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8 January 2011
Recovering ancient DNA from Homo floresiensis' teeth

Scientists are planning an attempt to extract DNA from the 'hobbit' Homo floresiensis, the 1-metre-tall extinct distant relative of modern humans that was unearthed in Indonesia, following a study that suggests problems in standard sampling methods in ancient-DNA research could have thwarted previous efforts.
     Geneticists at the Australian Centre for Ancient DNA (ACAD) at the University of Adelaide hope to recover DNA from a roughly 18,000-year-old H. floresiensis tooth, which was excavated in 2009 from the Liang Bua site on the Indonesian island of Flores. The premolar has been kept cold, and has been handled as little as possible to prevent contamination with modern DNA. But little, if any, of the ancient DNA is likely to have survived the heat and moisture of the tropics, and any that has may be highly fragmented. Five years ago, two teams attempted to recover DNA from another H. floresiensis tooth excavated in 2003. Both attempts failed.
     If the DNA can be extracted, comparing its sequence to that of other species could settle disputes over classification. For instance, Peter Brown, a palaeoanthropologist at the University of New England in Armidale, Australia, who described and named the species in 2001, is rethinking his initial classification. At first he put the species in the human genus Homo, but he now suspects that the hobbit's ancestors left Africa before Homo evolved so the species could belong to a different or new genus.
     A team led by Christina Adler, a geneticist at ACAD, compared the impacts of various sampling techniques on DNA from the mitochondria of 40 human specimens from around the world, which had been dated up to 7,500 years old. Most genetics research on ancient teeth has focused on the inner tooth tissue, dentine, but Adler's team found that cementum, the coating of the root, was a richer source of DNA. Adler's team found also that the heat generated at standard drill speeds of more than 1,000 revolutions per minute (RPM) destroys DNA rapidly, causing yields to be up to 30 times lower than for samples pulverized in a mill. Reducing the drill speed to 100 RPM alleviated the problem.
     Matthew Collins, a specialist in ancient-protein analysis who is based at the University of York, UK, says that Adler's team's results will "help to ensure that we minimize the destruction of molecules during sampling of precious fossils, and potentially enable us to reach even further back in time to recover sequence information". However, he is pessimistic about the chances of winkling DNA out of H. floresiensis, saying that the molecules are probably too fragmented owing to high temperatures at the excavation site.
     But the ACAD scientists think that it is worth making an attempt on their H. floresiensis tooth and they will target cementum in their next attempt.
     
Source: Nature News (5 January 2011)

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