Polymerase Chain Reaction Inhibition in Historical Fish Scale Mounting Cards

Abstract

In the case of Pacific salmon Oncorhynchus spp., as in that of other fish species, the ability to amplify specific DNA sequences from historical scale samples offers the opportunity to infer past population genetic structure and better understand how human activities may have changed natural populations. We extracted DNA from fish scales of various ages using two different methods and tested polymerase chain reaction (PCR) amplification of nuclear and mitochondrial products of various sizes. Our results provide further insight into some important limitations in working with historical DNA samples. We found evidence suggesting the presence of an inhibitory compound associated with the gummed scale collection cards that copurified with the DNA. Our results demonstrated that the putative inhibitory material was free in solution and not bound to the scale DNA. Long recognized in other genetic literature, PCR inhibition has only recently been reported in historical studies of fish. This paper provides the first detailed examination of the inhibition phenomenon and the first quantitative evaluation of DNA yield, sample dilution, and PCR success in the use of historical scale samples.