Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

Abstract The use of museum specimens held in natural history repositories for population and conservation genetic research is increasing tandem with the massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used markers wildlife studies. However, they traditionally suffered from a host issues including length homoplasy, high costs, low throughput, difficulties reproducibility across laboratories. Massively technologies can address these problems, but incorporation specimen derived DNA suffers significant fragmentation exogenous contamination. Combatting requires extra measures stringency lab during data analysis, yet there have not been any high-throughput studies evaluating allelic dropout extracted DNA. In this study, we evaluate genotyping errors mammalian skin extracts previously characterized microsatellites PCR replicates utilizing sequencing. We found it useful to classify samples based on concentration, which determined rate by genotypes were accurately recovered. Longer performed worse all specimens. Allelic rates loci dependent sample quantity, concentration performing as well recovering quality metrics nearly frozen tissue sample. Based our results, provide set best practices assurance reliable