Thursday, December 22, 2005

Mammoth Nuclear DNA says African Elephant, Mitochondrial DNA Says Asian

Okay, now I'm confused! I have posted on the Mammoth DNA study several times. One The articles I read stated that one of the conclusions was that Mammoths are more closely related to Asian elephants than African. Yet the story linked to above claims the exact opposite:

A mammoth was chosen for the study, in part, because of its close evolutionary relationship to the African elephant, whose nuclear DNA sequence has been made publicly available by the Broad Institute in Cambridge, Massachusetts (USA). Using comparisons with elephant DNA, the researchers identified 13-million base pairs as being nuclear DNA from the mammoth, which they showed to be 98.5 percent identical to nuclear DNA from an African elephant.

This, I hasten to point out, is a completely different study than the one I posted about previously. One obvious difference is that the first article used mitochondrial DNA while this one used nuclear DNA. I don't see how this would make a difference in basic results though. One of these studies has to be flawed...

At any rate here is what the Penn State (the mitochondrial DNA study was done by the Max Planck Institute)team did:

The project became possible through the discovery of exceptionally well preserved remains of a mammoth skeleton in the permafrost soil of northern Siberia, in combination with a novel high-throughput sequencing technique that could cope with the heavily fragmented DNA retrieved from the organism's mandible, its jaw bone. "The bone material used in this study is approximately 28,000 years old, as was shown by beta carbon dating analysis," said Hendrik N. Poinar, associate professor of anthropology at McMaster University. "This was a surprising finding, as it demonstrated that the analyzed material was frozen for more than 10,000 years before the maximum of the last ice age." The research team used a comparative computational approach to demonstrate that an unprecedented large percentage of the bone DNA was indeed mammoth DNA, while the remaining genetic material was shown to belong to microorganisms and plants living the tundra soil.
"Analyzing DNA from the organelles of mitochondria has been the only method of studying ancient DNA in the past, as it is more tractable due to its 1000-fold higher copy number per cell," Schuster explains. However, the mitochondrial genome codes for only a tiny fraction of an organism's genetic information -- 0.0006 percent in the case of a mammal. "We focused on sequencing nuclear DNA in this study because most hereditary information is organized on chromosomes located in the cell's nucleus," Schuster says.

The mitochondrial research appears in Nature and the Penn State research will appear in Science...

Added Later: Ahh, here is the explanation:

Poinar sent the DNA-rich sample to genomicist Stephan C. Schuster at Pennsylvania State University, University Park, who is working with a new genome sequencer developed by a team at Stanford University and 454 Life Sciences Corp. of Branford, Connecticut (Nature, 15 September, p. 376). This rapid, large-scale sequencing technology sidesteps the need to insert DNA into bacteria before amplifying and sequencing it. Instead, scientists break DNA into small fragments, each attached to a tiny bead and encapsulated by a lipid bubble where the DNA is multiplied into many copies for sequencing. Because each fragment is isolated before copying, the method avoids bias from copying large amounts of contaminant DNA from bacteria or humans.

The researchers were stunned by how well the method worked on ancient DNA, which is notoriously difficult to extract and sequence: "I would have been happy if we got 10,000 bases of mammoth DNA," said Poinar. Instead, they got 28 million basepairs, 13 million from the mammoth itself. Their preliminary analysis shows that the mammoth was a female who shared 98.55% of her DNA with modern African elephants. But mammoths were apparently closest kin to Asian elephants, as shown by Pääbo's mitochondrial study, which retrieved about 17,000 basepairs.

Apparently, both groups helped each other...