Hominin DNA suggests link to mystery population

A dig at the Sima de los Huesos cave in Spain, the site of ancient hominin fossils.

Hominin DNA baffles experts  Analysis of oldest sequence from a human ancestor suggests link to mystery population.

Hominin DNA baffles experts
Analysis of oldest sequence from a human ancestor suggests link to mystery population.

 

Another ancient genome, another mystery. DNA gleaned from a 400,000-year-old femur from Spain has revealed an unexpected link between Europe’s hominin inhabitants of the time and a cryptic population, the Denisovans, who are known to have lived much more recently in southwestern Siberia.

The DNA, which represents the oldest hominin sequence yet published, has left researchers baffled because most of them believed that the bones would be more closely linked to Neanderthals than to Denisovans. “That’s not what I would have expected; that’s not what anyone would have expected,” says Chris Stringer, a palaeoanthropologist at London’s Natural History Museum who was not involved in sequencing the femur DNA.

The fossil was excavated in the 1990s from a deep cave in a well-studied site in northern Spain called Sima de los Huesos (‘pit of bones’). This femur and the remains of more than two dozen other hominins found at the site have previously been attributed either to early forms of Neanderthals, who lived in Europe until about 30,000 years ago, or to Homo heidelbergensis, a loosely defined hominin population that gave rise to Neanderthals in Europe and possibly humans in Africa.

But a closer link to Neanderthals than to Denisovans was not what was discovered by the team led by Svante Pääbo, a molecular geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The team sequenced most of the femur’s mitochondrial genome, which is made up of DNA from the cell’s energy-producing structures and passed down the maternal line. The resulting phylogenetic analysis ­— which shows branches in evolutionary history — placed the DNA closer to that of Denisovans than to Neanderthals or modern humans. “This really raises more questions than it answers,” Pääbo says.

The team’s finding, published online in Nature this week, does not necessarily mean that the Sima de los Huesos hominins are more closely related to the Denisovans, a population that lived thousands of kilometres away and hundreds of thousands of years later, than to nearby Neanderthals. This is because the mitochondrial genome tells the history of just an individual’s mother, and her mother, and so on.

 

Nuclear DNA, by contrast, contains material from both parents (and all of their ancestors) and typically provides a more accurate overview of a population’s history. But this was not available from the femur.

With that caveat in mind, researchers interested in human evolution are scrambling to explain the surprising link, and everyone seems to have their own ideas.

Pääbo notes that previously published full nuclear genomes of Neanderthals and Denisovans suggest that the two had a common ancestor that lived up to 700,000 years ago. He suggests that the Sima de los Huesos hominins could represent a founder population that once lived all over Eurasia and gave rise to the two groups. Both may have then carried the mitochondrial sequence seen in the caves. But these mitochondrial lineages go extinct whenever a female does not give birth to a daughter, so the Neanderthals could have simply lost that sequence while it lived on in Denisovan women.

“I’ve got my own twist on it,” says Stringer, who has previously argued that the Sima de los Huesos hominins are indeed early Neanderthals. He thinks that the newly decoded mitochondrial genome may have come from another distinct group of hominins. Not far from the caves, researchers have discovered hominin bones from about 800,000 years ago that have been attributed to an archaic hominin called Homo antecessor, thought to be a European descendant of Homo erectus. Stringer proposes that this species interbred with a population that was ancestral to both Denisovans and Sima de los Huesos hominins, introducing the newly decoded mitochondrial lineage to both populations .

This scenario, Stringer says, explains another oddity thrown up by the sequencing of ancient hominin DNA. As part of a widely discussed and soon-to-be-released analysis of high-quality Denisovan and Neanderthal nuclear genomes, Pääbo’s team suggests that Denisovans seem to have interbred with a mysterious hominin group.

The situation will become clearer if Pääbo’s team can eke nuclear DNA out of the bones from the Sima de los Huesos hominins, which his team hopes to achieve within a year or so.

Obtaining such sequences will not be simple, because nuclear DNA is present in bone at much lower levels than mitochondrial DNA. And even obtaining the partial mitochondrial genome was not easy: the team had to grind up almost two grams of bone and relied on various technical and computational methods to sequence the contaminated and damaged DNA and to arrange it into a genome. To make sure that they had identified genuine ancient sequences, they analysed only very short DNA strands that contained chemical modifications characteristic of ancient DNA.

Clive Finlayson, an archaeologist at the Gibraltar Museum, calls the latest paper “sobering and refreshing”, and says that too many ideas about human evolution have been derived from limited samples and preconceived ideas. “The genetics, to me, don’t lie,” he adds.

Even Pääbo admits that he was befuddled by his team’s latest discovery. “My hope is, of course, eventually we will not bring turmoil but clarity to this world,” he says.

Earth’s evolutionary ancestor is a planet-spanning organism

The ancestor of all life on Earth might have been a gigantic planetary super-organism:

The ancestor of all life on Earth might have been a gigantic planetary super-organism

The ancestor of all life on Earth might have been a gigantic planetary super-organism

All life on Earth is related, which means we all must share a single common evolutionary ancestor. And now it appears that this ancestor might have been a single, planet-spanning organism that lived in a time that predates the development of survival of the fittest. That’s the idea put forward by researchers at the University of Illinois, who believe the last universal common ancestor, or LUCA, was actually a single organism that lived about three billion years ago. This organism was unlike anything we’ve ever seen, and was basically an amorphous conglomeration of cells. Instead of competing for resources and developing into separate lifeforms, cells spent hundreds of millions of years freely exchanging genetic material with each other, which allowed species to obtain the tools to survive without ever having to compete for anything. That’s maybe not an organism as we would comprehend it today, but that’s the closest term we have for this cooperative arrangement. All that we know about LUCA is based on conjecture, and the most promising recent research has been in figuring out what proteins and other structures are shared across all three domains of life: the unicellular bacteria and archaea and the multi-celled eukaryotes, which are where all plants and animals evolved from. This isn’t a foolproof method — it’s possible that two extremely similar but not identical structures could evolve independently after LUCA split into the three domains — but it’s a good starting point. Illinois researcher Gustavo Caetano-Anollés says about five to eleven percent of modern proteins could be traced back to LUCA. Based on the function of these particular proteins, it appears LUCA had the enzymes needed to break down nutrients and get energy from them, and it could also make proteins, but it probably didn’t have the tools necessary to make DNA. This fits with other research that suggests LUCA fed upon many different food sources, and that it had internal structures in its cells known as organelles. The big difference between LUCA and everything that came after, of course, is DNA. Because LUCA didn’t have the tools to deal with DNA, it probably used RNA instead, and it likely had very little control over the proteins that it made. The research suggests the ability to precisely control protein manufacture only came long after LUCA split apart, which means that protein-making was probably always a big crapshoot. That’s why LUCA had to be cooperative, with any cells that produced useful proteins able to pass them on throughout the world without competition. This was a weird variation on what we know as natural selections — helpful proteins could go from a single cell to global distribution, while harmful or useless proteins were quickly weeded out and discarded. The result was the equivalent of a planet-spanning organism. So why did this paradise of cellular cooperation give way to the last three billion years of cutthroat competition? The simple answer is that some cells probably outgrew this arrangement, as they had finally developed all the structures needed to survive without help. We don’t know quite why that happened, but it appears to coincide with the sharp increase of oxygen in the atmosphere. Whatever the cause, cells began eking out their own independent existences, ending the reign of LUCA that had lasted hundreds of millions of years… while beginning a new order that is still going strong 2.9 billion years later.