Complete Neanderthal Mitochondrial Genome Sequenced From 38,000-year-old Bone

"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 Neanderthals 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's not yet clear what it means.

"We also wanted to know about the history of the Neanderthals themselves," said Jeffrey Good, also of the Max-Planck Institute. For instance, the new sequence information revealed that the Neanderthals 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 Neanderthals 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.

This research was reported in the August 8th issue of the journal Cell, a Cell Press publication.

The researchers include Richard E. Green, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Anna-Sapfo Malaspinas, University of California, Berkeley, CA; Johannes Krause, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Adrian W. Briggs, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Philip L.F. Johnson, University of California, Berkeley, CA; Caroline Uhler, University of California, Berkeley, CA; Matthias Meyer, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Jeffrey M. Good, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Tomislav Maricic, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Udo Stenzel, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Kay Prüfer, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Michael Siebauer, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Hernán A. Burbano, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Michael Ronan, 454 Life Sciences, Branford, CT; Jonathan M. Rothberg, The Rothberg Institute for Childhood Diseases, Guilford, CT; Michael Egholm, 454 Life Sciences, Branford, CT; Pavao Rudan, Croatian Academy of Sciences and Arts, Zagreb, Croatia; Dejana Brajkovic, Croatian Academy of Sciences and Arts, Institute for Quaternary Paleontology and Geology, Zagreb, Croatia; Željko Kucan, Croatian Academy of Sciences and Arts, Zagreb, Croatia; Ivan Gušic, Croatian Academy of Sciences and Arts, Zagreb, Croatia; Mårten Wikström, University of Helsinki; Liisa Laakkonen, University of Helsinki; Janet Kelso, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Montgomery Slatkin, University of California, Berkeley, CA; and Svante Pääbo, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany.