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



Edible Kreb’s Cycle Models

In order to increase understanding and comprehension, Year 13 IB Biology (HL) students were asked to create edible Kreb’s Cycle models, which were absolutely fantastic and of course delicious! I’m so impressed with their projects!                        Kreb's Cycle Edible Cake Kreb's Cycle Edible Model-Brownies Kreb's Cycle Edible Model-Brownies 2 Kreb's Cycle Models Kreb's Cycle-edible models-cup cakes Edible Kreb's Cycle Model-Donuts Kreb's Cycle Model-Cupcake 2

# I wish my teacher knew

I am inspired by primary teacher Kyle Schwartz who posed the question: ‘I wish my teacher knew’? Obviously her students felt safe to be completely transparent about their ‘wishes’, and I think that speaks volumes about the type of safe learning environment that she has created for her students.  See video below. I will pose this question to my Year 12 tutor group and ask them to create a video log of their response ( to be uploaded shortly – stay tuned).

Investigating the Effect of Enzyme Concentration on the Rate of Reaction

Year 12 Biology HL girls were investigating the effect of enzyme concentration on the rate of reaction using hydrogen peroxide and liver. They learned that  2 H2O2 —-> 2 H2O + O2. The oxygen is given off as a gas and foam is formed. The volume of foam produced in a give time can be used as a measure of enzyme activity. 


IMG_20150327_075254 IMG_20150327_075357 IMG_20150327_075435 IMG_20150327_075754 IMG_20150327_075842 IMG_20150327_080000 IMG_20150327_080228 IMG_20150327_080507 IMG_20150327_080743

Vampire Crabs

By James Owen, National Geographic

Vampire crabs, so named because of their glowing yellow eyes, have become popular as pets, but the origin of some of these spooky-looking crustaceans has been cloaked in mystery.
Until now.

Now researchers have traced the freshwater crabs back to their wild source in Southeast Asia—and report that the two most sought-after species are new to science.

The newly described species, Geosesarma dennerle and Geosesarma hagen, were found in separate river valleys on the Indonesian island of Java (map).

“These crabs are kind of special because they’ve been around in the pet trade for ten years, but no one knew where they come from,” said study co-author and professional aquarist Christian Lukhaup of Waiblingen, Germany.

Scientists have identified other vampire crab species before, including those in the aquarium trade, but the newfound species are the most common pets, he said.

The new vampire crab G. dennerle is a deep purple with a creamy splotch on its back. G. hagen catches the eye with its bright orange shell and claws. (Also see “Pictures: New Purple Crab Species Found.”)

These crabs’ blazing eyes and spectacular colors explain their attraction to aquarists.

“Dealers working in Southeast Asia and other parts of the world know what their clients are looking for in terms of colors,” said study co-author Christoph Schubart, of Germany’s Regensburg University’s Institute of Zoology.

“They start collecting in areas where scientists may not have made any expeditions so far, and suddenly the market is formed with some animals that no one has ever given a name,” said Schubart, whose study appeared in January in the Raffles Bulletin of Zoology.

Vampire (Crab) Hunter
Measuring less than an inch wide, vampire crabs are also an ideal size for keeping in a small tank, said Lukhaup.

Picture of Geosesarma hagen crab with red claws
A Geosesarma hagen crab has red claws and yellow eyes—colors that help it communicate with its brethren.
The vampire crab hunter of the team, Lukhaup, fittingly, was born in Transylvania, home to the mythical Dracula. (See “Archaeologists Suspect Vampire Burial; An Undead Primer.”)
He used his contacts in the aquarium trade to scout out collectors who might know where the crabs came from.

“There were a lot of false rumors because people don’t want other collectors to go there,” he said.

Lukhaup, who has helped uncover the wild origins of various shrimps and other freshwater crustaceans sold as pets, finally tracked the crabs down in central Java.

Communicating With Color
Schubart suspects there are many more vampire crab species yet to be described on Indonesia’s islands.

Since these freshwater crabs don’t use the ocean as part of their life cycles and tend to stay put, many of Indonesia’s islands have their own vampire crab species, Schubart explained.

These crabs’ amphibious lifestyles also influenced the evolution of their bright coloration. On land, “visual communication becomes much more important,” he said.

“There’s much more emphasis on color and visual cues rather than chemical cues, as used in the water.”

Vulnerable Vamps
The two new vampire crab species are probably each confined to a single watershed, making them particularly vulnerable to collectors, the study team warned. (See “Do You Know Where Your Aquarium Fish Come From?”)

“For the local collectors, it’s their living,” Schubart said. “They just catch what they can get and export it.”

Lukhaup hopes that in the future commercial breeding will help prevent wild populations from being wiped out by the vampire crab craze.

Some private enthusiasts are breeding the crabs, he said, but most still come from Indonesia.

With vampire crabs and other exotic aquarium species, it seems there’s no silver bullet for salvation.

All information was taken from: http://news.nationalgeographic.com/2015/03/150316-vampire-crabs-animals-new-species-science-pets/

Ecology Community iMovie Trailers

Year 13 students were assigned one learning objective from Option G1: Ecology Community. The following three videos were class favorites and based on the following learning objectives:

Video One: Outline the factors that affect the distribution of plant species, including temperature, water, light, soil pH, salinity and mineral nutrients.

Video Two: Explain the principle of competitive exclusion.

Video Three: Explain the niche concept


iPad Digital Bioengineering and GMO Science Stories

Screen Shot 2015-02-25 at 7.04.17 AMScreen Shot 2015-02-25 at 7.02.48 AM


Year 12 Biology HL students were asked to create digital stories using the Book Creator app on their iPads. The stories needed to be linked to their learning objective applications from the Bioengineering and Genetic Modification Unit ( See the topics below).  It is no surprise that the stories that were created were unique, interesting and educational. I am so proud of their creations. There are two samples below. Enjoy!

TOPIC 1: Application: Use of DNA profiling in paternity and/or forensic investigations 
TOPIC 2: Gene transfer to bacteria using plasmids makes use of restriction endonucleases and DNA ligase 
TOPIC 3: Assessment of potential risks and benefits associated with genetic modification of crops (
TOPIC 4: Production of cloned embryos produced by somatic-cell nuclear transfer 


iBook:The Cloning Zoo: Maria Alba: CGB 2015

The secret of purple hood

TOK: We are not defined by what was taken -what was lost – We are defined by what we do with what remains. CARL WILKENS


Carl Wilkens, a humanitarian and author of the book: I’m not leaving, spoke to our TOK students about his role during the Rwandan genocide, but more specifically he came to talk about the importance of tolerance. Whilst thousands of expatriates were fleeing Rwanda to their respective countries, Carl Wilkens decided to stay. He felt that his presence could save the lives of not only his night watchman and maid, but also the lives of the orphans that remained. Between April 1994 and July 1994 Carl ventured out everyday to try to save the lives of orphans by bring them food, water and medicine to different orphanages around the city. His actions saved thousands of lives (worldoutsidemyshoes). At the end of his talk he wrote this powerful quote: We are not defined by what was taken or what was lost. We are defined by what remains -Carl Wilkens. As such, we asked out TOK students to reflect on the following Carl’s presentation, his documentary and the following questions:

BLOG QUESTIONS: To what extent do you find each ethical perspective offered in the film useful or insightful way of thinking about morality? We learned from the film that Carl stayed behind because he felt that his presence could save lives, thus begs the ethical question: Do  you have a responsibility to act on knowledge ie. are we responsible for for situations were we fail to act (poverty, famine, genocide etc) ? If you are aware of situations where you could act to improve them, are you obligated to act to the best of your ability?