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Sequencing Study Finds Amber-Preserved Insects Contain No DNA

NEW YORK (GenomeWeb News) – Insects trapped in an amber precursor contained no endogenous DNA, University of Manchester researchers reported in PLOS One yesterday, a finding that counters previous claims that such DNA could be successfully extracted and could potentially be used in a Jurassic Park-style re-creation of extinct animals.

Studies dating back to the 1990s had indicated that DNA could be PCR-amplified from amber-ensconced specimens, an idea that captured the imagination of many. Indeed, in both the 1990 book by Michael Crichton and the subsequent 1993 movie from Universal Pictures, the dinosaurs of Jurassic Park were resurrected by recovering dinosaur DNA from the guts of biting insects that had fed on dinosaurs before being swallowed themselves by tree resin and preserved as amber.

"Intuitively, one might imagine that the complete and rapid engulfment in resin, resulting in almost instantaneous demise, might promote the preservation of DNA in a resin-entombed insect," the researchers noted in their new paper. "Within this protective environment, DNA preservation might be better than in an air-dried museum specimen."

Recent studies, though, have called those early findings into question, suggesting that what was actually amplified were modern DNA contaminants.

For this study, Terry Brown, a professor at Manchester, and his colleagues turned to next-generation sequencing to try to detect DNA in preserved insects, arguing that such an approach would be less swayed by modern contaminants.

"[PCR] will preferentially amplify any modern, undamaged DNA molecules that contaminate an extract of partially degraded ancient ones to give false-positive results that might be mistaken for genuine ancient DNA," Brown said in a statement. "Our approach, using next-generation sequencing methods is ideal for ancient DNA because it provides sequences for all the DNA molecules in an extract, regardless of their length, and is less likely to give preference to contaminating modern molecules."

To see whether such preserved insect samples could house DNA, Brown and his colleagues examined two stingless bees, Trigonisca ameliae, that were encased in copal, the sub-fossilized resin precursor of amber. One sample was approximately 60 years old while the other was about 10,600 years old.

In the ancient DNA facility at Manchester, the researchers removed the samples from the resin and prepared them for sequencing. Both non-destructive and destructive extracts were taken from each sample.

The samples were then sequenced using the Roche GS Junior 454 System.

Read numbers for all samples were low, the researchers reported. For example, the younger specimen yielded 30 reads with an average length of about 50 nucleotides and 460 reads with a 100-nucleotide average length for the non-destructive and destructive preparation methods, respectively.

Brown and his colleagues searched all the reads they generated against Blast and Megan4, a metagenome analyzer, finding a limited number of hits. For the younger sample, two hits were found for the non-destructive extract and eight for the destructive extract. None were to stingless bees, though one 76-nucleotide long read aligned with non-contiguous portions of the mitochondrial cytochrome oxidase subunit I gene of Bombus hypocrita, the East Asian bumblebee. Reads from the older specimen appeared to all be artifacts.

"We were unable to obtain any convincing evidence for the preservation of endogenous DNA in either of the two copal inclusions that we studied," the researchers said.

The investigators argued that their negative results could not be attributed solely to a lack of technical skill as they have successfully isolated and sequenced ancient Mycobacterium tubercolosis DNA from human bones as well as DNA from archaeological plant samples, nor to their extraction and preparation methods as those approaches have been used to isolate DNA from air-dried specimens.

"We therefore conclude that our failure to obtain sequence reads was because the copal specimens contained no preserved DNA," Brown and his colleagues said.

First author David Penney noted that "unfortunately, the Jurassic Park scenario must remain in the realms of fiction."