Viewpoint: Human evolution, from tree to braid

If one human evolution paper published in 2013 sticks in my mind above all others, it has to be the wonderful report in the 18 October issue of the journal Science.

The article in question described the beautiful fifth skull from Dmanisi in Georgia. Most commentators and colleagues were full of praise, but controversy soon reared its ugly head.


What was, in my view, a logical conclusion reached by the authors was too much for some researchers to take.

The conclusion of the Dmanisi study was that the variation in skull shape and morphology observed in this small sample, derived from a single population of Homo erectus, matched the entire variation observed among African fossils ascribed to three species – H. erectus, H. habilis and H. rudolfensis.

The five highly variable Dmanisi fossils belonged to a single population of H. erectus, so how could we argue any longer that similar variation among spatially and temporally widely distributed fossils in Africa reflected differences between species? They all had to be the same species.

I have been advocating that the morphological differences observed within fossils typically ascribed to Homo sapiens (the so-called modern humans) and the Neanderthals fall within the variation observable in a single species.

It was not surprising to find that Neanderthals and modern humans interbred, a clear expectation of the biological species concept.

But most people were surprised with that particular discovery, as indeed they were with the fifth skull and many other recent discoveries, for example the “Hobbit” from the Indonesian island of Flores.

It seems that almost every other discovery in palaeoanthropology is reported as a surprise. I wonder when the penny will drop: when we have five pieces of a 5,000-piece jigsaw puzzle, every new bit that we add is likely to change the picture.

Did we really think that having just a minuscule residue of our long and diverse past was enough for us to tell humanity’s story?

If the fossils of 1.8 or so million years ago and those of the more recent Neanderthal-modern human era were all part of a single, morphologically diverse, species with a wide geographical range, what is there to suggest that it would have been any different in the intervening periods?

Probably not so different if we take the latest finds from the Altai Mountains in Siberia into account. Denisova Cave has produced yet another surprise, revealing that, not only was there gene flow between Neanderthals, Denisovans and modern humans, but that a fourth player was also involved in the gene-exchange game.

The identity of the fourth player remains unknown but it was an ancient lineage that had been separate for probably over a million years. H. erectus seems a likely candidate. Whatever the name we choose to give this mystery lineage, what these results show is that gene flow was possible not just among contemporaries but also between ancient and more modern lineages.

Pit of Bones
A femur recovered from the famed “Pit of Bones” site in Spain yielded 400,000-year-old DNA

Just to show how little we really know of the human story, another genetic surprise has confounded palaeoanthropologists. Scientists succeeded in extracting the most ancient mitochondrial DNA so far, from the Sima de los Huesos site in Atapuerca, Spain.

The morphology of these well-known Middle Pleistocene (approximately 400,000 years old) fossils have long been thought to represent a lineage leading to the Neanderthals.

When the results came in they were actually closer to the 40,000 year-old Denisovans from Siberia. We can speculate on the result but others have offered enough alternatives for me to not to have to add to them.

The conclusion that I derive takes me back to Dmanisi: We have built a picture of our evolution based on the morphology of fossils and it was wrong.

We just cannot place so much taxonomic weight on a handful of skulls when we know how plastic – or easily changeable – skull shape is in humans. And our paradigms must also change.

The Panel of Hands at El Castillo Cave, Spain
Old assumptions are being challenged as new thinking emerges

Some time ago we replaced a linear view of our evolution by one represented by a branching tree. It is now time to replace it with that of an interwoven plexus of genetic lineages that branch out and fuse once again with the passage of time.

This means, of course, that we must abandon, once and for all, views of modern human superiority over archaic (ancient) humans. The terms “archaic” and “modern” lose all meaning as do concepts of modern human replacement of all other lineages.

It also releases us from the deep-rooted shackles that have sought to link human evolution with stone tool-making technological stages – the Stone Ages – even when we have known that these have overlapped with each other for half-a-million years in some instances.

The world of our biological and cultural evolution was far too fluid for us to constrain it into a few stages linked by transitions.

The challenge must now be to try and learn as much as we can of the detail. We have to flesh out the genetic information and this is where archaeology comes into the picture. We may never know how the Denisovans earned a living, after all we have mere fragments of their anatomy at our disposal, let alone other populations that we may not even be aware of.

What we can do is try to understand the spectrum of potential responses of human populations to different environmental conditions and how culture has intervened in these relationships. The Neanderthals will be central to our understanding of the possibilities because they have been so well studied.

A recent paper, for example, supports the view that Neanderthals at La Chapelle-aux-Saints in France intentionally buried their dead which contrasts with reports of cannibalistic behaviour not far away at El Sidron in northern Spain.

Here we have two very different behavioural patterns within Neanderthals. Similarly, modern humans in south-western Europe painted in cave walls for a limited period but many contemporaries did not. Some Neanderthals did it in a completely different way it seems, by selecting raptor feathers of particular colours. Rather than focus on differences between modern humans and Neanderthals, what the examples show is the range of possibilities open to humans (Neanderthals included) in different circumstances.

The future of human origins research will need to focus along three axes:

  • further genetic research to clarify the relationship of lineages and the history of humans;
  • research using new technology on old archaeological sites, as at La Chapelle; and
  • research at sites that currently retain huge potential for new discoveries.

Sites in the latter category are few and far between. In Europe at least, many were excavated during the last century but there are some outstanding examples remaining. Gorham’s and Vanguard Caves in Gibraltar, where I work, are among those because they span over 100,000 years of occupation and are veritable repositories of data.

There is another dimension to this story. It seems that the global community is coming round to recognising the value of key sites that document human evolution.

In 2012, the caves on Mount Carmel were inscribed on the Unesco World Heritage List and the UK Government will be putting Gorham’s and associated caves on the Rock of Gibraltar forward for similar status in January 2015. It is recognition of the value of these caves as archives of the way of life and the environments of people long gone but who are very much a part of our story.

Prof Clive Finlayson is director of the Gibraltar Museum and author of the book The Improbable Primate.

Gorham's Cave The UK government is to seek World Heritage status for Gorham’s and associated caves on the Rock

Neanderthals Passed Along Diabetes Risk Gene.

Kermanshah Pal Museum-Neanderthal

Scientists have determined that a variation of a gene that increases the risk of a person developing type 2 diabetes by 25 percent was likely introduced into human populations by Neanderthals more than 60,000 years ago. Half of people with a recent Native American lineage, including Latin Americans, have the gene, SLC16A11, as do 20 percent of East Asians. The newly seqeuenced, high quality Neanderthal genome, taken from a female toe found in Siberia‘s Denisova Cave, also included the variant, and researchers say that analysis suggests that Neanderthals introduced it into the human genome when they intermixed with modern humans, after the latter left Africa 60,000 to 70,000 years ago. According to the findings from the completed Neanderthal genome, roughly two percent of the genomes of today’s non-African humans are comprised of Neanderthal DNA.

Genome Brings Ancient Girl to Life

In a stunning technical feat, an international team of scientists has sequenced the genome of an archaic Siberian girl 31 times over, using a new method that amplifies single strands of DNA. The sequencing is so complete that researchers have as sharp a picture of this ancient genome as they would of a living person’s, revealing, for example that the girl had brown eyes, hair, and skin. “No one thought we would have an archaic human genome of such quality,” says Matthias Meyer, a postdoc at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “Everyone was shocked by the counts. That includes me.”

That precision allows the team to compare the nuclear genome of this girl, who lived in Siberia’s Denisova Cave more than 50,000 years ago, directly to the genomes of living people, producing a “near-complete” catalog of the small number of genetic changes that make us different from the Denisovans, who were close relatives of Neandertals. “This is the genetic recipe for being a modern human,” says team leader Svante Pääbo, a paleogeneticist at the institute.

Ironically, this high-resolution genome means that the Denisovans, who are represented in the fossil record by only one tiny finger bone and two teeth, are much better known genetically than any other ancient human—including Neandertals, of which there are hundreds of specimens. The team confirms that the Denisovans interbred with the ancestors of some living humans and found that Denisovans had little genetic diversity, suggesting that their small population waned further as populations of modern humans expanded. “Meyer and the consortium have set up the field of ancient DNA to be revolutionized—again,” says Beth Shapiro, an evolutionary biologist at the University of California, Santa Cruz, who was not part of the team. Evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania agrees: “It’s really going to move the field forward.”

Pääbo’s group first gave the field a jolt in May 2010 by reporting a low-coverage sequence (1.3 copies on average) of the composite nuclear genome from three Neandertals. They found that 1% to 4% of the DNA of Europeans and Asians, but not of Africans, was shared with Neandertals and concluded that modern humans interbred with Neandertals at low levels.

Just 7 months later, the same group published 1.9 copies on average of a nuclear genome from a girl’s pinky finger bone from Denisova Cave. They found she was neither a Neandertal nor a modern human—although bones of both species had been found in the cave—but a new lineage that they called Denisovan. The team found “Denisovan DNA” in some island Southeast Asians and concluded that their ancestors also interbred with the ancestors of Denisovans, probably in Asia.

But these genomes were too low quality to produce a reliable catalog of differences. Part of the problem was that ancient DNA is fragmentary, and most of it breaks down into single strands after it is extracted from bone.

Meyer’s breakthrough came in developing a method to start the sequencing process with single strands of DNA instead of double strands, as is usually done. By binding special molecules to the ends of a single strand, the ancient DNA was held in place while enzymes copied its sequence. The result was a sixfold to 22-fold increase in the amount of Denisovan DNA sequenced from a meager 10-milligram sample from the girl’s finger. The team was able to cover 99.9% of the mappable nucleotide positions in the genome at least once, and more than 92% of the sites at least 20 times, which is considered a benchmark for identifying sites reliably. About half of the 31 copies came from the girl’s mother and half from her father, producing a genome “of equivalent quality to a recent human genome,” says paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not part of the team.

Now, the view of the ancient genome is so clear that Meyer and his colleagues were able to detect for the first time that Denisovans, like modern humans, had 23 pairs of chromosomes, rather than 24 pairs, as in chimpanzees. By aligning the Denisovan genome with that of the reference human genome and counting mutations, the team calculated that the Denisovan and modern human populations finally split between 170,000 and 700,000 years ago.

The researchers also estimated ancient Denisovan population sizes by using methods to estimate the age of various gene lineages and the amount of difference between the chromosomes the girl inherited from her mother and father. They found that Denisovan genetic diversity, already low, shrank even more 400,000 years ago, reflecting small populations at that time. By contrast, our ancestors’ population apparently doubled before their exodus from Africa.

The team also counted the differences between Denisovans and chimps, and found that they have fewer differences than do modern people and chimps. The girl’s lineage had less time to accumulate mutations, and the “missing evolution” suggests she died about 80,000 years ago, although the date is tentative, says co-author David Reich, a population geneticist at Harvard University. If this date—the first proof that a fossil can be directly dated from its genome—holds up, it is considerably older than the very rough dates of 30,000 to more than 50,000 years for the layer of sediment where the fossils of Denisovans, Neandertals, and modern humans all were found.

The team says the new genome confirms their previous findings, showing that about 3% of the genomes of living people in Papua New Guinea come from Denisovans, while the Han and Dai on mainland China have only a trace of Denisovan DNA. Furthermore, the team determined that Papuans have more Denisovan DNA on their autosomes, inherited equally often from both parents, than on their X chromosomes, inherited twice as often from the mother. This curious pattern suggests several possible scenarios, including that male Denisovans interbred with female modern humans, or that these unions were genetically incompatible, with natural selection weeding out some of the X chromosomes, Reich says.

The new genome also suggests one odd result. By using the detailed Denisovan genome to sharpen the view of their close cousins the Neandertals, the team concludes that living East Asians have more Neandertal DNA than Europeans have. But most Neandertal fossils are from Europe; paleoanthropologist Richard Klein of Stanford University in Palo Alto, California, calls the result “peculiar.”

Most exciting to Pääbo is the “nearly complete catalog” of differences in genes between the groups. This includes 111,812 single nucleotides that changed in modern humans in the past 100,000 years or so. Of those, eight were in genes associated with the wiring of the nervous system, including those involved in the growth of axons and dendrites and a gene implicated in autism. Pääbo is intrigued in particular by a change in a gene that is regulated by the so-called FOXP2 gene, implicated in speech disorders. It is “tempting to speculate that crucial aspects of synaptic transmission may have changed in modern humans,” the team wrote. Thirty-four genes are associated with disease in humans. The list suggests some obvious candidates for gene-expression studies. “The cool thing is that it isn’t an astronomically large list,” Pääbo says. “Our group and others will probably be able to analyze most of them in the next decade or two.”

Back in Leipzig, the mood is upbeat, as researchers pull fossil samples off the shelf to test anew with “Matthias’s method.” First on Pääbo’s list: Neandertal bone samples, to try to produce a Neandertal genome to rival that of the little Denisovan girl.

Source: Scientific American.