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

随着大规模平行测序技术的使用，自然历史资料库中保存的博物馆标本用于种群和保护遗传研究的情况正在增加。短串联重复序列 (STR) 或微卫星位点是野生动物和种群遗传研究中常用的遗传标记。然而，它们传统上受到许多问题的困扰，包括长度同质性、高成本、低通量以及跨实验室重现性困难。大规模平行测序技术可以解决这些问题，但博物馆标本衍生 DNA 的掺入会遭受严重的碎片化和外源性 DNA 污染。解决这些问题需要在实验室和数据分析过程中采取额外的严格措施，然而，还没有任何高通量测序研究评估博物馆标本提取的 DNA 中微卫星等位基因丢失。在这项研究中，我们利用高通量测序评估了先前表征的微卫星的哺乳动物博物馆皮肤 DNA 提取物的基因分型错误。我们发现根据 DNA 浓度对样本进行分类很有用，这决定了准确恢复基因型的比率。更长的微卫星在所有博物馆标本中表现更差。跨位点的等位基因丢失率取决于样本数量，高浓度博物馆标本的表现与冷冻组织样本一样高，恢复的质量指标几乎与冷冻组织样本一样高。根据我们的结果，