Gene trouble
A POPULAR type of deoxyribose nucleic-acid (DNA) fingerprinting used by conservation biologists may give false results with some species of animals, say researchers in Germany. DNA fingerprinting is a fairly recent innovation that involves taking samples of an organism's genetic structure. Like the human fingerprint - which has a pattern unique only to that person - these genetic patterns, too, are characteristic of a particular organism. In the recent years, DNA fingerprinting has emerged as a popular identification method, employed for a wide range of purposes- from immigration monitoring to plant and animal conservation. However, in the past few months, there have been reports of how, contrary to the claims of geneticists the world over, DNA fingerprinting may not be as foolproof as was claimed. Now, the researchers have merely stumbled upon another factor that serves to question the efficacy of DNA fingerprinting once more.
There are two sources of DNA in animals: the nucleus of a cell, and the cell's powerhouse, the mitochondria.
Researchers usually resort to mitochon-drial fingerprinting when the genetic material in a sample is degraded, for while there are only two copies of each nuclear gene in a cell, there are often hundreds of copies of mitochondrial DNA (mtDNA).
In these circumstances, a technique called polymerese chain reaction (PCR) is used to enhance or "amplify" the undamaged strains of mtDNA so that these can be analysed. PCR analysis of mtDNA is being increasingly used to trace the relationships or numbers of animals in the wild. It is also used by forensic experts to pin down criminals.
However, Alex Greenwood and Svante Paabo of the University of Munich, Germany, came across a potential flaw in the fingerprinting technique while studying woolly mammoths. The team wanted to use tissue from hundreds of mammoth carcasses found in permafrost - a perennial layer of snow - to work out the relationships among the animals and compare these with their distant cousins, the modern-day elephants.
To begin with, they took hairs from an Asian elephant (Elephas maximus) at a nearby zoo and amplified a fragment of its mtDNA. But when the duo tried to sequence the products of the PCR, they found they were scrambled. "So we suspected we were dealing with a mixture," says Paabo. The suspicion was confirmed when they purified and sequenced individual DNA strands from the PCR. They found four different classes of sequence.
When the researchers looked at elephant blood, however, they found only one of the four sequence classes found in the hair. They also discovered that it was the only active sequence of mtDNA, implying that the other three found in the hair were fragments of mtDNA that had migrated to the nucleus during the early stages of evolution. This suggests that elephant hair has few mitochon dria, giving a high chance that PCK would amplify one of these "pseudo-genes", rather than the true sequence. Paabo points out that if no blood had been available for analysis - as is often the case in forensics or molecular ecology - it may have been impossible to sort out the true sequence.
Mitchell Holland, a DNA identification expert at the Armed Forces Institute of Pathology in Maryland, USA, says the finding highlights the great care that must be taken in analysing mtDNA data. "You cannot just get a PCR result and walk away from it," he says. However, he adds that nuclear pseudogenes are not a problem in human hair analysis. He says that researchers can recognise the sequences of mtDNA that have migrated to the nucleus, and that they rarely see them in their PCR reactions.
Paabo agrees that "contaminating" nuclear mtDNA sequences are possibly only an issue for particular tissues in particular animals. "Most sequences out there are probably fine," he says. "This is just a warning to people that you have to be aware of this possibility and be really careful." But his plans to map familial relationships of mammoths seem to have been scrapped. PCR amplification of mtDNA from hair of one of these ancient beasts reveals a variety of mito-chondrial sequences as confusing as that of their modern-day counterpart - the elephant.