Ancient Gene Yield: New methods retrieve Neandertals’ DNA

Welcome to the era of Neandertal genetics. Researchers announced this week that they have retrieved and analyzed a huge chunk of Neandertal DNA, covering more than 1 million of the roughly 3 billion* paired chemical constituents of an individual’s genetic makeup.

Until now, scientists had extracted small DNA segments from Neandertal bones, mainly from mitochondria outside cell nuclei (SN: 4/1/00, p. 213). Two new techniques have now recovered large amounts of genetic material from nuclei. One also permits tagging of ancient DNA sequences that correspond to modern human genes.

A team led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, presents results from the first new technique in the Nov. 16 Nature. A group directed by Edward M. Rubin of the U.S. Department of Energy Joint Genome Institute in Walnut Creek, Calif., describes results from the second technique in the Nov. 17 Science.

These new studies “foreshadow an exciting development—the recovery of the complete Neandertal genome,” comment David M. Lambert of Massey University in Auckland, New Zealand, and Craig D. Millar of the University of Auckland, in an editorial published with the Nature report. Pääbo and his colleagues expect to complete the genome within 2 years.

Pääbo’s team extracted DNA from a 38,000-year-old Neandertal fossil previously discovered in Croatia. Because of the conditions in the cave where the fossil was interred, it retained much DNA that could be analyzed.

In this new approach, unlike in traditional methods, DNA is sequenced directly from fragments. About 6 percent of sequences identified in this way were uncontaminated and presumed to be Neandertal DNA.

The scientists sorted the genetic material into appropriate chromosome locations by matching each fragment to similar sequences in human DNA.

The result indicates that humans diverged from Neandertals about 516,000 years ago. The investigators say that it will take additional sequencing of Neandertal DNA to determine whether that species interbred with Stone Age people.

Rubin’s group sequenced DNA from the same Croatian fossil using a method that makes many copies of DNA fragments by putting them into bacteria. The authors then used DNA sequences from people to identify corresponding Neandertal-DNA strands.

With this technique, the scientists identified 29 of 35 genes that they had targeted for recovery. Rubin and his coworkers place the evolutionary split of modern humans and Neandertals at around 370,000 years ago.

Another new genetic study, slated to appear in the Nov. 28 Proceedings of the National Academy of Sciences, suggests that modern humans and a closely related species, possibly Neandertals, occasionally interbred. Those contacts led to the spread in human populations of a particular gene that regulates brain size, contends a team led by geneticist Bruce T. Lahn of the University of Chicago.

Lahn’s team reported last year that this gene originated in people 37,000 years ago and now appears in 70 percent of the world’s population (SN: 9/24/05, p. 206). The new analysis indicates that Neandertals or some other now-extinct Homo lineage first possessed the gene about 1 million years ago and eventually passed it to Stone Age people.

Although the specific function of this gene remains unclear, it adds to growing genetic evidence of interbreeding among various lines of human ancestors within and outside Africa, remarks geneticist Michael F. Hammer of the University of Arizona in Tucson.

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* The online version of this sentence has been edited to correct an error.