Sitting on my kitchen counter, atop a pile of junk mail I have yet to throw away, is the current issue (May 2009) of the National Geographic. Emblazoned in red letters are the words “Ice Baby: Secrets of a Frozen Mammoth” under the picture of an incredibly well preserved wooly mammoth baby. The feature article tells the story of “Baby Lyuba” a baby mammoth discovered in 2007 on the Yamal Peninsula in Siberia. A companion article focuses on the possibility of bringing extinct animals—like the mammoth— back to life.
This article heralds the sequencing of a large portion of the nuclear genome of the mammoth by a team from Pennsylvania State University led by Webb Miller and Stephan C. Schuster (1). A happy coincidence because I was working on a blog about this same subject. The idea of sequencing the genome of an animal that last walked this earth tens of thousands of years ago captures my imagination.
Why the Mammoth?
Wooly mammoths are ideal targets for ancient DNA studies because so many well-preserved remains have been found. Locked in the permafrost for thousands of years, they emerge like time capsules of tissue, bone and hair. And as it turns out, the hair could be the key to obtaining sequencing results with fewer damage-derived errors, the errors that often plague studies of DNA extracted from other ancient sources (2). DNA studies using hair samples suffer less from exogenous DNA contamination because hair samples can be subjected to highly efficient decontamination processes. Decontamination removes any exogenous DNA but leaves the endogenous DNA unharmed, well protected by the highly keratinized hair shaft (3).
In 2007, Gilbert and colleagues used DNA isolated from hair samples and a process called the sequence-by-synthesis method or 454 method (4; commercially developed by 454 Life Sciences) to successfully sequence the mitochondrial DNA (mtDNA) from 10 Siberian mammoths (Mammuthus primigenius) with up to 48-fold coverage (2). Most remarkably, they were able to isolate and sequence DNA from hair samples from the so called “Adams Mammoth”. This almost perfectly preserved permafrost mummy was discovered in 1799 and collected in 1806 (5). Hair from the mummy was collected in 1806 and has been stored at room temperature for the last 200 years.
From Mitochondrial DNA to the Nuclear Genome
Obtaining a sequence of a nuclear genome from ancient DNA, which is highly fragmented, had always seemed impossible. The mitochondrial genome of the mammoth is relatively small (~16,770bp); however, the nuclear genome of the mammoth is estimated to be 4.2 to 4.8Gb in size (that’s 4 to 5 billion bases), based on estimates of the elephant genome size (1). Traditional large-scale sequencing (6) produces sequences of up to 800 bases from a single reaction, whereas the method described by Margulies et al (4) can produce up to 10 billion base pairs in a single run. The difference is that these are all in rather short sequence reads (as little as 30bp). This “shotgun” approach can have a high rate of error. Therefore, to get a reliable sequence, each nucleotide position needs to be sequenced multiple times (7). Miller and colleagues (1) suggest the mammoth sequence would need 10–20-fold coverage for reliable results to be obtained.
The Penn State team used DNA isolated from the hair of two mammoth mummies for their nuclear sequencing project. One mummy was ~20,000 years old, and the other was over 60,000 years old. They produced 4.7Gb of sequence and estimate that 80% of it is from mammoth. They obtained 0.7-fold coverage, suggesting that the total length of their genome read is 70% of the genomes length. This estimation is, however, based on a rough approximation (1).
So what can we learn from sequencing a mammoth? Stephen C. Schuster says they already know that the individual mammoths were so genetically similar to each other that they would have been highly susceptible to disease, climate change and perhapse even humans (8). By comparing the mammoth sequence to that of the present-day elephant, they may be able to identify genetic causes for some of the mammoth’s unique characteristics, like their adaptation to cold, and perhaps even for their extinction.
Today the Mammoth, Tomorrow the Neanderthal?
The work done by the Penn State team opens up a new horizon for science. If we can isolate and sequence DNA from ancient hair that has been stored at room temperature for the past 200 years, then every musty animal skin stored in museums around the world becomes a potential gold mine of information. Imagine being able to study the genes of animals long since extinct. What might we learn about why one species survives and another doesn’t?
Finally, using the 454 method of sequencing means that badly fragmented or degraded ancient DNA, such as that isolated from bone fragments, might now yield useable sequences. This is illustrated by the February announcement by team of scientists in Germany that they had sequenced the entire genome of a 38.000-year-old Neanderthal (9). Almost all of the genome comes from DNA isolated from a single bone that was discovered in a cave in Croatia. An entire genome from a single, 38,000-year-old bone— it seems that the mammoth may have been just the tip of the iceberg.
- Miller, W. et al. (2008) Nature 456, 387–90.
- Gilbert, M.T. et al. (2007) Science 317, 1927–30.
- Glibert, M.T. et al. (2006) Forensic Science International 156, 208–12.
- Margulies, M. et al. (2005) Nature 437, 376–80.
- Tolmachoff (1929) Siberia Trans. Am. Phils. Soc. 23, 1
- Sanger, F., Nicklen, S. and Coulson, A.R. (1977) Pcroc. Natl Acad. Sci USA 74, 5463–7
- Hofreiter, M. (2008) Nature 456, 330-31
- Science Centric News, 19, Nov 2008
- Dalton, R. (2009) Nature 457, 645.
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