Comparison and optimization for DNA extraction of archived fish specimens

Abstract

The DNA extracted from museum alcohol-fixed specimens can be a valuable source of information for solving taxonomic, phylogenetic, ecological and conservational questions. However, this type of DNA, also called ancient DNA, is routinely obtained in small portions and highly fragmented. We have tested two different extraction kits in museum type-specimens of the fish family Characidae. Aiming to increase the DNA yield, we made modifications on a Qiagen manufacturer protocol, in the elution step. Also, to overcome the issue of DNA fragmentation, we applied our efforts in Sanger sequencing, to find a highly variable and, in result, informative COI fragment. Based on our results, there is no correlation between amount of the DNA extracted and the age of the sample. The Sanger sequencing generated sequences which are useful in solving taxonomic puzzles. Here are presented the customization and guidelines that allowed us to recover DNA from the archived fish specimens. • DNA extraction from archived fish specimens is more effective when using silica columns. • Change of the elution times from minutes in room temperature to 24 h in freezer greatly improved the DNA yielded. • Short but highly variable sequences replace the need to sequence the entire gene to identify a species. Method name: DNA extraction for museum fish specimens, Keywords: Ancient DNA, Sanger methodology, Neotropical fish, Museum specimens, Characidae