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.

Possible Mollusk Etching by Homo erectus

Science Magazine (and quite a few other outlets) is running a story involving the discovery of a 500, 000 year-old mollusk that shows some rudimentary carving.  Michael Balter writes:

In 2007, Stephen Munro got the shock of his life. The archaeology graduate student was studying mollusk shells gathered more than 100 years ago on the Indonesian island of Java, where an early human ancestor, Homo erectus, had roamed at least 1 million years ago. As he studied photographs of the shells, Munro spotted one apparently engraved with a pattern of zigzag lines. “I almost fell off my chair,” he says. That’s because the oldest known engravings date back 100,000 years and were made by modern humans—the only species thought to be capable of making abstract designs.

If this has been accurately interpreted, this suggests that Homo erectus was capable of considerably more cognition than is generally ascribed to this form. While there is evidence that Homo erectus controlled fire and, perhaps, had hafted tools, there has been, as of this point, no evidence of symbolic thought.

Some are not convinced:

Yet even if ancient humans engraved the shell, says Russell Ciochon, a paleoanthropologist at the University of Iowa in Iowa City, the team has not shown that H. erectus did it. Ciochon, who has spent many years working at sites in Java, agrees with criticisms that the shells have been taken out of context, because Trinil was not an occupation site where early humans actually lived. Rather, Ciochon argues, the human fossils found there (which include a skullcap widely agreed to be H. erectus and a thigh bone that could belong to either H. erectus or H. sapiens, a matter of sharp debate) were washed into the site by a powerful flood, and nothing found with them—including the shells—can be assumed to have been associated with them originally.

Here is the shell.

Possible New Hominid Species Discovered in Siberia

Reuters is running with a story about genetic research being done on hominid material discovered in Siberia that, according to researchers, suggests the presence of a new species of hominid that lived until around 30 thousand years ago. The author writes:

"It really just looked like something we had never seen before," Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, told a telephone briefing.

"It was a sequence that looked something like humans but really quite different."

Writing in Nature, Krause and colleagues said they sequenced DNA from the mitochondria, a part of the cell, which is passed down virtually intact from a woman to her children. They compared it to DNA from humans, Neanderthals and apes.

The sequence indicates the hominin's line diverged about a million years ago from the line that gave rise to both humans and Neanderthals and that split about 500,000 years ago.

I always have grave misgivings when geneticists, in the complete absence of diagnostic palaeontological material, proclaim that a new species has been discovered. For one thing, we don't have the genetic sequences for the intermediates between the find in Siberia and contemporary humans. How many substitutions denote a different species? This is where systematics can get away from us. If we don't have the intermediates, how do we know where the proper branch is? To be fair, the researchers, themselves, are reticent to go the 'new species' route yet but it seems they are leaning that way.

Modern Human Evolution

Daily Galaxy has an article on how human evolution has proceeded in the recent past and how it might continue into the future.

A team led by University of Wisconsin-Madison anthropologist John Hawks estimates that positive selection just in the past 5,000 years alone -dating back to the Stone Age - has occurred at a rate roughly 100 times higher than any other period of human evolution. Many of the new genetic adjustments are occurring around changes in the human diet brought on by the advent of agriculture, and resistance to epidemic diseases that became major killers after the growth of human civilizations.

"In evolutionary terms, cultures that grow slowly are at a disadvantage, but the massive growth of human populations has led to far more genetic mutations," says Hawks. "And every mutation that is advantageous to people has a chance of being selected and driven toward fixation. What we are catching is an exceptional time."

While the correlation between population size and natural selection is nothing new - it was a core premise of Charles Darwin, Hawks says - the ability to bring quantifiable evidence to the table is a new and exciting outgrowth of the Human Genome Project.

This is the convergence of population genetics, comparative anatomy and palaeontology to explain how humans have evolved. About natural selection, he writes:

Another recently discovered gene, CCR5, originated about 4,000 years ago and now exists in about 10 percent of the European population. It was discovered recently because it makes people resistant to HIV/AIDS. But its original value might have come from obstructing the pathway for smallpox.

"There are many things under selection that are making it harder for pathogens to kill us," Hawks says.

Population growth is making all of this change occur much faster, Hawks says, giving a tribute to Charles Darwin. When Darwin wrote in "Origin of the Species" about challenges in animal breeding, he always emphasized that herd size "is of the highest importance for success" because large populations have more genetic variation, Hawks says.

This is contrary to popular wisdom that shows that evolution proceeds faster in smaller populations because traits are expressed more often. Typically, larger populations slow evolution down because they are much closer to Hardy-Weinberg equlibrium. I also wonder about the statement that human evolution is proceeding faster now than at any time in the past. I do not think we have the resolution to determine that, even genetically. The human "bush" has gone through some remarkable changes even in the last 200 thousand years, with the successive appearance of archaic Homo sapiens and modern Homo sapiens, with regional characteristics present in many populations. It is doubtful that any of these changes would have happened had the population been as global as it now is.


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Light-Colored Skin a Recent Trait

The Times Online is reporting research that strongly suggests that light-colored skin, characteristic of northern Europeans, is a recent genetic trait. Jonathan Leake writes:

Johan Moan, of the Institute of Physics at the University of Oslo, said in a research paper: “In England, from 5,500-5,200 years ago the food changed rapidly away from fish as an important food source. This led to a rapid development of ... light skin.”

Moan, who worked with Richard Setlow, a biophysicist at Brookhaven National Laboratory in New York state, said vitamin D deficiency could be lethal. Research links it with heart disease, diabetes, arthritis and reduced immunity.

Their research says: “Cold climates and high latitudes would speed up the need for skin lightening. Agricultural food was an insufficient source of vitamin D, and solar radiation was too low to produce enough vitamin D in dark skin.”

Conventional wisdom is that the recent light pigments appeared in the last 20 to 30 ky, so this moves the evolution of light pigmentation up considerably.

Homo floresiensis: An Early Split?

Debbie Argue of the Australian National University has published research suggesting that the remains consisting of Homo floresiensis diverged from the main hominin/hominid line as early as the early Pleistocene or late Pliocene, between 2 and 2.5 million years ago. The story, in ANU News, reports:

“Until now much of the debate about H. floresiensis has rested on analysis of the morphology and measurements of the remains found on the Indonesian island of Flores in 2004,” Ms Argue said. “Despite evidence supporting the idea that H. floresiensis constitutes a new species, some researchers continue to argue that it is the remains of a sick modern human or a near-human ancestor affected by island miniaturisation.”

To try to settle the debate, Ms Argue and her colleagues compared up to 60 characteristics from a range of early hominins, including H. erectus, and modern humans. They used two different computer-based modelling systems, testing relationships between the species to find the most parsimonious, or simplest, evolutionary line.

“Our cladistic analyses created two very similar evolutionary trees that establish a very early origin for H. floresiensis back around the emergence of the very first members of the Homo family. This suggests that H. floresiensis was not a sick modern human, not even a very close relative.

This, of course, assumes that the remains are not pathological, a position that has adherents. Recent studies have suggested that this is not the case, however. One has to be very careful in conducting cladistic analyses, which are trait driven, not morphologically driven. The specimen involved cannot have post-mortem deformation and the traits must be extremely clear. The article continues:

“The late survival of H. floresiensis on Flores could turn over the idea that H. sapiens was the only hominin around after the extinction of H. erectus and the Neanderthals,” Ms Argue said. “These two ideas represent paradigm shifts in the field of anthropology, forcing us to reconsider our long-held ideas about our species and its place in the world.”

If there was a second species running around after the transition from Homo erectus to Homo sapiens, it does raise questions about how many there might have been at other times. There is, for example, considerable morphological variation in Homo erectus in China, when compared to that of South East Asia and Africa. Whether this is suggestive of more than one species is not quite clear, though. If human evolutionary history is more like a bush than a tree, then this finding is in keeping with that idea. It is the same thinking that drove the idea to split Homo erectus into Homo erectus and Homo ergaster.


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