DNA Proteins Revealing Information About Human Evolution

Since the advent of population genetics and modern techniques to examine DNA, research has focused on, first, Mitochondrial DNA and then nuclear DNA.  Now we have another weapon in our arsenal.  Matthew Warren of Nature News relates new research done on palaeoproteomics.  This is the study of proteins found in fossilized human ancestors.  How is this possible, you ask?

Some time in the past 160,000 years or so, the remains of an ancient human ended up in a cave high on the Tibetan Plateau in China. Perhaps the individual died there, or parts were taken there by its kin or an animal scavenger. In just a few years, the flesh disappeared and the bones started to deteriorate. Then millennia dripped by. Glaciers retreated and then returned and retreated again, and all that was left behind was a bit of jawbone with some teeth. The bone gradually became coated in a mineral crust, and the DNA from this ancient ancestor was lost to time and weather. But some signal from the past persisted.

Deep in the hominin’s teeth, proteins lingered, degraded but still identifiable. When scientists analysed them earlier this year, they detected collagen, a structural support protein found in bone and other tissues. And in its chemical signature was a single amino-acid variant that isn’t present in the collagen of modern humans or Neanderthals — instead, it flagged the jawbone as belonging to a member of the mysterious hominin group called Denisovans. The discovery of a Denisovan in China was a major landmark. It was the first individual found outside Denisova Cave in Siberia, where all other remains of its kind had previously been identified. And the site’s location on the Tibetan Plateau — more than 3,000 metres above sea level — suggested that Denisovans had been able to live in very cold, low-oxygen environments.

As the author notes, this kind of research has opened many other doors that, up until now, have been shut to researchers. The realization that proteins have much longer staying power than DNA could radically reshape our understanding of human evolution:

Previously, scientists had recovered proteins from 1.8-million-year-old animal teeth and a 3.8-million-year-old eggshell. Now, they hope that palaeoproteomics could be used to provide insights about other ancient hominin fossils that have lost all traces of DNA — from Homo erectus, which roamed parts of the world from about 1.9 million to 140,000 years ago, to Homo floresiensis, the diminutive ‘hobbit’ species that lived in Indonesia as recently as 60,000 years ago. By looking at variations in these proteins, scientists hope to answer long-standing questions about the evolution of ancient human groups, such as which lineages were direct ancestors of Homo sapiens.

Whether that level of resolution will ever be possible remains to be seen, especially given that the modus operandi of modern palaeontology is focused on clade relationships. It will be interesting to see.

The Ancient History of Neanderthals in Europe

The Max Planck Society has a post in PhysOrg, a highly-regarded science site, on the history of Neandertals (they have used the old spelling). 

Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have retrieved nuclear genome sequences from the femur of a male Neanderthal discovered in 1937 in Hohlenstein-Stadel Cave, Germany, and from the maxillary bone of a Neanderthal girl found in 1993 in Scladina Cave, Belgium. Both Neanderthals lived around 120,000 years ago, and therefore predate most of the Neanderthals whose genomes have been sequenced to date.

Perhaps the most interesting aspect of the research was how much evolution within Neandertals was revealed:

Intriguingly, unlike the nuclear genome, the mitochondrial genome of the Neanderthal from Hohlenstein-Stadel Cave in Germany is quite different from that of later Neanderthals—a previous report showed that more than 70 mutations distinguish it from the mitochondrial genomes of other Neanderthals. The researchers suggest that early European Neanderthals may have inherited DNA from a yet undescribed population.

As with what is going on in human fossil research in China, it seems as though there is a tangled web of relationships between human populations extending through both time and space.  Whatever complexity we envision for these groups, it is probably far more so.  As I wrote about the Chinese material:

The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well.  As Chris Davis of China Daily News put it: “One big happy family.”

It is becoming increasingly clear that our simplistic notions of population replacement and regional continuity are probably wrong. Is evolution occurring in these human groups? It absolutely is. Just how these puzzle pieces relate to each other is the question.

Oldest Human DNA Recovered

Using the fossil material from the Sima de Los Huesos cave, at the Spanish site of Atapuerca, geneticists have recovered DNA.   From the National Geographic story by Karl Gruber:

Analysis of the bones challenges conventional thinking about the geographical spread of our ancient cousins, the early human species called Neanderthals and Denisovans. Until now, these sister families of early humans were thought to have resided in prehistoric Europe and Siberia, respectively. (See also: "The New Age of Exploration.")

But paleontologists write in a new study that the bones of what they thought were European Neanderthals appear genetically closer to the Siberian Denisovans, as shown by maternally inherited "mitochondrial" DNA found in a fossil thighbone uncovered at Spain's Sima de los Huesos cave.

"The fact that they show a mitochondrial genome sequence similar to that of Denisovans is irritating," says Matthias Meyer of Germany's Max Planck Institute for Evolutionary Anthropology in Leipzig, lead author of the study, published Wednesday in Nature.

"Our results suggest that the evolutionary history of Neanderthals and Denisovans may be very complicated and possibly involved mixing between different archaic human groups," he said.

Although the report argues that the Atapuerca remains show a greater similarity to Denisovans than Neandertals, we already know that modern Europeans and East Asians have Neandertal genes in them, indicating that admixture was occurring.  Milford Wolpoff has been arguing for decades that archaic Homo sapiens represents a polytypic species that has genetic ties to modern human groups in different parts of the Old World.  While it certainly appears that Neandertals were distinctive, this information, in conjunction with various studies (here and here) of the Denisovans and African archaics indicates that this model may be the more correct one. 

Lost in the shuffle, however, is that the ability to recover this DNA is an astounding feat of science and portends for great advances in human palaeontology in the future. 

“Out-of-Africa Replacement Model”: Piling On

On the heels of the recent DNA arguments supporting hybridization between early modern Homo sapiens and archaic Homo sapiens in Africa comes fossil skeletal evidence.  As the Telegraph reports:

A study on human remains found in the Iwo Eleru cave in Nigeria, West Africa, shows that Stone Age humans in the area shared characteristics with much older human relatives. Palaeontologists leading the study believe their findings provide evidence that modern humans and older subspecies of human might have coexisted and even crossbred in Africa. The findings add weight to theories that ancient species of human lived alongside the anatomically modern humans after they first appeared in Africa 200,000 years ago.

Quoted in the article is Chris Stringer, one of the progenitors of the Out-of-Africa replacement model of modern human origins which was based on mitochondrial DNA studies done in the late 1980s.The article continues:

Professor Stringer said: "The majority view was that once modern humans emerged in Africa 150,000 years ago, it was kind of the end of the story and modern humans took over. "I think the reality is that the ancestral forms didn't just disappear but hung around alongside those that had evolved into modern humans. "Somewhere lurking in bits of Africa were these more archaic people and we are starting to get a picture of that."

I suspect that it is going to get very hard to pin down exactly where Homo sapiens starts. It is becoming more and more clear that anatomically modern Homo sapiens and archaic Homo sapiens went for the occasional “roll in the hay.” If so, as I pointed out earlier, there simply was no “speciation event.” This goes more to supporting the multiregional evolution model, as it applies to Africa, in which there was selection for more modern genes. This model may also apply to Europe, with the mixing of modern humans and archaic humans there. I suspect that this will spur reexamination of the early modern material from there, such as Mladeč, where the material dates from the Early Würm/Late Würm interglacial period.