45,000-year-old modern human bone yields a genome

The femur from which the DNA samples originated.

Bence Viola, MPI EVA

Svante Pbo's lab at the Max Planck Institute for Evolutionary Anthropology in Germany has mastered the process of obtaining DNA from ancient bones. With the techniques in hand, the research group has set about obtaining samples from just about any bones they can find that come from the ancestors and relatives of modern humans. In their latest feat, they've obtained a genome from a human femur found in Siberia that dates from roughly the time of our species' earliest arrival there. The genome indicates that the individual it came from lived at a time where our interbreeding with Neanderthals was relatively recent, and Europeans and Asians hadn't yet split into distinct populations.

The femur comes from near the town of Ust-Ishim in western Siberia. It eroded out of a riverbank that contains a mixture of bones, some from the time where the sediments were deposited (roughly 30 to 50,000 years ago), and some likely older that had been washed into the sediments from other sites. The femur shows features that are a mixture of those of paleolithic and modern humans and lacks features that are typical of Neanderthal skeletons.

Two separate samples gave identical carbon radioisotope dates; after calibration to the 14C record, this places the bone at 45,000 years old, give or take a thousand years. That's roughly when modern humans first arrived in the region. That also turned out to be consistent with dates estimated by looking at the DNA sequence, which placed it at 49,000 years old (the 95 percent confidence interval was 30 to 65,000 years).

Even though the majority of the DNA obtained from similar bones is typically bacterial, Pbo's group managed to obtain collections of short DNA molecules that were between two and 10 percent human. Contamination with current human sequences, which was often a problem in earlier work, appears to be less than half a percent of the total sequences.

The short DNA fragments that persist in these ancient samples limit the areas of the human genome that you can match the fragments tolots of the human genome is repetitive, and you can't tell which repeat a fragment comes from. Of the 1.9 billion bases that can be matched uniquely, the genome the researchers obtained covered the typical base over 40 times (in the lingo of the field, it provided 42-fold coverage). That's more than enough to do some comparisons with other humans, current and past.

Because the human population is genetically diverse, the two copies of each chromosome we possess differ at known rates. In Africans, the oldest and thus most genetically diverse populations, there are about 10 differences for every 10,000 DNA bases. Non-Africans, by contrast, typically only have six or seven differences in the same amount of DNA. The Ust-Ishim genome clearly groups with non-Africans, at 7.7 differences every 10,000 bases. This is consistent with the idea that the migration out of Africa created a bottleneck, with only a fraction of our genetic diversity getting exported to populations that left the continent.

So, who was this individual related to? Based on Y chromosome and mitochondrial genome, the Ust-Ishim DNA appears to reside at the base of a broad group of populations that exist in current Eurasia. The rest of the genome indicates that it lacks many of the individual DNA changes that have appeared in current populations. All of which suggests that the population it belongs to is ancestral to Europeans and Asians.

But if you look at overall relatedness, the genome is slightly closer to current Asian populations than it is to Europeans. The authors note that other data has led researchers to hypothesize that Europeans have had an influx of DNA from a population that did not participate in the initial migration out of Africaperhaps a second wave out of Africa.

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45,000-year-old modern human bone yields a genome