Fossil DNA.

Abstract

Also known as… ancient DNA. The New Shorter Oxford Dictionary offers the precise explanation of ‘ancient’ as ‘belonging or pertaining to the period before the fall of the Western Roman Empire in AD 476.’ DNA can be recovered from fossils much older than 1500 years, but the inevitable time-dependent decay of the DNA structure due to oxidation and hydrolysis makes retrieval increasingly difficult with age. How is it recovered? The advent of the polymerase chain reaction (PCR) allowed for amplification and sequencing of the minute amounts of DNA fragments sometimes found in fossils. DNA is better preserved in ancient bones than in soft tissues and multicopy mitochondrial DNA is more easily recovered than nuclear DNA; some fascinating sources have been used. So what is possible? The oldest authentic samples are short sequences of 100–250 nucleotides from Neandertal and mammoth fossils, which had remained in a cold environment for 40,000–100,000 years. Low temperature slows the DNA decay process. But hasn’t dinosaur DNA been reported? Attempts in many laboratories to isolate DNA from dinosaur bones and other antediluvian sources have yielded nothing but modern contaminants. As late as April 2000, one of the major scientific journals contained as a News item a breathless account on the similarity between retrieved dinosaur DNA and bird DNA, starting “They said it couldn’t be done. But …” Scientists at University of Alabama sequenced a 130-nucleotide long mitochondrial DNA sequence from dinosaur vertebrae, and found that it was 100% homologous to mitochondrial DNA from turkeys. However, the scientists themselves “remain quite sceptical of our own work” and noted that they had been consuming turkey sandwiches in the laboratory. Are there other such reports? Unfortunately, yes. Insects entombed in amber are a perennial favourite. A 1996 paper in the same journal from another group described how a piece of amber containing an insect was cracked open over an agar plate. Subsequently, a yeast colony grew out on the plate, which was interpreted as a Jurassic yeast, and therefore published. So how do you avoid contamination problems? Fossils are regularly contaminated with present-day DNA. For this reason, it seems difficult to be certain of DNA purported to come from, for example, ancient bacteria in fossil glacier ice, primitive human tribes, or other likely antecedents of extant modern species. Extinct animals with a good taxonomic record offer a safer source. Svante Pääbo’s group in Leipzig has set the standards for everybody else by their meticulous and highly credible work. What extinct species have been analyzed? The most archaic are mammoths, which turn out, not surprisingly, to have had DNA more similar to that of elephants than other big mammals. Being more reminiscent of Asian than African elephants also fits with the known geographic distribution of mammoths. Another well studied example is the giant ground sloth, which was eradicated in connection with the human invasion of Latin America 11,000 years ago. Interesting, but are there any revelatory scientific achievements in this field? Yes. Palaeontologists had been unable to agree from the fossil record whether Neandertals were a separate species or direct precursors of humans. Isolation and sequencing of DNA from Neandertal bones over the last couple of years has shown that those anthropologists were right who subscribed to the former hypothesis. Note that the palaeontologists continue their skirmishes just as before, essentially ignoring the new molecular evidence. Can the complete genome of a Neandertal be sequenced? Possibly, although it would be very difficult to recover all single-copy nuclear DNA sequences, and fossils are scarce. Also, the DNA fragments are so short that it would be a major computing task to assemble all those bits into a correct sequence. Can ancient DNA be repaired? Some base damage could most likely be corrected, offering modest quality improvement. But the main problem is extensive fragmentation of very old DNA by double-strand breaks, apparently occurring as a consequence of prolonged drying. Don’t say… ‘We have found a frozen mammoth and intend to clone it’ Do say… ‘From DNA sequencing we now have irrefutable evidence that Neandertals represented a distinct species, different from humans.’ Where can I find out more? Greenwood AD, Capelli C, Possnert G, Pääbo S: Nuclear DNA sequences from late pleistocene megafauna.Mol Biol Evol 1999, 16:1466-1473. Höss M: Neanderthal population genetics.Nature 2000, 404:453-454. Kimberly KO, Robertson HM: Ancient DNA from amber fossil bees?Mol Biol Evol 1997, 14:1075-1077. Willerslev E, Hansen AJ, Christensen B, Steffensen JP, Arctander P: Diversity of Holocene life forms in fossil glacier ice.Proc Natl Acad Sci USA 1999, 96:8017-8021.