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



Oldest genitals found. Went out of fashion for eons

If you’re going through a dry patch, it’s nothing compared to the entire animal kingdom – which appears to have gone millions of years without copulating. A new analysis of 380-million-year-old fossils tucked away in boxes in museums is rewriting the textbooks on the origins of sex and genitalia. It shows genitals started out bony, were used sideways, and then copulation went out of fashion for tens of millions of years.

John Long from Flinders University in Adelaide, Australia, and colleagues have found fossil evidence that one of the earliest jawed vertebrates calledMicrobrachius dicki – from a group known as gnathostomes – reproduced via internal fertilisation. This suggests that all gnathostomes were doing it too.

The find shows that vertebrates lost and regained the ability to efficiently deliver sperm internally, many times over. Copulation was such fun, evolution discovered it again and again.

It also shows that the first jawed vertebrates were copulating. But close descendants of Microbrachius have been found with clear evidence showing that they used external fertilisation, Long says. So the evolution of both external and internal fertilisation must have happened repeatedly.

“Among the roughly 50,000 species of extant vertebrates, we have no evidence that internal fertilisation has ever reverted to external fertilisation,” says Daniel Blackburn from Trinity College in Hartford, Connecticut, who was not involved in the study. “Once a lineage has evolved a way for males to introduce sperm into the reproductive tract of the female, they tend to retain that mode of fertilisation.”

Missing, no more

Apparently, not, since Long’s work provides this missing evidence, Blackburn says. “Under this interpretation, internal fertilisation must have been lost prior to the evolution of the two major lineages of living jawed fishes.” From them evolved the cartilaginous fishes – modern day sharks, skates, and rays – and the bony fishes and their descendants – including us.

Around the time the bony fishes and sharks evolved, internal fertilisation went AWOL, says Long. And then nobody was doing it until internal fertilisation re-evolved about 20 to 40 million years later. And when that happened, animals adopted a different way of locking on to each other.

Long says there are genetic clues as to how the ability could be lost and then come back. “The HOXD13 gene can develop limbs and genital organs in mammals and in sharks as well,” he says. “Early fish probably originated the capability of evolving these things and then they were lost. But once that gene was set in the vertebrate body plan, it could come back later.”

Examining fossil specimens of the earliest known jawed fish, M. dicki, Long and colleagues found both male and female genitalia that had gone unnoticed. On the male they found bony structures that spread out on each side of the fish, with a groove that would have delivered the sperm. On the female, there were spiny plates that would have acted like Velcro, holding the male in place.

The real clincher showing that the fish went for internal fertilisation is that their genitals are nearly identical to those of later fish, where females have been found complete with embryos, Long says. “There’s no other interpretation of what they could be,” he says. The new find shows that it was a feature of the very earliest ones.

It even reveals how they did it (see video, above). “Fundamentally they couldn’t have done it in a missionary position,” says Long, pointing out that the genital structures are bony, immobile and are on the sides of the fishes. It also explains why the fish have spiny arms: they were probably used to hold hands, to help lock the genitals in place, as the did it side-by-side. “We’ve wondered for over 100 years what these tiny little jointed arms were used for in these peculiar fishes,” Long says. “The very first act of copulation was done sideways, square-dance style.”

Blackburn, who himself studies reproductive anatomy, says he finds the analysis of how the genitals were used convincing. “It is most surprising to find evidence for a loss of internal fertilisation in a fossil lineage,” he says.

Journal Reference: Nature, DOI: 10.1038/nature13825


The Cosmos E2: Some Of The Things That Molecules Do

In The Cosmos: A Space Time Odyssey Episode two entitled: Some Of The Things That Molecules Do,depicts that life is in constant transformation. Artificial selection turned the wolf into man’s best friend and is ultimately responsible for all the other canine breeds we love today. And over the eons, natural selection is responsible for all of the  domesticated animals and plant, and .has sculpted the exquisitely complex human eye out of a microscopic patch of pigment. And reiterates that evolution is just the change in inheritable traits over time.

What did you learn from this episode and what did you find particularly interesting?

Music Video: Protobionts

Year 13 students were assigned a presentation to discuss learning objective D.1.6: State that living cells may have been preceded by protobionts with an internal chemical environment different from their surroundings. In order to make the presentation more interesting and accessible,  two students decided to create this song using Taylor Swift’s tune to enhance their overall presentation. It’s fantastic!


The Cosmos E1: “Standing Up in the Milky Way”

Neil deGrasse Tyson  makes science accessible and engaging for viewers.Cosmos-A Space Odyssey Episode One: Standing up in the Milky Way is an overview of the beginning of time. It briefly explains the Big Bang Theory, the Geologic Time Scale, Evolution and Astronomy. We are also introduced to Giordano Bruno, a rebel thinker of the times who thought that the Universe was infinite.

What did you find particularly fascinating about Cosmos-A Space Odyssey Episode One: Standing up in the Milky Way?

Visual Notes: Homo sapien VS. Australopithecus afarensis

Another fantastic illustration of how we use Visual Notes in IBDP Biology. Students were asked to compare the morphological skeletal features of Homo sapien and Australopithecus afarensis and this is what they created! unnamed

TOK: Are Homo floresiensis a separate species or remains of a diseased homo sapiens?: Nathalie

TOK: The Little People of Flores

Posted by Nathalie Istanto in Biology SL on Tuesday, May 20th, 2014 at 4:39 pm

Are Homo floresiensis a separate species or remains of a diseased homo sapiens?

Based on the video in PBS on Homo floresiensis, I think that they are a separate species. It is highly improbable that the Homo floresiensis are a diseased homo sapiens because of the shape of their brain cavity. It does not look like a normal human’s brain cavity, which meant that the skull found on Flores is unlikely to be a human’s.

There might be a small chance seeing that a certain disease could reduce the brain size, known as microencephaly. However, I think that there are more than one Homo florensiensis alive during that time, and the probability that they all had the same disease affecting them the same way over a few thousand years is highly unlikely. I think that the Homo floresiensis might act like human in some ways, which might lead to some people thinking that they are part of a diseased homo sapiens.

The Homo floresiensis built bridges and are able to catch animals. It also seemed that they lived together in caves. This shows some capability for them to think before they act, which is similar to humans in a sense, though not as advanced. A smaller brain cavity does not mean that they are less advanced. If the disease were to affect the brain, wouldn’t it affect their brain capability too? Yet, the Homo floresiensis were able to use tools. Their small size is theorized to be from island isolation, which leads to them growing smaller to make use of what limited resources they have in that island. I just knew that species adapt to a smaller size in an isolated island overtime, although it makes sense as they want to use as little resource as they can.

From the video, I disagree with the scientist that said that the Ebu Gogo does not exist. I think that there might be a small chance that they still exist, but they might be hiding somewhere in the jungle or caves of Flores. It might be that they feel threatened by the Homo sapiens because of their smaller size. It might also be that their behavior differs to our behavior, which is another indication of them being a separate species.

The Namibian Fog Basking Beetle

The Namibian Fog Basking Beetle lives in the Namibian Desert, where water is scarce. Seeing as water is necessary for the survival of any form of life, this poses a challenge to organisms. The Namibian Fog Basking Beetle has an extremely innovative method of obtaining moisture in its harsh environment.

The Namib Desert is the site of a remarkable natural phenomenon. The cold Benguela current causes a fog to roll into the desert, serving as a source of water. This fog occurs roughly 30 days every year and in a single day can deposit up to 1 litre of water per square meter (on the mesh of an artificial fog screen).

The Fog Basking Beetles exploit this rare occurrence by climbing to the top of sand dunes and face the wind with their backs in the air. They then turn their bodies into literal water collectors. Water droplets form on their elytra* and roll down into their mouths. In some varieties of Fog Basking Beetle, it is thought that their elytra are hydrophobic surfaces. This causes the water in the fog to bead up and slide down into their mouths.

This resource exploitation is extremely successful. Other similar beetles that do not exhibit such fog basking behaviour have serious decline in population during times of drought. However, the fog-basking beetle is still present in large numbers at such periods of scarcity.

*Elytra: The forewings of the beetle

Read all about it: http://1.usa.gov/1eGK3HQ
Image URL: http://bit.ly/15sSKNv
Watch a video: http://bit.ly/11vHwKO

World’s Biggest Dinosaur Discovered

May 17, 2014 | by Lisa Winter
Read more at http://www.iflscience.com/plants-and-animals/%E2%80%9Cworld%E2%80%99s-biggest-dinosaur%E2%80%9D-discovered#PYvu2t7RE1B5SleW.99

A farmer in Chubut, Argentina made an incredible dinosaur discovery about three years ago. While working out in his fields, he stumbled across some fossilized dinosaur remains. Paleontologists from the nearby Museum of Paleontology Egidio Feruglio excavated the area and found about 150 incredibly well-preserved bones from seven individuals of a species that is likely the largest to ever walk the Earth.

The remains come from a newly-described species of titanosaur, which are large herbivorous sauropods. It lived in the late Mesozoic about 95 million years ago. This behemoth will not have a name until the findings are published in a scientific journal, but the researchers have claimed they will choose a title that pays tribute to the region, the farmer, and the dinosaur’s incredible size.

It is estimated to be an astonishing 40 meters (130 feet) long from head to tail and 20 meters (65 feet) tall. A creature this large would have likely weighed in at a hefty 77 tonnes (85 short tons), which is over eleven times more than Tyrannosaurs rex.

Researchers are currently comparing this species to Argentinosaurus, which is currently regarded as the largest dinosaur ever. However, Argentinosaurus is believed to weigh about 7 tonnes (7.7 tons) less than this new species, and has likely been officially dethroned as the largest terrestrial animal ever.

Understanding the true size of the dinosaurs is always open for some debate when there isn’t a complete skeleton. Assumptions must be made about the size and shape of missing bones, based on what they know about related species. However, there may be many more clues that have not yet been surfaced at the dig site.

José Luis Carballido, who is leading the dig has said in a press release on the museum’s website that the team is “[s]till working on this extraordinary site. We estimate that one fifth of the excavation process is completed, so there is still much work to do and probably much to discover.”

The researchers also found more than 60 teeth belonging to carnivorous species, who likely scavenged on the dead titanosaurs. Carballido claims that this opportunity came at a price, as the giant herbivores likely had incredibly thick skin that would have broken the carnivores’ teeth, though the teeth would have grown back.

Other fossils from the site indicate that when this giant dinosaur lived, the local landscape was quite green and lush with flowers and trees. The titanosaurs likely gathered near a source of water, and may have died after getting caught in mud.

The researchers note that the farmer’s family has been very accommodating during the excavation process as many pieces of large digging equipment have been brought in onto the land.

[All images credited to: Museum of Paleontology Egidio Feruglio]

Read more at http://www.iflscience.com/plants-and-animals/%E2%80%9Cworld%E2%80%99s-biggest-dinosaur%E2%80%9D-discovered#PYvu2t7RE1B5SleW.99