Non-destructive sampling of ancient insect DNA

TY - JOUR

T1 - Non-destructive sampling of ancient insect DNA

AU - Thomsen, Philip Francis

AU - Elias, Scott

AU - Gilbert, Tom

AU - Haile, James

AU - Munch, Kasper

AU - Kuzmina, Svetlana

AU - Froese, Duane G

AU - Sher, Andrei

AU - Holdaway, Richard N

AU - Willerslev, Eske

N1 - Keywords: Animals; DNA; Fossils; Insects; Polymerase Chain Reaction; Species Specificity

PY - 2009

Y1 - 2009

N2 - BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago -- an alternative approach that also does not involve destruction of valuable material. METHODOLOGY/PRINCIPAL FINDINGS: The success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA) fragments of 77-204 base pairs (-bp) in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.

AB - BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago -- an alternative approach that also does not involve destruction of valuable material. METHODOLOGY/PRINCIPAL FINDINGS: The success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA) fragments of 77-204 base pairs (-bp) in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.

U2 - 10.1371/journal.pone.0005048

DO - 10.1371/journal.pone.0005048

M3 - Journal article

C2 - 19337382

SN - 1932-6203

VL - 4

SP - e5048

JO - PLoS Computational Biology

JF - PLoS Computational Biology

IS - 4

ER -