Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

中文翻译：

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用于群体基因组学的福尔马林固定组织和等位酶上清液的基因组文库制备和杂交捕获以及结合捕获和基于 RADseq 的单核苷酸多态性数据集的考虑

直到最近，许多历史博物馆标本在很大程度上无法进行基因组调查，但高通量测序 (HTS) 方法使研究人员能够成功地从干燥和液体保存的博物馆标本中对基因组 DNA 进行测序。除了保存的标本外，许多博物馆还收藏了大量的等位酶上清液样本，但尚未评估这些样本对 HTS 的适应性。在这里，我们比较了使用来自 10 个春蝾螈（Plethodontidae： Gyrinophilus porphyriticus）样本的基因组 DNA 替代来源的目标捕获方法的性能) 1985 年至 1990 年间收集的：等位酶上清液、等位酶匀浆颗粒和福尔马林固定的组织。我们设计了基于双酶切限制性位点相关测序 (RADseq) 衍生基因座的捕获探针，这些位点来自可用于 7 个样本的冷冻血液样本，并评估了捕获和 RADseq 方法的成功和一致性。该研究设计能够直接比较系统基因组和群体基因组分析的不同数据集之间的数据质量和潜在偏差。我们发现，在系统发育分析中，给定标本的所有富集类型都聚集在一起。在主成分空间中，所有基于捕获的样本都聚集在一起，但 RADseq 样本没有与相应的基于捕获的样本聚集在一起。单核苷酸多态性调用平均为 18。给定个体的富集类型之间有 3% 的差异，但这些差异主要是由于杂合/纯合单核苷酸多态性调用的差异。我们证明了等位酶上清液和福尔马林固定的样本都可以成功地用于群体基因组分析，我们讨论了识别和减少与捕获和 RADseq 数据结合相关的偏差的方法。