January 15, 2014 (Vol. 34, No. 2)

Genomics Sheds More Light on Journey from Early Ancestors to Modern Humans

The study of human evolution stands on a cusp. A discipline that once depended on the study of bones, teeth and artefacts is, just now, being given added color and meaning by molecular genetics.

It’s now possible to sketch evolutionary relationships between various human species in a way that is simply not possible by looking at anatomy. Because of this, people are now coming to look at human evolution in a whole new way and, hopefully, shedding a few misconceptions as they go. Misconceptions such as the one in which human evolution is an orderly line of progression from primitive to advanced, into which you can slot “missing links” as if they were pieces in an existing jigsaw puzzle.

There never was any justification for that view. As I show in my new book “The Accidental Species: Misunderstandings of Human Evolution,” it represents a gross misreading of the Darwinian concept of evolution. Now, evidence from molecular biology, added to the existing fossil record, shows it up for the simple-minded notion it is. Human evolution is far more complicated than anyone could have imagined just 30 years ago.

Thirty years after ancient DNA was first cloned, it’s now possible to stretch the fingers of molecular genetics back in time to find previously unknowable details of humans living almost half a million years ago. That’s 3,000 centuries years before Homo sapiens emerged, and well before Neanderthals came onto the scene. The work stretches ancient DNA technology to the limits, coaxing fragments of mitochondrial DNA no more than 20 or 30 base-pairs long into the light, and at the same time ensuring that there aren’t contaminants.

But technology is improving daily, and it could be that within the next 30 years we could be able to extract meaningful genetic information from fossils up to a million years old.


Henry Gee, Ph.D.

New Genomics Dimension

The several different Neanderthal nuclear-DNA genomes now available have been extracted from bones several tens of thousands of years apart, to give genomics a whole new dimension—time. More startling still, genomes have been extracted from unremarkable bones, otherwise not attributable to species, but which have rocked our understanding of human evolution.

From a cave in southern Siberia came a tiny finger bone, no bigger than a grain of rice, yielding a genome of a completely unknown human species, known as the Denisovans. These were neither Neanderthals nor modern humans, but related to both. They lived in eastern Asia until as recently as 30,000 years ago, but before their genome had been discovered, nobody had any idea that they existed.

Because of this work, we now know that there’s a little bit of Neanderthal in everyone of European or Asian ancestry and that many modern humans living in South-East Asia and Oceania also contain small but appreciable amounts of Denisovan DNA.

What’s more, analysis of Denisovan, Neanderthal, and human DNA suggests that there are traces of genetic introgression from yet other undiscovered species, archaic humans that have left no other trace in the fossil record that we know about.

These new results have prompted palaeontologists to look anew at skulls and skeletons which somehow looked a bit strange, but were dismissed as oddities because they couldn’t be made to fit into the current, simple paradigm of human evolution. There are fossil skulls and skeletons from across the Old World that don’t seem to fit into any known human species.

Do these represent hitherto unknown species, rather than deformed examples of species we know? Could some puzzling skulls from China represent Denisovans, or other, even more shadowy species? Some modern African genomes show traces of some non-human archaic past: might this have some connection with two peculiar skulls from Iwo Eleru in Nigeria—dated to approximately 13,000 b.p.—but which look very much more archaic than one would expect from their age?


Still commonly perceived as an orderly progression from primitive to advanced, human evolution is actually far more complicated, as genomics studies have already demonstrated.

What About the Hobbit?

The best known fly in the ointment is the ‘Hobbit’, the skeleton of a small and very weird human, now called Homo floresiensis, that lived on the small island of Flores in Indonesia until almost historical times. Vociferously dismissed by many as a pathological modern human, it is now as certain as anything can be in science that it represents a relic of a phase of human evolution that had hitherto been completely unknown, even unsuspected.

Now, given that the chances of any creature becoming a fossil are exceedingly remote, you have to ask yourself the following question: If the Hobbit were the only hitherto unknown, enigmatic fossil human that ever existed, how likely do you think it is that a group of researchers, who were, incidentally, looking for something else, just happened to have stumbled on it, in just this one cave, in an archipelago full of similar deep, unexplored caves?

To be sure, someone has to win the lottery. But it’s more likely that many other weird human fossils remain to be discovered. The DNA from Denisova, and the hints from genomes of the existence of further, undiscovered, archaic forms, supports that view.

Because we H. sapiens are members of the only species of human left on Earth, we tend to think that the world has always been that way. Creation myths (including the one in the Bible) have humans created in their modern forms, without antecedents.

When evolution came along, a misreading of natural selection as a kind of progressive force for improvement (the result of a bastard fusion of Darwinism with older currents of thought) gave us a single line of ancestors which were presumably there in the rocks for us to find, if we knew where to look, whose evolution would naturally lead to our current exalted state, higher than apes, but beneath the angels.

The current evidence, from fossils and lately from DNA, reveals a very different picture. There have been humans of various sorts scattered across the world for millions of years. At first in Africa, where the human family appears to have evolved, but, some time around two million years ago, across the Old World.

The human family has always been very thinly spread, separated into groups that are more or less genetically distinct, interacting and interbreeding only rarely. If we wish to find a model for most of our existence, there is one—modern chimpanzees. There is more genetic diversity in the few scattered populations of chimps in West Africa than in the entirety of H. sapiens.

This speaks to another feature of our genetic past. H. sapiens has been through one or more severe genetic bottlenecks in the past, when our species declined to almost nothing, but recovered. Who knows how many other human species declined to extinction, leaving no trace at all in the fossil record, except perhaps a few hundred bases in some other human’s genome?

Henry Gee, Ph.D. ([email protected]), is an evolutionary biologist, paleontologist, and a senior editor at Nature. He is the author of “The Accidental Species: Misunderstandings of Human Evolution.”

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