We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167-175,2018) and Thines et al. (IMA Fungus9: 177-183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with "false negatives" surpassing "false positives"; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as "nom. seq." (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.

中文翻译：

---

基于序列的命名法：对Thines等人的答复。和Zamora等。以及“从头开始”修改提案的条款，以允许将DNA序列作为名称的类型。

我们回复了基于序列命名法的反对者Zamora等人最近发表的两篇多论意见书。（IMA Fungus9：167-175，2018）和Thines等人。（IMA Fungus9：177-183，2018）。尽管我们同意这些作者提出的一些主要论点，但我们解决了误解，并证明这些论文中提出的某些假定证据已被错误地解释。我们不同意允许将序列作为类型​​从根本上改变类型的性质，因为在《守则》（第40.5条）中已经允许抽象特征作为类型的类似性质，即插图。我们还不同意引入人为分类单元的高风险，因为考虑到各种类型的高通量测序错误，这种风险可以量化为远低于5％。与表面上普遍的误解相反，基于序列的命名不能基于相似性的OTU及其共有序列，而必须使用严格的，基于多个比对的系统发育方法和定量的单标记物种识别算法（使用原始序列读取）得出; 因此，它在基于物理类型的单标记研究方法上是相同的，这是本规范允许的方法。我们认识到ITS作为单一真菌条形码标记的局限性，但指出这些导致了一种保守的方法，“假阴性”超过“假阳性”。基于序列的术语的理想功能。基于序列的命名法并非旨在准确解析物种，但是命名序列代表未知的真菌谱系，这样它们就可以作为一种交流手段，从而结束了填充在线存储库的未标记真菌序列呈指数增长的局面。由命名序列的参考文库获得的，跨越整个真菌多样性阵列的收获所带来的收益远远超过了风险。最后，除了修订提案的原始提案外，我们还详细制定了​​条款，以解决反对者对此方​​法提出的问题。尤其是，考虑到原核生物术语中无效的临时名称的假丝酵母状态的想法，我们提出了一个折衷方案，即允许以一致的方式有效发布无凭证，基于序列的名称，但必须指定为“ nom”。序列。” （nomen sequentiae）。此类名称将不优先于标本名称或文化名称，除非根据实际的基础名称进行严格的质量控制评估后，以物理类型进行了典型化或根据国际真菌分类学委员会的建议将其用于保护。根据既定规则或建议进行研究。