Data from: Next-generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)

Historical museum specimens are invaluable for morphological and taxonomic research,
but typically the DNA is degraded making traditional sequencing techniques difficult to
impossible for many specimens. Recent advances in Next-Generation Sequencing, specifically
target capture, makes use of short fragment sizes typical of degraded DNA, opening up the
possibilities for gathering genomic data from museum specimens. This study uses museum
specimens and recent target capture sequencing techniques to sequence both Ultra-Conserved
Elements (UCE) and exonic regions for lineages that span the modern spiders, Araneomorphae,
with a focus on Palpimanoidea. While many previous studies have used target capture techniques
on dried museum specimens (for example, skins, pinned insects), this study includes specimens
that were collected over the last two decades and stored in 70% ethanol at room temperature. Our
findings support the utility of target capture methods for examining deep relationships within
Araneomorphae: sequences from both UCE and exonic loci were important for resolving
relationships; a monophyletic Palpimanoidea was recovered in many analyses and there was
strong support for family and generic-level palpimanoid relationships. Ancestral character state
reconstructions reveal that the highly modified carapace observed in mecysmaucheniids and
archaeids has evolved independently.

馆藏历史标本对于形态学与分类学研究而言具有不可估量的价值，但多数标本的DNA均已发生降解，使得传统测序技术难以甚至无法应用于此类材料。近年来下一代测序（Next-Generation Sequencing）技术的进展，尤其是靶向捕获（target capture）技术，可利用降解DNA特有的短片段特征，为从馆藏标本中获取基因组数据开辟了新的可能。本研究采用馆藏标本与新型靶向捕获测序技术，对涵盖现代蜘蛛类群新蛛亚目（Araneomorphae）的谱系开展超保守元件（Ultra-Conserved Elements, UCE）与外显子区域测序，研究聚焦于触形蛛总科（Palpimanoidea）。尽管此前诸多研究已将靶向捕获技术应用于干燥馆藏标本（如皮肤标本、针插昆虫），但本研究的标本采集于近二十年间，并以70%乙醇在室温条件下保存。本研究结果证实了靶向捕获方法在解析新蛛亚目内部深层系统发育关系中的应用价值：超保守元件与外显子基因座的测序数据均对系统发育关系的解析起到关键作用；多项分析均推断得到单系的触形蛛总科（Palpimanoidea），且该类群的科级与属级系统发育关系得到了强有力的支持。祖先性状状态重建结果显示，微螯蛛科（Mecysmaucheniidae）与古蛛科（Archaeidae）所特有的高度特化头胸部，是独立演化而来的。