Complete Neanderthal Mitochondrial Genome Sequenced
Thursday, 07 August 2008
A study reported in the August 8th issue of the journal Cell, a Cell Press publication, reveals the complete mitochondrial genome of a 38,000-year-old Neanderthal. The findings open a window into the Neanderthals past and helps answer lingering questions about our relationship to them.
"For the first time, we've built a sequence from ancient DNA that is essentially without error," said Richard Green of Max-Planck Institute for Evolutionary Anthropology in Germany.
The key is that they sequenced the Neanderthal mitochondria — powerhouses of the cell with their own DNA including 13 protein-coding genes — nearly 35 times over. That impressive coverage allowed them to sort out those differences between the Neanderthal and human genomes resulting from damage to the degraded DNA extracted from ancient bone versus true evolutionary changes.
Although it is well established that Neanderthals are the hominid form most closely related to present-day humans, their exact relationship to us remains uncertain, according to the researchers. The notion that Neanderthals and humans may have "mixed" is still a matter of some controversy. Analysis of the new sequence confirms that the mitochondria of Neanderthal’s falls outside the variation found in humans today, offering no evidence of admixture between the two lineages although it remains a possibility.
It also shows that the last common ancestor of Neanderthals and humans lived about 660,000 years ago, give or take 140,000 years. Of the 13 proteins encoded in the mitochondrial DNA, they found that one, known as subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain or COX2, had experienced a surprising number of amino acid substitutions in humans since the separation from Neanderthals.
While the finding is intriguing, Green said, it is not yet clear what it means.
"We also wanted to know about the history of the Neanderthal’s themselves," said Jeffrey Good, also of the Max-Planck Institute.
For instance, the new sequence information revealed that the Neanderthal’s have fewer evolutionary changes overall, but a greater number that alter the amino acid building blocks of proteins. One straightforward interpretation of that finding is that the Neanderthal’s had a smaller population size than humans do, which makes natural selection less effective in removing mutations. That notion is consistent with arguments made by other scientists based upon the geological record, said co-author Johannes Krause.
"Most argue there were a few thousand Neanderthals that roamed over Europe 40,000 years ago."
That smaller population might have been the result of the smaller size of Europe compared to Africa. The Neanderthals also would have had to deal with repeated glaciations, he noted.
"It's still an open question for the future whether this small group of Neanderthals was a general feature, or was this caused by some bottleneck in their population size that happened late in the game?" Green said.
Ultimately, they hope to get DNA sequence information for Neanderthals that predated the Ice Age, to look for a signature that their populations had been larger in the past. Technically, the Neanderthal mitochondrial genome presented in the new study is a useful forerunner for the sequencing of the complete Neanderthal nuclear genome, the researchers said, a feat that their team already has well underway and expected to be unveiled later this year.
The complete Neanderthal nuclear genome sequence, together with comparison with the great apes DNA sequences, many hope will reveal the key genetic changes that propelled the evolution of human behaviour.
A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing
Richard E. Green, Anna-Sapfo Malaspinas, Johannes Krause, Adrian W. Briggs, Philip L.F. Johnson, Caroline Uhler, Matthias Meyer, Jeffrey M. Good, Tomislav Maricic, Udo Stenzel, Kay Prüfer, Michael Siebauer, Hernán A. Burbano, Michael Ronan, Jonathan M. Rothberg, Michael Egholm, Pavao Rudan, Dejana Brajković, Željko Kućan, Ivan Gušić, Mårten Wikström, Liisa Laakkonen, Janet Kelso, Montgomery Slatkin, and Svante Pääbo
Cell, Vol 134, 416-426, 08 August 2008
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