The potential of 'museomics' to revitalize taxonomy - a case study on aplacophoran Mollusca

毫无疑问，分子数据在系统学中对于检验已建立的系统发育假说和描述物种的价值。然而，有些分支仍然无法用分子方法，因为回忆新鲜材料并不总是可行的，例如濒危物种或深海谱系。根据现有的分类学知识，正确地将新标本分配给有效物种可能是有问题的。在处理自然历史收藏品中储存的模式标本时，正确的分配是有保证的。但储存的遗传资源仍然没有得到充分利用，尽管最近的开创性研究成功地证明了大量的遗传数据（整个线粒体基因组和“超保守”元素）可以从博物馆收藏的百年类型材料中提取（“博物馆组学”）。管腹目（或称Neomeniomorpha）是软体动物门中一个被忽视的小类，其系统发育位置存在争议，对理解早期软体动物的进化至关重要。主要分布在深海，对其物种多样性的了解仍然很少。由于庞大而耗时的分类过程需要组织切片以及齿舌和巩膜的准备，以确定科的水平和超越，大多数新收集的材料仍然无法识别。因此，它们在加强我们对深海多样性、分布模式和生物相互作用的了解方面的潜力在很大程度上仍然被忽视。本研究旨在通过使用基于NGS的“museomics”通过靶向捕获线粒体标记（理想情况下是整个线粒体基因组）和“保守元件”或来自所有264个有效物种的类型材料的核基因组来振兴Solenogastres的分类学。我们将选择一系列快速进化的标记，并比较执行树和成对距离的分子物种划分方法，以测试传统的，主要是基于巩膜的分类。在分子和形态学数据之间存在矛盾的情况下，我们将使用现代组织学和超微结构方法重新研究显微解剖学。这一综合性的物种划分将补充第一次全面的基因组学分析的系统关系的Solenogastres，最终导致一个整体更新的分类学这支蠕虫软体动物。Solenogaster 'museomics'将作为一个具有成本效益的展示大规模应用的DNA杂交捕获旧类型的材料存储在自然历史收藏的分支，其分类既不能可靠地通过传统的分类学通过形态特征，也不能通过经典的条形码。建立的多位点条形码库将有助于在未来的生物多样性研究中可靠地识别和描绘新的谱系，同时提供一个基于林奈系统的分子分类学。

There is no doubt about the value of molecular data in systematics for testing established phylogenetic hypotheses and delineating species. Yet some clades remain inaccessible to molecular approaches, as recollection of fresh material is not always feasible, e.g. in the case of endangered species or deep-sea lineages. And depending on the available taxonomic knowledge, correctly assigning new specimens to valid species can be problematic. Correct assignment is assured when dealing with type material stored in natural history collections. But stored genetic resources remain underutilized despite recent pioneering studies which successfully demonstrate how vast amounts of genetic data (entire mitochondrial genomes and 'ultraconserved' elements) can be extracted from century-old type material stored in museum collections ('museomics'). Solenogastres (or Neomeniomorpha) form a small, neglected class of Mollusca with controversial phylogenetic placement and a crucial importance to understanding early molluscan evolution. Distributed mainly in the deep sea, knowledge of their species diversity remains scant. And due to a bulky and time-consuming taxonomic process requiring histological sectioning as well as radula and scleritome preparation for identification to family level and beyond, the majority of the newly collected material stays unidentified. Consequently, their potential to enhance our understanding of diversity, distribution patterns and biological interactions in the deep sea remains largely neglected. This study aims to revitalize the taxonomy of Solenogastres through the use of NGS-based 'museomics' via target capture of mitochondrial markers (ideally entire mitochondrial genomes) and 'conserved elements' or the nuclear genome from type material of all 264 valid species. We will select a range of fast-evolving markers and comparatively perform tree and pairwise-distance methods of molecular species delineation to test traditional, largely scleritome-based taxonomy. In the case of contradicting lines of evidence between molecular and morphological data, we will reinvestigate the microanatomy using modern histological and ultrastructural approaches. This integrative species delineation will be supplemented by the first comprehensive phylogenomic analyses on the systematic relationship of Solenogastres, ultimately leading to an overall renewed taxonomy of this clade of worm-molluscs. Solenogaster 'museomics' will serve as a cost-efficient showcase for the large-scale application of DNA hybridization capture from old type material stored in natural history collections for clades, whose taxonomy can neither be reliably accessed through traditional taxonomy via morphological characters nor through classical barcoding. The established multi-loci barcoding-library will serve to identify and delineate novel lineages in future biodiversity research reliably, while providing a molecular taxonomy well founded in the Linnaean System.