Sunday, January 22, 2006

Paleogenomics, the Future of Evolutionary Biology?

Last month, scientists sequenced 28 million base pairs of DNA from the genome of Mammuthus primigenius, this DNA was was found to be 98.5% sequence identical to that of Loxodonta africana. Interestingly, the wooly mammoth appears to have diverged from the Asian elephant more recently than Asian elephants and African elephants diverged from their common ancestor. All three shared a common ancestor about 5 to 6 million years ago.

The DNA from one sample, extracted from Mammoth bones frozen for 27,740 years in Siberia, was surprisingly intact and free of other (fungal, bacterial, or human) DNA contamination, indicating that it would be possible to sequence the entire nuclear genome of the woolly mammoth using such samples.

"To find the ideal sample and analytical approach for paleogenomics, we screened eight of the morphologically best preserved mammoth remains in the collections of the Mammoth Museum, a dedicated permafrost ice cave facility in the town of Khatanga in the southeastern part of the Taimyr Peninsula, Russian Federation, and maintained by Cerpolex/Mammuthus Expeditions (CME)."
Although ancient DNA such as this is always degraded due to breaks in the phosphodiester backbone of the DNA and chemical alterations of the DNA bases, the extreme conditions under which these mammoth bones were preserved, -10 C, slowed down the rate of chemical alteration and degradation of the DNA. Additionally, using PCR to amplify the DNA for sequencing would avoid some of the degraded DNA strands because they are unsuitable for complete amplification. This would allow the PCR reaction to selectively amplify the more intact molecules.

From the paper:
"Recently, a whole-genome approach was attempted from DNA of the extinct cave bear Ursus spelaeus, yielding È27,000 bp of endogenous genetic material from 1.1 to 5.8% of all DNA reads (29). We have produced 13 million bp of endogenous genetic material from 45% of all DNA reads, some 480 times as much DNA sequence and 15 times the percentage. The ability to obtain this level of genetic information from extinct species makes it possible to consider detailed analysis of functional genes and fine-scale refinement of mutation rates. A rapid identification assay of single nucleotide polymorphisms (SNPs) would be of great value for studying population genetics of Pleistocene mammals and plants, which in turn could help elucidate their responses to climate changes during late glacial and early postglacial time and ultimately shed new light on the cause and consequences of late Quaternary extinctions.

The woolly mammoth isn't the only extinct species whose genome is receiving such close attention. Initial experiments using nuclear DNA extracted from Cave Bear fossils, which are similar in age and preserved under similar conditions to Neanderthals, have suggested that a Neanderthal genome project might be successful.

The ability to reference ancient genomes as benchmarks would be a powerful tool for evolutionary biologist to study how species have changed over time, and perhaps to determine some of the genetic differences between us and our Neanderthal cousins that has allowed us to prosper while they perished.

Speaking of mammoths: This is an AWESOME fossil!

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Comments on "Paleogenomics, the Future of Evolutionary Biology?"

 

Blogger gaw3 said ... (2/02/2006 7:41 AM) : 

I have also seen a taxonomy of modern and fossil hyenas using the metagenomics approach. In that case, the extinct European cave hyenas were essentially identical to one of the two African species.

Very cool.

 

Blogger Moment of Science said ... (2/02/2006 2:33 PM) : 

Is this the one you're talking about?

http://email.eva.mpg.de/~paabo/pdf1/Rohland_Population_MBE_2005.pdf

Paabo's group at the Max Planck was also involved with that work. But it looks like they were looking at mitochondrial DNA in that paper rather than the nuclear genome. Mitochondrial DNA is a lot easier to find in those old bones because there was so much of it.

Thanks for stopping by.

 

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