Now, ancient human genome studied

Published in The Hindu on February 11, 2010

For the first time ever the genome of an ancient human has been studied. The about 4,000-year-old sample studied was a human hair of an Eskimo recovered from permafrost sediments in Qeqertasussuk, Greenland. Four hair tufts were recovered and only one was studied (sequenced).

The hair was from a Saqqaq man. Very little information is available about Saqqaq culture as their remains are hard to find. The results are published today (February 11) in Nature.

Samples need to be well preserved and free of any contamination by foreign DNA if a detailed genomic study is to be done. The Eskimo sample met both the criteria.

Well preserved

The sample obtained has been excellently preserved. This is because it was preserved in permafrost sediments. And this allowed the scientists to study the sample in great detail.

The sample was relatively free of contamination with DNA of the scientists or others who handled them. About 80 per cent of the DNA recovered was that of the ancient Eskimo.

Apart from studying 79 per cent of diploid genome, the scientists studied the mitochondrial DNA (mtDNA) and Y-chromosome DNA. Mitochondrial DNA remains unchanged through generations and provides information of the maternal lineage. The Y-chromosome reveals the details of paternal lineage.

Northeast Asian origin

Based on the data generated, scientists were able to describe many characteristics of the Saqqaq individual. The characteristics are typical of northeast Asian origin.

For instance, he had black thick hair, skin colour that was more Asian, eyes were brown, and teeth were typical of Asians. Metabolism and body mass index clearly showed that the Saqqaq individual was adapted to living in cold regions.

It became possible to describe the physical characteristics as the genome had undergone specific point mutations (single-nucleotide polymorphisms – SNP) in the coding region of the human genome.

Though all humans share about 99.9 per cent of the genome, specific SNPs make Asians look different from Caucasians or play a role in diseases by affecting the gene’s function. SNPs can also help predict the risk of developing particular diseases.

Based on the physical characteristics, scientists have been able to deduce the migration of Saqqaq from East Siberia across the Bering Strait.

Across Bering Strait

“A single individual may, or may not, be representative of the extinct culture that inhabited Greenland some 4,000 years ago,” notes the paper. Yet, they go on to conclude that this individual or a group did indeed cross the Bering Strait, and they did it “independently of the ancestors of present-day Native Americans and Inuit.”

But they are unequivocal about the northeast Asian characteristics (phenotype) of the individual.

Geneticists have been particularly interested in studying samples of ancient humans to understand the dispersal of humans out of Africa.

But to do this, several well-preserved samples from different locations have to be studied.

Though human remains, particularly bones and teeth, can be found, the DNA is very often degraded and is not suitable for undertaking complete genome analysis. Moreover, contamination with modern human DNA should not be present or should be only negligible.

Unlike in this case where the sample was preserved in permafrost, cold conditions were absent in Africa, south Asia and Australia, especially in the last few thousand years.

The next challenge

To study samples that have not been deposited in permafrost will be the next challenge.

“Although undoubtedly challenging [studying samples not deposited in permafrost], it will, if successful, take the emerging field of palaeogenomics to yet another level,” the scientists write.