We have specimens at home: efficacy comparison of methods for genomic DNA capture in fluid-preserved crayfish specimens

Jesse R. Wallace, Quinton M. Skelly, Bryan C. Carstens, Marymegan Daly. Natural History Collections and Museomics 3: e189111. DOI: 10.3897/nhcm.3.189111

Abstract

Fluid-preserved specimens housed in museums represent a wealth of potential genomic data. Historically, museum wet specimens have been difficult to use as a source for genomic DNA due to the damage that fixative mediums may cause to the DNA. In this study, we explore several methods for DNA extraction to evaluate their efficacy when applied to fluid-preserved specimens, considering yield of DNA and the quality of short-read sequences that result from the extractions. We evaluated these methods as well as specimen age and starting tissue mass on the axes of DNA yield and sequencing quality. We found that across extraction methods, as sample age increased, DNA yield was reduced. Starting sample mass had no significant effect on DNA yield. Lastly, although each extraction was capable of yielding sequences with accurate base calls, loci recovery was highly variable across our tested extraction methods. Our results demonstrate the viability of wet museum specimens as a source of genomic DNA when processed with extraction and sequencing methods that account for their unique characteristics.