by Greg Mayer
In a paper published today in Nature, Qiaomei Fu and colleagues report a high quality genome sequence derived from a 45,000 year old, anatomically modern human femur found in western Siberia. “Ust’-Ishim Man” has provided the oldest known genome of an anatomically modern human (there are earlier genomes of archaic humans).
So, why is this interesting? First, it is a marvelous technical achievement to be able to get a high quality sequence out of a bone of such great age recovered from a riverbank. Kudos to Fu and her colleagues for this achievement. Second, Ust’-Ishim Man proves to be very interesting phylogenetically. While definitely non-African in his genetic affinities, he appears to be equidistant from both modern Europeans and modern East Asians. Fu et al. interpret him as being at or near the point in time when the split occurred between these two branches of humanity, making him part of the lineage of modern humans that had left Africa, but had not yet split into European and East Asian sub-lineages. Third, by being able to identify the genetic differences between Ust’-Ishim and modern man, they were able to estimate the mutation rate in both the nuclear and mitochondrial genomes. The autosomal mutation rate was about .5X10E-9 per site per year, the Y chromosome mutation rate was higher, about .75X10E-9 per site per year, and the mitochondrial rate much higher, about 2.5X10E-8 per site per year. These rates and their mutual relations are about exactly what we would expect, but it’s nice to have fairly direct estimates, over a long time base, to confirm estimates based on short term de novo mutation studies and comparison of contemporaneous sequences.
And, finally, there’s what we learn about the interbreeding between anatomically modern humans and Neanderthals. As Jerry, John Hawks, and I have all argued before (and as I recently summarized at The Dish— see the update at end of Andrew’s post), Neanderthals and early non-African anatomically modern humans (along with Denisovans), were all parts of a group of interbreeding populations in nature, and thus were all members of the species Homo sapiens. Ust’-Ishim Man’s genome is about 2% Neanderthal, just like modern Europeans and East Asians. This means that the level of admixture characterizing modern populations was already in place by 45,000 years ago. This is not too surprising. Neanderthals were going or gone by about then, so whatever interbreeding occurred should have (mostly) occurred by then. So Neanderthals are us.
But that’s not all. Modern humans are separated by some tens of thousands of years, and thousands of generations, from the time our forebears interbred with one another. During this time, recombination between the chromosomes of our anatomically modern and Neanderthal ancestors will have broken up the originally contiguous chromosome segments, dispersing the two sets among one another. Since the great majority of our genome is from anatomically modern ancestors, this will most easily be seen in our Neanderthal genetic component, which will become scattered throughout the anatomically modern part. This is exactly what is seen in the 15 modern non-African genomes in the figure above– the yellow and blue Neanderthal segments are scattered throughout the black anatomically modern background.
But when interbreeding first occurs, the two genomes will be separate. The first “hybrid” child will have one set of Neanderthal chromosomes, and one set of anatomically modern chromosomes. When that child produces gametes, its chromosomes will undergo crossing over— an exchange of chromosome segments– during meiosis, so that its children will receive a chromosomal gemisch: each chromosome will consist of alternating stretches of Neanderthal and anatomically modern parts. In subsequent generations, crossing over occurs again, so the contiguous segments from the founding generation keep getting broken up into smaller and smaller bits. So, if we catch the genome fairly soon after the genetic admixture has occurred, we should see that the chromosome segments occur in larger, contiguous blocks– and that’s exactly what Fu and colleagues found!
Look at the top row in the figure above. That’s Ust’-Ishim Man– note that his Neanderthal DNA occurs in larger blocks, indicating that it has not yet been fully broken up by crossing over. His genome represents an earlier stage in the genetic admixture of Neanderthals and anatomically modern humans. The actual interbreeding has already occurred– he’s 2% Neanderthal– but his Neanderthal DNA still largely occurs in unrecombined blocks. Based on this, Fu and colleagues have been able to calculate about how long before Ust’-Ishim Man the interbreeding occurred, and come up with a figure of about 300 generations, or about 10,000 years before Ust’-Ishim Man. So, the interbreeding occurred on the order of 50-60,000 years ago.
You might also wonder why our genomes are mostly from anatomically modern humans. If they and Neanderthals interbred, shouldn’t it be 50-50? Well, no– it would be 50-50 only if there were an equal number of ancestors from the two groups, but that’s not necessarily the case (in fact, we know it’s not the case in this instance). Most of the “hybrids” must have backcrossed (i.e. had children) with anatomically modern humans. There are many instance in history of two modern human groups meeting and interbreeding, but with a rather unqequal genetic contribution to the descendant populations. In the case of Neanderthals, the ratio was about 1 to 49. It’s easy to imagine how this might happen– a lone Neanderthal being adopted into a modern group, with its descendants therefore breeding mostly with the numerically predominant moderns. Many other scenarios could be posited, but they would be mostly speculative.
Whenever I see interesting results in human evolution, I always check to see what John Hawks has to say, but he’s not posted on this yet; fortunately Carl Zimmer at the NY Times has been able to get a hold of John personally, and ask him what he thinks:
“It’s irreplaceable evidence of what once existed that we can’t reconstruct from what people are now,” said John Hawks, a paleoanthropologist at the University of Wisconsin who was not involved in the study. “It speaks to us with information about a time that’s lost to us.”
That’s absolutely right of course, but I’d like to hear more of what he has to say, and I hope he will post something on the new discoveries.
Fu, Q., et al. 2014.Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514:445-449. abstract