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

毫无疑问，分子数据在系统分类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，由于回忆起新鲜的材料并不总是可行的，例如在濒危物种或深海谱系的情况下，一些分支仍然无法用分子方法来研究。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会有问题。在处理保存在自然史收藏中的字型材料时，确保正确的赋值。但是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如何从博物馆收藏的百年历史的材料中提取大量的遗传数据（整个线粒体基因组和“超保守”元素）（“博物馆组学”）。螺螺肌动物（或新门形动物）是一个小的，被忽视的软体动物类，有争议的系统发育位置，对理解早期软体动物的进化至关重要。它们主要分布在深海，对其物种多样性的了解仍然很少。由于分类学过程庞大且耗时，需要进行组织学切片，以及为科级及科级以上的鉴定需要准备孔道和巩膜，因此大多数新收集的材料仍未得到鉴定。因此，它们增强我们对深海多样性、分布模式和生物相互作用的理解的潜力在很大程度上被忽视了。本研究旨在通过使用基于ngs的“博物馆组学”，通过目标捕获所有264个有效物种的线粒体标记（理想情况下是整个线粒体基因组）和“保守元件”或核基因组的类型材料，重振螺线管属的分类学。我们将选择一系列快速进化的标记，比较执行分子物种描述的树和成对距离方法，以测试传统的、主要基于硬体的分类方法。在分子和形态数据之间矛盾的证据线的情况下，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。这一整合的物种描述将被第一次对螺螺肌系系统关系的全面系统基因组分析所补充，最终导致这一蠕虫软体动物分支的全面更新分类。螺线管“博物馆组学”将为大规模应用从保存在自然历史收藏品中的旧类型材料中捕获DNA提供经济高效的展示，这些材料既不能通过传统的形态特征分类方法可靠地获取，也不能通过经典的条形码进行分类。建立的多位点条形码文库将为今后的生物多样性研究提供可靠的新谱系识别和描述，同时为林奈系统提供一个良好的分子分类学基础。

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.