Oldest human genome dug up in Spain’s pit of bones

A 400,000-year-old genome from ancient human bone could herald a missing link species – taking us closer than ever to our common ancestor with Neanderthals
DEEP inside the Atapuerca cave system in northern Spain, 30 metres beneath the surface, lies the Sima de los Huesos, or the “pit of bones”. The remains of at least 28 ancient humans have been found at the bottom of this 12-metre-long vertical shaft. Now a thigh bone pulled out of the pit has yielded 400,000-year-old DNA – by far the oldest human DNA ever sequenced.

The results suggest the thigh bone belonged to a previously unknown human species – perhaps even a missing link between the Neanderthals and their mysterious cousins the Denisovans. This, say palaeontologists, brings us closer than ever before to understanding who our own common ancestor with the Neanderthals was.
Video: Pit of bones hides our oldest DNA

The bones at Sima de los Huesos pre-date the origin of Homo sapiens, who appeared around 200,000 years ago, and most closely resemble those of Neanderthals. Fred Spoor of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, calls them “Neanderthals in the making”.

Until now, it had only been possible to sequence the genomes of hominin fossils found in cold climates; DNA breaks down faster in warmer climates like Spain’s. But spurred by the successful sequencing of a 300,000-year-old cave bear genome from the same area, Matthias Meyer, also at the Max Planck Institute in Leipzig, and colleagues decided to give it a go.

They drilled into a hominin thigh bone from the cave and extracted 1.95 grams of material, processed it for DNA, and filtered out a large amount of modern human DNA – the bones had been heavily contaminated as they were removed and handled.

The end result was a near-complete mitochondrial genome – the DNA found inside the organelles that power cells. By comparing it with that of modern humans, chimpanzees and bonobos, plus Neanderthals and Denisovans, Meyer estimated its age at 400,000 years, twice as old as our own species and far older than any hominin genome previously sequenced (Nature, DOI: 10.1038/nature12788). The Neanderthal and Denisovan genomes sequenced in recent years are each around 40,000 years old.

“The genomes we have [up until now] are really very recent,” says Chris Stringer of the Natural History Museum in London. “This takes us at least a few hundred thousand years back, towards our common ancestor with other hominins.”

“This takes us back a few hundred thousand years, to our common ancestor with other hominins”
“This paper is the dream,” says David Reich of Harvard Medical School in Boston, Massachusetts. It is the latest in a series of breakthroughs in ancient DNA, coming just months after the sequencing of the oldest-ever genome, from a 700,000-year-old horse.

Since the Sima de los Huesos hominins look like Neanderthals, and lived in Europe where the Neanderthals would soon dominate, Meyer expected their DNA to look Neanderthal. But to his surprise, it proved quite distinct. It is most closely related to the Denisovans, a species known only from a finger bone and two molars found in a Siberian cave.

“We don’t quite know what to make of it,” says Meyer. “There’s no evidence the Denisovans ranged anywhere near Atapuerca,” says Stringer.

The biggest mystery is how and when our lineage diverged from that of the Neanderthals and Denisovans. Also unclear are the circumstances of the later split between Neanderthals and Denisovans. All we know is that both of these events happened around the time the Sima de los Huesos hominins were living in Spain.

One possibility is that the fossils belong to the common ancestor of Neanderthals and Denisovans, and some of their descendants later headed east and became the Denisovans. “I think that’s the most likely scenario,” says Meyer.

But that doesn’t explain why the Sima de los Huesos bones look so much like Neanderthals, says Stringer. He thinks they were Neanderthal ancestors, and came after the species split from Denisovans. The Neanderthals could easily have lost the mitochondrial genes they shared with Denisovans later on, he says, as mitochondrial DNA is only passed down the female line. “Mitochondrial DNA can be lost if a woman only has sons,” says Stringer.

That means the only way to settle exactly what happened is to sequence a full genome from the Sima de los Huesos fossils. Meyer is working on this now. “It is extremely difficult,” he says.

The Sima de los Huesos genome is particularly exciting because it is from a time that is very close to the origin of our human line. The archaeological evidence suggests these early humans were developing significant new behaviours. On the one hand, they were still using fairly primitive stone tools like a crafted hand axe – nicknamed Excalibur – that was found in the pit. But the bones also suggest more modern traits.

For instance, some believe the pit might have been an early burial site, part of a simple funeral rite. Excalibur could be a tribute to the dead, suggests Stringer.

And the deformed skull of a girl who lived to be around 12 years old, also found in the pit, suggests that the tribe cared for her. “There’s a hint of something human – caring for the disabled,” says Stringer.

Elsewhere in Atapuerca, archaeologists have discovered the remains of an elderly man with severe back problems, who couldn’t have fended for himself. Here, too, the man’s age suggests a community must have protected him.

The possibility of peering into the Sima people’s genes as well as their bones is a huge step forward. A full genome would be invaluable, says Reich. We could find out which of our modern genes were already in place, and which ones had to change to produce modern humans. As Reich puts it: “It’s about what makes us human.”

“A full genome from these bones would tell us which genes had to change to produce modern humans”

A brief history of human fossils

The fossil remains found in Sima de los Huesos, Spain, offer important clues to unravelling the origins of our species (see main story). Here are five other key ancestors.

Lucy Modern humans are descended from the ape-like Australopithecus, which lived in Africa. The most famous specimen is Lucy, a 3.2-million-year-old Australopithecus afarensis found in Ethiopia in 1974. She got her name from The Beatles’ song Lucy in the Sky with Diamonds.

Karabo This 1.9-million-year-old boy was found in South Africa in 2008, alongside an adult female. He belongs to the species Australopithecus sediba, has a mix of ape-like and human-like features, and was named “Answer” by a 17-year-old South African student in a competition.

Turkana Boy An almost complete 1.5-million-year-old Homo erectus fossil was found by Kenya’s Lake Turkana in 1984. The species spread as far as Java, and may be our direct ancestors.

Neanderthal 1 The first recognised Neanderthal was found in 1856 in Germany’s Neander valley. It didn’t get a snappy name, but was the first primitive human identified, and in 1997 became the first to yield DNA.

X-Woman A female finger bone from the Denisova cave in Siberia turned out to belong to a new species when its genome was sequenced in 2010. The Denisovans are most closely related to Neanderthals. Genetics show they roamed as far as Indonesia, where they interbred with modern humans.

This article appeared in print under the headline “Pit of bones hides our oldest DNA”

By Michael MarshallMagazine issue 2946 published 7 December 2013


Article: Controlling Genes with your thoughts

Controlling genes with your thoughts

November 11, 2014
ETH Zurich
Researchers have constructed the first gene network that can be controlled by our thoughts. Scientists have developed a novel gene regulation method that enables thought-specific brainwaves to control the conversion of genes into proteins (gene expression). The inspiration was a game that picks up brainwaves in order to guide a ball through an obstacle course.

It sounds like something from the scene in Star Wars where Master Yoda instructs the young Luke Skywalker to use the force to release his stricken X-Wing from the swamp: Marc Folcher and other researchers from the group led by Martin Fussenegger, Professor of Biotechnology and Bioengineering at the Department of Biosystems (D-BSSE) in Basel, have developed a novel gene regulation method that enables thought-specific brainwaves to control the conversion of genes into proteins — called gene expression in technical terms.

“For the first time, we have been able to tap into human brainwaves, transfer them wirelessly to a gene network and regulate the expression of a gene depending on the type of thought. Being able to control gene expression via the power of thought is a dream that we’ve been chasing for over a decade,” says Fussenegger.

A source of inspiration for the new thought-controlled gene regulation system was the game Mindflex, where the player wears a special headset with a sensor on the forehead that records brainwaves. The registered electroencephalogram (EEG) is then transferred into the playing environment. The EEG controls a fan that enables a small ball to be thought-guided through an obstacle course.

Wireless Transmission to Implant

The system, which the Basel-based bioengineers recently presented in the journalNature Communications, also makes use of an EEG headset. The recorded brainwaves are analysed and wirelessly transmitted via Bluetooth to a controller, which in turn controls a field generator that generates an electromagnetic field; this supplies an implant with an induction current.

A light then literally goes on in the implant: an integrated LED lamp that emits light in the near-infrared range turns on and illuminates a culture chamber containing genetically modified cells. When the near-infrared light illuminates the cells, they start to produce the desired protein.

Thoughts Control Protein Quantity

The implant was initially tested in cell cultures and mice, and controlled by the thoughts of various test subjects. The researchers used SEAP for the tests, an easy-to-detect human model protein which diffuses from the culture chamber of the implant into the mouse’s bloodstream.

To regulate the quantity of released protein, the test subjects were categorised according to three states of mind: bio-feedback, meditation and concentration. Test subjects who played Minecraft on the computer, i.e. who were concentrating, induced average SEAP values in the bloodstream of the mice. When completely relaxed (meditation), the researchers recorded very high SEAP values in the test animals. For bio-feedback, the test subjects observed the LED light of the implant in the body of the mouse and were able to consciously switch the LED light on or off via the visual feedback. This in turn was reflected by the varying amounts of SEAP in the bloodstream of the mice.

New Light-sensitive Gene Construct

“Controlling genes in this way is completely new and is unique in its simplicity,” explains Fussenegger. The light-sensitive optogenetic module that reacts to near-infrared light is a particular advancement. The light shines on a modified light-sensitive protein within the gene-modified cells and triggers an artificial signal cascade, resulting in the production of SEAP. Near-infrared light was used because it is generally not harmful to human cells, can penetrate deep into the tissue and enables the function of the implant to be visually tracked.

The system functions efficiently and effectively in the human-cell culture and human-mouse system. Fussenegger hopes that a thought-controlled implant could one day help to combat neurological diseases, such as chronic headaches, back pain and epilepsy, by detecting specific brainwaves at an early stage and triggering and controlling the creation of certain agents in the implant at exactly the right time.

Story Source:

The above story is based on materials provided by ETH Zurich. Note: Materials may be edited for content and length.

Journal Reference:

  1. Marc Folcher, Sabine Oesterle, Katharina Zwicky, Thushara Thekkottil, Julie Heymoz, Muriel Hohmann, Matthias Christen, Marie Daoud El-Baba, Peter Buchmann, Martin Fussenegger. Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant. Nature Communications, 2014; 5: 5392 DOI: 10.1038/ncomms6392

Science In The News: Blonde Hair Caused By DNA Mutation (A to G)

Photo of a young boy with curly blond hair.

A new study that found blond hair is the result of a small genetic “tweak” could provide clues for how to genetically treat illnesses.


Karen Weintraub

for National Geographic News


For thousands of years, people have both prized and mocked blond hair. Now, a new study shows that many can thank a tiny genetic mutationa single letter change from an A to a G among the 3 billion letters in the book ofhuman DNAfor their golden locks.

The mutation “is the biological mechanism that helps create that [blond] color naturally,” said David Kingsley, a professor of developmental biology at Stanford University and a Howard Hughes Medical Institute investigator, who led the research. “This is a great biological example of how traits can be controlled, and what a superficial difference blond hair color really is.”

Kingsley, a brunet, said the study, published today in Nature Genetics, also offers a powerful insight into the workings of the human genome. The mutation doesn’t alter the protein production of any of the 20,000 genes in the human genome, he said. Instead, in people of European ancestry, it causes blond hair through a 20 percent “turn of the thermostat dial” that regulates a signaling gene in the hair follicles of the skin.

Elsewhere in the body, that signaling gene is involved in the formation of blood, egg, sperm, and stem cells. Turning such a gene entirely on or off could be devastating. But a tiny mutation that tweaks the gene’s activity in only one area—in this case the skin—allows for harmless changes, he said.

Pardis Sabeti, a computational biologist at Harvard University and Broad Institute who was not involved in the research, said the study is a “beautiful demonstration” of this kind of tweaking, which has previously been poorly understood. To find a single letter change and prove that it is a big driver of blond hair is a major scientific accomplishment, she said.

Photo of a young girl with blond hair.

Blond hair, like this young girl’s, is caused by a single DNA base pair change.

A Subtle Change With Big Results

To find the blond-hair gene mutation, Kingsley and his team looked at an area of the genome previously linked to blondness in people fromIceland and the Netherlands. They painstakingly identified the exact letter change that gives a person blond hair.

The researchers tested what that letter change did in human skin cells grown in a petri dish. The cells showed a reduction in activity in the switch that controls the signaling gene. Then Kingley’s group bred lines of mice that either had the mutation or didn’t have it. The single-letter change didn’t create blond mice, but those with the mutation had coats of a lighter color than those without.

Learning the mechanism behind something as common—and as universally recognizable—as hair color, can help explain how genes work in other contexts, such as illnesses, where the stakes are higher, Kingsley said. “Understanding these principles will help people … trying to find drugs for diseases.”

Hopi Hoekstra, a professor of genetics at Harvard who was not involved in the research, said the new finding confirms what researchers had long suspected: that small changes in gene expression caused by only a single DNA base pair change can lead to major changes in traits.

Hair color “is a great starting point to do this type of molecular dissection” because it’s simple to see whether the mutation results in a change in appearance, she said. “But it highlights how difficult this is going to be for more complex human traits, like mental illness, which we’ve never been very good at measuring.”

The blond hair mutation—or variant—is not genetically linked to any other traits, even eye color, Kingsley said, showing that none of our stereotypes about blonds are true. In contrast, many other human variants, such as some that cause red hair, are known to affect the protein structure of genes, and therefore trigger changes everywhere in the body the gene is expressed. Red hair, fair skin, and lighter eyes tend to travel as a package, he said, and may even be genetically paired with greater sensitivity to pain and temperature changes—though probably not fiery temper


Video Reflection: Ghost in our Genes-Christy

Biology: Ghost In Your Genes

Posted by Christy Zakarias in Science on Monday, February 24th, 2014 at 10:39 am


What is ‘epigenetics’?

Heritable changes in gene expression that does not involve changes to the underlying DNA sequence; a change in phenotype without a change in genotype (“Fundamentals”).

What is the most interesting information you learnt from the documentary?

From the documentary, I learnt that there is another side to genetics aside from the human genome, epigenetics. Dubbed epigenetics are chemical markers along the DNA that control a person’s development by turning genes on and off. These markers vary widely for each person, and are influenced by one’s environment as well as experiences.

What responsibilities do you have to your grandchildren?

Just like genetic information, epigenetics can be passed down from generation to generation. Hence, what I do and experience today can impact the characteristics and health of my future grandchildren. Bearing this in mind, it is then important for me to adopt a healthy lifestyle, one that, for the most part, does not involve starvation, junk food, drinking and smoking. The change in epigenetics might not be immediately apparent in my next generation, however this is only because, as illustrated by the documentary, those changes tend to become increasingly visible two to three generations thereafter.

Works Cited

“Fundamentals.” What Is Epigenetics. N.p., n.d. Web. 23 Feb. 2014. <http://www.whatisepigenetics.com/fundamentals/&gt;.

Video Reflection: Ghost in our Genes-Nabila

The Ghost in Your Gene

Posted by Nabilla Gunawan in Biology HL on Monday, February 24th, 2014 at 03:40

Human Genome Project might be considered a break through ten years ago, however there is somehting further. We might think that the traits we obtained comes purely from the DNA we have in our bodies, but in fact, even identical twins with the same exact  DNA can appear differently. This is due to epigenetics. Epigenetic is behaviour that are caused by external factors other than genetics. The environment we live in, mainly contributes to the epigenetic factor. Genes are the same throughout the whole body, but epigenetics varies from different tissue. Epigenetics alter the gene functions but not the gene sequence itself, the gene sequence does not change, however what turns on and off in a gene

What do you find fascinating? The fact that identical twins can still have different behaviour and character even though they are considered to be ‘identical’ twin. It is fascinating how  the several generations before the offsprings can causes disease to the current generation. It gives an understanding for us regarding the origin of a disease, where both mother and father doesn’t have. It also gives clue about how human adapt and how it affects the next generation.

What is my responsibility for my grand children (next generation)? Personally, I do feel like one of my responsibility for my grand children is to stay as healthy as possible. Live a healthy lifestyle so that I don’t develop diseases such as stroke or diabetes in my late fifties. Consume healthy food and exercise would strengthened my organ functions, which means I will pass on a good quality genes on my next generation.

Video Reflection: Ghost in our Genes-Nathalie

Ghost in Our Genes

Posted by Nathalie Istanto in Biology SL on Monday, February 24th, 2014 at 3:39 am

What is epigenetics?
Epigenetics are traits that are results of environmental influences instead of genetic influences.

What do you find fascinating about the video?
I found it interesting that the environment arounds us affects what genes are activated and what genes are turned off. In the video, we can see that the mice with a more caring mother will see a smaller increase in stress levels as opposed to mice with neglecting mothers. It is also interesting to see that this epigenetic change is also seen in humans and lasts for generations.

It is also interesting to see how we are dealing with problems that arise from the epigenetic traits. This is shown in the documentary with the cancer drug trials and also the autistic children. As it can be seen that epigenetic traits arise due to the lifestyles of our grandparents, we can try to reduce it by living a healthier lifestyle, which will have a smaller impact on our future generations.

Responsibility to our grandchildren
We have a responsibility in keeping the gene that we pass on to our grandchildren healthy. As can be seen from the video, epigenetic traits are passed on due to our lifestyle. This is shown when the grandfather suffers from famine, his grandchildren are less likely to have diabetes in the future. We now know that smoking and drinking affects our life with diseases such as lung cancer. To avoid this fate for our grandchildren, we must stop doing all these things and start living a healthy lifestyle.

The affects might not be visible during the time that we are alive. However, our children and grandchildren might suffer from it. Epigenetic traits can even be passed down for up to 4 generations. Therefore, as a responsibility to our grandchildren and future generations, we have to think of the consequences our actions might bring later in their life.

Human Genome Project-Nathalie

4.4.5 Biology TOK: Human Genome Project

Posted by Nathalie Istanto in Biology SL on Tuesday, March 18th, 2014 at 6:41 am

The Human Genome Project was an international endeavor, with laboratories throughout the world collaborating. However, there were also efforts in some parts of the world to gain commercial benefits from the outcomes of the project.

The data from the Human Genome Project can be viewed in different ways: it could be seen as a complete account of what makes up a human, if one takes a reductionist view of life, or, alternatively, as merely the chemical instructions that have allowed a huge range of more significant human characteristics to develop. This could lead to a discussion about the essential nature of humanity.

The data of the Human Genome Project can be viewed in many ways. It can be viewed as something that makes us human, because only humans have that certain gene. This genes arranged in a certain way is essential to making a human, and will result into a human when combined together. Plants and other animals don’t have the same genetic sequence as us humans. The data collected from the Human Genome Project can be considered as what is essential to form human life. In my view, I think that the project shows us what we are made of as humans. It shows us how we differ from other animals or plants by certain parts of our genetic sequence. It shows that we are something different from everything else.

However, other people may view it differently. The data from the Human Genome Project can also show that we are not as complex as we think. Our body and the way it functions can be explained through a chemical arrangement, which can be manipulated by certain drugs. This view for the data of the Human Genome Project might make it seem like humans are not that great, and that we are just the same as every other living thing. We are just a bunch of chemicals arranged in a certain way.

Some religious people might also disagree with the data collected from the Human Genome Project. They might think that it is impossible to have just a whole list of chemicals which determines us as human. They think that we still need to have a “soul”, which is not found as part of the Human Genome Project.

Human Genome Project-Nabila

Biology TOK: Human Genome Project

Posted by Nabilla Gunawan in Biology HL on Tuesday, March 18th, 2014 at 06:45

The Human Genome Project was an international endeavour, with laboratories throughout the world collaborating. However, there were also efforts in some parts of the world to gain commercial benefits from the outcomes of the project.

The data from the Human Genome Project can be viewed in different ways: it could be seen as a complete account of what makes up a human, if one takes a reductionist view of life, or, alternatively, as merely the chemical instructions that have allowed a huge range of more significant human characteristics to develop. This could lead to a discussion about the essential nature of humanity. 

How do I view Human Genome Project? The data from the Human Genome Project can be viewed as an outbreak in scientific world, particularly in genetics. Human genome project can create greater benefits and milestone for scientist to develop genetics, however, if applied to the society, the genome project can brings up pros and cons. The cons, for an example would be some people are unable to afford the cost to in human genome project. Although it has a lot of benefits, but the benefits cannot be equally distributed in the society.

Human Genome Project-Geun Myo

Human Genome Project – TOK Q

Posted by Geun Kim in Biology 11 on Tuesday, March 18th, 2014 at 6:50 am

TOK: The Human Genome Project was an international endeavour, with laboratories throughout the world collaborating. However, there were also efforts in some parts of the world to gain commercial benefits from the outcomes of the project.
The data from the Human Genome Project can be viewed in different ways: it could be seen as a complete account of what makes up a human, if one takes a reductionist view of life, or, alternatively, as merely the chemical instructions that have allowed a huge range of more significant human characteristics to develop. This could lead to a discussion about the essential nature of humanity.

Although the human genome project was first set to research and discover the amount of human genomes in the human body, I believe it makes the nature humanity seem significant and important. The fact that a single DNA strand can be coded up to thousands of letters is amazing. The tiniest bits of life fills more than 100 books of just letters is amazing. This just tells us people that the human body is so complexed, work of the Gods. Everything in the body, cell, and DNA is made to work together and is so complexed that it codes up to fill more than 100 books.