Successful extraction of insect DNA from recent copal inclusions: limits and perspectives

Abstract

Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.

The significance of cephalopod beaks as a research tool: An update

“…Nevertheless, the use of the transparent part of the beak could be a limitation for these methodologies in smaller species in which the transparent part is reduced, as well as in beaks from predators' stomachs since the transparent part disappears with the action of the gastric acids (Clarke, 1986;Duffy and Jackson, 1986). Furthermore, we suggest trying different methodologies, including approaches that have been used to successfully extracted DNA from other difficult-to-handle issues e.g., Frontiers in Physiology frontiersin.org bones or fossils (Vecchione et al, 2009;Xavier et al, 2016;Campos and Gilbert, 2019;Modi et al, 2021).…”

Rapid and zero-cost DNA extraction from soft-bodied insects for routine PCR-based applications

“…The quantity of extracted DNA gradually decreased over time irrespective of the methods. The possible explanation for this gradual decline in yield and purity is the degradation of DNA over time [43,44]. The reduction in concentration and purity was faster in the case of rapid approaches than standard methods.…”

Comparison of DNA extraction techniques for the recovery of bovine DNA from fly larvae crops

“…Chitin can affect cell lysis; therefore, precautions, such as adding dithiothreitol (DTT), can be taken to reduce chitin content when extracting human DNA from fly larvae. 20,21 Also, the fat body of fly larvae and other insects contain lipids and other tissue that could inhibit PCR. 22,23 Along with potential inhibitors, preservation methods can also affect the recovery of human DNA.…”

“…An additional consideration for recovering host DNA is the presence of the insect cuticle, which contains chitin and lines the crop of fly larvae. Chitin can affect cell lysis; therefore, precautions, such as adding dithiothreitol (DTT), can be taken to reduce chitin content when extracting human DNA from fly larvae 20,21 . Also, the fat body of fly larvae and other insects contain lipids and other tissue that could inhibit PCR 22,23 .…”