Non-Destructive Sampling of Ancient Insect DNA

Abstract

BackgroundA 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 FindingsThe 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/SignificanceThe 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.

The ecology of environmental DNA and implications for conservation genetics

“…Although preservative ethanol is not an environmental sample per se, we note the work of Hajibabaei et al (2012) and others using nondestructive DNA sampling methods (e.g. Thomsen et al 2009) with excitement in the present section because of the potential for this eDNA-inspired method to enable genetic analysis of museum specimens and other archived samples from the past which may benefit contemporary conservation challenges and ecological understanding.…”

Real-Time Polymerase Chain Reaction For Detection Of Optimal Thermal Profile For DNA Templates From Air-Dried Insect Collection Material

“…Such types of samples should be analyzed several times to ensure the quality of the data. For some samples it is possible that PCR reliability may be enhanced, for example, by optimising the PCR profile, increasing the amount of template, using E. coli colonies or double PCR (Folmer et al, 1994;Thomsen et al, 2009;Gavarâne et al, 2011;Demeke et al, 2012). Real-time PCR could be used for samples that have low success of amplification, as it allows to control the reaction profile and to determine parameters associated with the effectiveness of reaction.…”

“…Molecular systematics involves many approaches in which phylogenetic relationships are included by using information from molecular sequences of the organisms under study (Lemey et al, 2009;Wiley and Lieberman, 2011). Nowadays, air-dried collection material is used for different studies of evolution, ecology and systematics (Krishtalka et al, 2000;Suarez & Tsutsui, 2004;Thomsen et al, 2009).…”

“…DNA extraction from ancient insects is limited by the destructive sampling methods, which may destroy important morphological characteristics. Many museum specimens have suffered from such sampling procedures, but there are several methods to obtain DNA by using non-destructive sampling methods (Rohland et al, 2004;Gilbert et al, 2007;Thomsen et al, 2009).…”

“…The universal primer pair LCO/HCO has been used in studies for several species using the mitochondrial DNA cytochrome oxidase I. The most popular primers for mitochondrial DNA genes are for specimens from air-dried collection materials (Gilbert et al, 2007;Thomsen et al, 2009). This might be because the amount of isolated mitochondrial DNA is higher than the amount of nuclear DNA from airdried collection material (Goldsen and DeSalle, 2003;Gavarâne et al, 2011).…”