Foto: Eremitagemuseet i Skt. Petersborg

DNA analysis sensation: Origin of Indians linked to Europe

Thursday 21 Nov 13
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by Iben Julie Schmidt

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Simon Rasmussen
Associate Professor
DTU Bioinformatics
+4545 25 61 27

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Thomas Sicheritz-Pontén
Professor
DTU Bioinformatics
+4545 25 24 22

Calculations performed on supercomputers at DTU are impacting the debate on the origins of indigenous American Indians.

A showcase in the Hermitage Museum in St Petersburg contains the fossil remains of a four-year-old boy who lived near Lake Baikal in Siberia 24,000 years ago and who has suddenly taken on a key role in the debate on the genetic origins of the Indian population.

From Siberia to America

The reason for is that Danish researchers have successfully mapped the boy's entire genome. When comparing his genome to the genomes of present-day people from various regions of the world, his closest genetic relatives are the Indian population in North and South America, while he has virtually no kinship with modern East Asians. This result—just published in the journal Nature—is a major surprise and runs contrary to the existing theory that East Asians crossed the Bering Strait during the last ice age and founded America's indigenous population.

It now appears that the Siberian boy and the Indians had a common ancestor who lived in Europe and West Asia. It also means that the European traits in the Indians' genome are not simply a result of European immigration to America from the 1400s, but also have a prehistoric explanation.

The significance of the reconstructed genome—which also represents the world's oldest complete human genome—has already created much debate in scientific circles and is sure to be followed up by further similar studies.

"We will see many results like this in the years ahead, which will allow us to suddenly pinpoint human emigration and migration patterns. This is linked to the rapid changes happening within sequencing technology, which go hand-in-hand with expanding computer power and the development of new methods to analyse the data coming in," explains Professor Thomas Sicheritz Pontén. Professor Pontén leads a research group at the Centre for Biological Sequence Analysis, DTU Systems Biology, which has worked closely for several years with researcher Eske Willerslev and his team from the Centre for GeoGenetics at the University of Copenhagen to map and analyse DNA from fossil finds.

From St. Petersburg to DTU

The boy's bones were originally discovered during excavation in 1920, but the technologies and methods which allow valuable genetic information to be extracted from the microscopic amounts of original DNA remaining in a fossil bone have only recently been developed. Professor Eske Willerslev and Kelly Graf of USA therefore travelled to the museum in St. Petersburg to take a sample from the boy in the showcase. Even though carbon dating set the age of the bones at 24,000 years, they found it was possible to extract useful sequence information from the sample. This data was sent to DTU's genome assembly experts.

"It was our job to take the billions of tiny DNA fragments resulting from sequencing and determine with the aid of supercomputers how they should be assembled to recreate his genome," explains Associate Professor Simon Rasmussen from DTU Systems Biology, who was responsible for putting together the 24,000-year-old jigsaw puzzle. The older the DNA, the more pieces to the puzzle, because DNA breaks down over time, with the result that the pieces derived from sequencing are shorter.
There are many possible sources of error that need to be taken into account when working with prehistoric DNA. It can be very expensive if you only discover the errors along the way.

"Having worked on several projects involving this type of sample, we have become aware of the possible sources of error. We therefore now have a very clear strategy for how to approach such a task. Part of this strategy involves being in dialogue with the people performing the sequencing at the Centre for GeoGenetics. While running their sequencing they send their data to us continually, so we can check it and make suggestions for how to proceed. This saves both computer time and money," explains Simon Rasmussen.

This is important in relation to the future studies necessary to allow us to determine with certainty whether the boy from Siberia really is the missing link that explains the origin of the Indians. 

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