Data_Sheet_2_Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study.xlsx

Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.

博物馆基因组学（museomics）领域的进展，推动了自然历史馆藏（Natural History Collections, NHCs）的高采样需求，最终对用于解析历史生物多样性的珍贵资源造成了损害。因此，就何种历史组织为最佳DNA来源达成共识至关重要。本研究针对伊比利亚狼的自然历史馆藏样本，评估了不同历史组织在全基因组分析中的表现。我们选取了哺乳动物食肉动物传统标本剥制术中常用的三种组织：骨骼（下颌骨与股骨）、鼻甲骨以及皮肤。具体而言，我们对1912年至2005年间采集的103份样本，分别开展了鸟枪测序，以及针对从商业犬类高密度芯片（Canine HD BeadChip）中筛选出的10万个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）的靶向捕获富集实验。不同组织的表现通过以下三类指标进行评估：内源DNA含量、捕获后唯一高质量比对读数数量，以及富集比例。所有样本均可作为合格的DNA来源，不受采集年份或样本类型的影响。皮肤样本的内源DNA含量显著高于两种骨骼组织，而两种骨骼组织的内源DNA含量相当。未发现组织类型对捕获效率存在直接影响；然而，基因分型的单核苷酸多态性数量与起始内源DNA含量严格相关。针对不同组织类型在不同最低测序深度下的基因分型准确率评估显示，整体基因分型错误率始终维持在较低水平（<7%），即便在3×低覆盖度条件下亦是如此。我们建议，在哺乳动物食肉动物的全基因组测序及靶向捕获富集实验中，可采用皮肤作为可靠且破坏性极小的内源DNA来源。此外，我们开发了一款全新的10万SNP捕获芯片，该芯片针对历史DNA（historical DNA, hDNA）进行了验证，可与用于高质量DNA样本的犬类高密度芯片兼容。随着自然历史馆藏作为DNA来源的需求日益增长，应推动生成可在不同研究间进行横向比较的基因组数据集。