdated material as well.

“I felt bad knowing that we had this very much better version of the same genome and that it would be a few months before it became available,” says Pääbo.

Even though Pääbo and colleagues have yet to release the paper they’ve been working on for such a long time, the researchers decided to allow their colleagues to download the sequence data for the high-resolution genome today. The sequence can be freely downloaded from  both on Max Planck website and through Amazon’s Web Services. Speaking of which,  this latest version of the genome they’ve released online and which will be presented shortly for scientific publishing, has every position sequenced an average of 30 times – all based on DNA extracted from less than 10 milligrams of the finger bone of the ancient girl found in the Denisovan caves, in Siberia.

Ancestors of homo sapiens breeding

With this higher resolution of the genome in their hands, the scientists can now more accurately determine how our hominid ancestors influenced modern man, since DNA differences can be precisely extracted from that of living humans and Neanderthals. It’s believed that early humans interbred with both Neanderthals and Denisovans. We all currently have Neanderthal genes inside our DNA, however they’re inactive; modern humans in Melanesia and other parts of Asia have inherited about 4% of their DNA from Denisovans.

A third group of extinct humans, Homo floresiensis, nicknamed “the hobbits” because they were so small, also walked the Earth until about 17,000 years ago. It is not known whether modern humans bred with them because the hot, humid climate of the Indonesian island of Flores, where their remains were found, impairs the preservation of DNA.

Of course, to protect their ability to publish a paper, the Max Planck team is releasing the sequence under a license that prohibits anyone else from doing an analysis of the complete genome, nevertheless anyone, scientist or not, is now free to analyze specific genes in the genome without having to wait for the study to pass peer review.

Visitors of the Museum for Prehistory in Eyzies-de-Tayac, France observe a Neanderthal man ancestor's reconstruction (AFP/File, Patrick Bernard)

Human mating with Neanderthals made our immune system stronger

The mating between Neanderthals and modern homo sapiens has been a highly controversial matter between scientists in the anthropology scene for decades now. That was until last year, however, when anthropologists convened that the two related species did indeed mate, but the genes passed down from Neanderthals were inactive.

Recently, there’s been another reason for contradiction, once with the publishing of a new study this Thursday by Stanford scientists in which they outline how DNA inherited from Neanderthals and newly discovered hominids, dubbed the Denisovans, has contributed to the immune system of modern day man among populations in Europe, Asia and Oceania. Just so you can get an idea of how volatile studies and discoveries in the scientific world can be.

Prehistoric interbreeding is considered responsible for 4% of the homo sapiens genome; the Standford research, lead by Peter Parham from Stanford University School of Medicine in California, identifies stretches of DNA derived from our distant relatives.

Sex with Neanderthals made modern day humans stronger

The researchers focuses their attention  on a small set of genes on chromosome six, known as the human leukocyte antigen (HLA) class I genes, which help the immune system adapt to fight off new pathogens that could cause various infections, viruses and diseases. HLA-B*73, one of the types, was traced down to the newly discovered hominids called Denisovans, who likely  mated with humans arriving in West Asia on their way out of Africa. The variant is rare in modern African populations but is common in people in west Asia.

“The HLA genes that the Neanderthals and Denisovans had, had been adapted to life in Europe and Asia for several hundred thousand years, whereas the recent migrants from Africa wouldn’t have had these genes,” said Dr. Peter Parham.

“So getting these genes by mating would have given an advantage to populations that acquired them.”

A similar scenario was found with HLA gene types in the Neanderthal genome.

“We are finding frequencies in Asia and Europe that are far greater than the whole genome estimates of archaic DNA in modern humans, which is 1-6%,” said Professor Parham.

From the analysis, the scientists estimated that more than half of the genetic variants in one HLA gene in Europeans could be traced back to Neanderthal or Denisovan DNA. Asians owe up to 80%, and Papua New Guineans up to 95%.

Skepticism among other scientists

While this is a remarkable, ground-breaking study by all means, some scientists are still reluctant to accept its impact on the immune system and, consequently, passing on off active genes.

“I’m cautious about the conclusions because the HLA system is so variable in living people,” commented John Hawks, assistant professor of anthropology at the University of Wisconsin-Madison, US.
Denisovan tooth DNA from a tooth (pictured) and a finger bone show the Denisovans were a distinct group

“It is difficult to align ancient genes in this part of the genome.

“Also, we don’t know what the value of these genes really was, although we can hypothesise that they are related to the disease environment in some way.”

The study was published in the latest edition of the journal Science.