The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (“mgDNA”) from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these ‘dark taxa’ or ‘dark matter fungi’ that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

中文翻译：

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我们可以使用环境DNA作为全型吗？

有效命名从环境标本中检测到的DNA序列的优缺点目前是真菌学界的热门话题。考虑到可以提供的“暗类群”或“暗物质真菌”中知识的扩展，使用环境样品中的细胞内DNA（“ mgDNA”）作为完整型的想法似乎是一个好主意。基于序列的分类单元，没有物理标本和正式的命名法）。但是，将mgDNA用作全型的局限性需要仔细考虑，即我们是否可以使用一个短的mgDNA片段（该片段可能包含少量的遗传信息）来区分物种？为mgDNA赋予有效的科学名称有什么意义？潜在的问题是什么？许多真菌学家和分类学家，谁拥有多年从事不同真菌分类和系统发育研究的经验，他们担心为mgDNA提供有效名称的后果。通过几篇出版物，关于使用mgDNA作为全型的重大问题已经引起了很多争论。支持者们试图辩论使用mgDNA作为全型的优点。反对者表明，使用mgDNA进行物种鉴定在许多真菌类中不起作用，而反对者则表明可以使用mgDNA鉴定物种。不同学科对于使用mgDNA作为全型有不同的理由和见解，但是即使是同一学科的团体也有不同的想法。在本文中，我们探索了mgDNA作为全型的用途。我们根据自己的经验提供有关将mgDNA用作全型的证据和见解。我们决不会试图破坏对环境样本中DNA的研究以及将知识扩展到黑暗分类中的方法，而是将这些问题与真菌分类法联系起来。实际上，我们展示了使用这些方法中的序列数据处理已命名的分类单元，分类单元编号和生态角色的发现的价值。我们讨论了使用环境样品中的mgDNA作为全型的优势和陷阱。还讨论了扩展命名法概念以允许使用来自环境样品的mgDNA作为全型的影响。我们从以下案例研究中提供证据 在处理已经命名的分类单元，分类单元编号和生态角色方面的发现。我们讨论了使用环境样品中的mgDNA作为全型的优势和陷阱。还讨论了扩展命名法概念以允许使用来自环境样品的mgDNA作为全型的影响。我们从以下案例研究中提供证据 在处理已经命名的分类单元，分类单元编号和生态角色方面的发现。我们讨论了使用环境样品中的mgDNA作为全型的优势和陷阱。还讨论了扩展命名法概念以允许使用来自环境样品的mgDNA作为全型的影响。我们从以下案例研究中提供证据葡萄球菌，炭疽菌，青霉和Xylaria。案例研究表明，由于mgDNA的短片段以及目前大多数ITS序列数据来自环境测序这一事实，我们无法使用mgDNA。我们从证据中得出结论，在命名真菌物种时，非常不希望使用mgDNA作为全型。如果采用这种方法，将导致许多问题，由于可用于整型的序列数据有限，无法确认物种识别。我们还提出了一种用于命名基于DNA的物种的基于DNA的替代系统，该系统所产生的问题要少得多，应该采用。