Copenhagen, Denmark. For the first time, scientists have performed a detailed reconstruction of an ancient human being's genome. The individual was a male who lived in Greenland 4,000 years ago and belonged to the first culture to settle in the New World Arctic.

The team garnered international attention on 2009 when they reconstructed the complete mitochondrial genomes of a woolly mammoth and an ancient human. However, the current discovery advances this work in that for the first time scientists were able to reconstruct the 80% of the nuclear genome that is possible to retrieve from fossil remains.

Up intil now, only limited remains have been recovered, but the new techniques can be applied to museum materials and ancient remains found in nature and help reconstruct the human phenotypic traits of extinct cultures. The discovery provides pathways for tracing relationships between ancient cultures and contemporary populations, revealing the patterns of human expansions and migrations. Scientists expect substantial improvements in our understanding of heredity, human development, and disease risks passed down from our ancestors.

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Human Genome Project (HGP)

A genome is all the DNA in an organism, including its genes and other materials.

Genes carry information for making all the proteins required by all organisms. These proteins determine, among other things, how the organism looks, how well its body metabolizes food or fights infection, and to an extent even how it behaves.

The HGP identified all of the genes in the human genome and mapped their individual sequencing. Basic work began in 1990 and reached completion in 2005, sparking continuous refinements and new projects. Though the HGP is finished, data analyses will continue for many years.

DNA is made up of four similar chemicals (called bases and abbreviated A, T, C, and G) that are repeated millions or billions of times throughout a genome.

The human genome, for example, has 3 billion pairs of bases. The particular order of As, Ts, Cs, and Gs is extremely important.

The order underlies all of life's diversity, even dictating whether an organism is human or another species such as yeast, rice, or fruit fly, all of which have their own genomes and are themselves the focus of genome projects.

Because all organisms are related through similarities in DNA sequences, insights gained from nonhuman genomes often lead to new knowledge about human biology.

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Video: An introduction to the ongoing Human Genome Project, courtesy of the US National Institutes of Health (NIH) (18 May 2007). Time: 00:03:33. Creative Commons license: Attribution-NonCommercial-NoDerivs.

For more information see the TS-Si.org section, Genetics & Genome.

Sequencing the genome

The discovery was made by analysing a tuft of hair that belonged to a man from the Saqqaq culture from north-western Greenland 4,000 years ago. The scientists have named the ancient human "Inuk," which means "man" or "human" in Greenlandic. Although Inuk is more closely related to contemporary north-eastern Siberian tribes than to modern Inuits of the present day New World Arctic, the scientists wanted to acknowledge that the discovery was made in Greenland.

Professor Willerslev discovered the existence of the hair tuft by coincidence after several unsuccessful attempts to find early human remains in Greenland.

"I was speaking with the Director of the Natural History Museum in Denmark, Dr. Morten Meldgaard, when we started discussing the early peopling of the Arctic," Willerslev recalls. "Meldgaard who had participated in several excavations in Greenland told me about a large tuft of hair, which was found during an excavation in north-western Greenland in the 1980's, and now stored at the National Museum in Denmark.

"After the Greenland National Museum and Archives granted permission, we analysed the hair for DNA using various techniques and found it to be from a human male. For several months, we were uncertain as to whether our efforts would be fruitful. However, through the hard work of a large international team, we finally managed to sequence the first complete genome of an extinct human.," Willerslev says.

Blueprint of the ancient man

The reconstruction serves as blueprint that scientists can use to give a description of how the pre-historic Greenlander, Inuk, looked — including his tendency to baldness, dry earwax, brown eyes, dark skin, the blood type A+, shovel-shaped front teeth, and that he was genetically adapted to cold temperatures, and to what extend he was predisposed to certain illnesses.

This is important as besides four small pieces of bone and hair, no human remains have been found of the first people that settled the New World Arctic. Willerslev's team can also reveal that Inuk's ancestors crossed into the New World from north-eastern Siberia between 4,400 and 6,400 years ago in a migration wave that was independent of those of Native Americans and Inuit ancestors. Thus, Inuk and his people have no descendents among contemporary indigenous people of the New World.

"Previous efforts to reconstruct the mammoth nuclear genome resulted in a sequence filled with gaps and errors due to DNA damage because the technology was in its infancy. The genome of Inuk is comparable in quality to that of a modern human ," Willerslev says.

"Our findings can be of significant help to archaeologists and others as they seek to determine what happened to people from extinct cultures. Doing so requires organic material — bones or hair kept as museum pieces or found at archaeological sites. Previously, the DNA needed to have been frozen or buried in a layer of permafrost. But with the new methods developed here at the Centre, that is not a premise anymore."

Much of the hands-on work analysing and joining the DNA sequences and the chemical analyses of what little was left of the damaged genetic material together to form a complete profile of Inuk was done by Morten Rasmussen. The work was carried out in close collaboration with other scientists at the University of Copenhagen and in China, where they have far more sequencing machines than in Denmark.

"Not so long ago, reconstructing an entire modern human genome took years," Rasmussen says. But the new methods and the abundance of sequencing machines allow us to do it in just a few months — and that includes the time-consuming task of analysing the results.

The interesting thing about compiling a human genome is that we can look at the genes to see traits like why Scandinavians are blonde, why some are predisposed to certain illnesses and why others more easily become addicted to alcohol or tobacco.

But the genome we've reconstructed is no Frankenstein's Monster; it's more like we've got the blueprints for a house, but we don't know how to build it."

ParticipantsAnders Krogh's bioinformatics group, University of Copenhagen, Denmark
Søren Brunak and Thomas Sicheritz-Ponten's bioinformatics groups, Technical University of Denmark
Rasmus Nielsen's evolution group, University of California, Berkeley, USA
Richard Villem's genetic anthropology group, Latvia
Toomas Kivisild's genetic anthropology group, Cambridge, UK
Jun Wang's sequencing centre, BGI, China
Bjarne Grønnow, National Museum of Denmark, Denmark
Claus Andreasen, Greenland National Museum and Archives, Greenland

CitationAncient human genome sequence of an extinct Palaeo-Eskimo. Morten Rasmussen, Yingrui Li, Stinus Lindgreen, Jakob Skou Pedersen, Anders Albrechtsen, Ida Moltke, Mait Metspalu, Ene Metspalu, Toomas Kivisild, Ramneek Gupta, Marcelo Bertalan, Kasper Nielsen, M. Thomas P. Gilbert, Yong Wang, Maanasa Raghavan, Paula F. Campos, Hanne Munkholm Kamp, Andrew S. Wilson, Andrew Gledhill, Silvana Tridico, Michael Bunce, Eline D. Lorenzen, Jonas Binladen, Xiaosen Guo, Jing Zhao, Xiuqing Zhang, Hao Zhang, Zhuo Li, Minfeng Chen, Ludovic Orlando, Karsten Kristiansen, Mads Bak, Niels Tommerup, Christian Bendixen, Tracey L. Pierre, Bjarne Grønnow, Morten Meldgaard, Claus Andreasen, Sardana A. Fedorova, Ludmila P. Osipova, Thomas F. G. Higham, Christopher Bronk Ramsey, Thomas v. O. Hansen, Finn C. Nielsen, Michael H. Crawford, Søren Brunak, Thomas Sicheritz-Pontén, Richard Villems, Rasmus Nielsen, Anders Krogh, Jun Wang and Eske Willerslev. Nature 2010; 463: 757-762. doi:10.1038/nature08835.
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Abstract

We report here the genome sequence of an ancient human. Obtained from ~4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single- nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

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