There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, 'hijacking' species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.

中文翻译：

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基于序列的无凭证真菌的正式描述：承诺和陷阱，以及如何解决它们。


鉴于环境测序已在序列读取存档中积累了超过 10 亿真菌 ITS 读取，大约是 GenBank 中真菌 ITS 序列的 1,000 倍，因此迫切需要基于序列的无凭证真菌的正式命名法。这些未命名的真菌可以帮助缩小目前已接受的 115,000 至 140,000 种真菌与预测的 2.2 至 380 万种真菌之间的差距，而使用标本或基于培养物的库存实际上无法填补这一空白。该守则从未旨在对分类学所选择的字符的性质进行限制，而对物理类型的要求现在正在成为科学进步的限制。我们详细阐述了基于序列的命名法的前景和陷阱，并为真菌学界的主要问题提供了潜在的解决方案。基于序列的分类单元的类型默认缺乏物理样本或培养物，可以通过四种替代方式指定：（1）基础样本（“袋”类型），（2）DNA提取物，（3）荧光原位杂交 (FISH)，或 (4) 类型序列本身。只有 (4) 需要对规范进行修改，而后者将是最直接的方法，比物理标本更好地符合类型的五个主要功能中的三个。第五种方式，即用插图表示序列，在守则中已被裁定为不可接受。序列数据中的潜在缺陷类似于物理类型中的缺陷，如果应用严格的分析方法，则伪影是可以管理的。同质性、基因组内变异、基因重复、杂交和水平基因转移等概念错误适用于所有分子方法，不能用作反对基于序列的命名法的具体论据。 这些现象的潜在影响是可控的，因为系统发育物种界定在真菌中取得了令人满意的效果。基于序列的命名法最严重的缺点是并行分类的可能性，要么通过描述已经根据物理类型命名的类群，要么通过使用不同的标记来界定同一谱系内的物种。无意中建立具有可用名称的基于序列的物种的概率在 20.4% 到 1.5% 之间，具体取决于全球预测的真菌物种的数量。这与基于物理类型的约 30% 的历史错误率相比是有利的，并且通过在准则中对此方法添加具体规定，可以将该错误率降低到几乎为零。为了避免基于不同标记的平行分类，基于序列的命名法应限于单个标记，最好是真菌 ITS 条形码标记；这是可能的，因为基于序列的命名法的目的不是准确的物种界定，而是命名谱系以生成参考数据库，而与这些谱系是否代表物种、密切相关的物种复合体或种下无关。我们认为聚类方法不适合基于序列的命名法；这种方法必须使用基于多重比对的系统发育方法，并结合定量物种识别方法。我们概述了获得基于 ITS 的无凭证物种的更高级别系统发育的策略，包括系统发育分箱、“劫持”物种定界方法和时间带。 我们的结论是，无凭证、基于序列的命名法不会对基于标本和培养的真菌分类学构成威胁，而是一种补充方法，能够大大缩小已知和预测的真菌多样性之间的差距，这种方法需要仔细的工作和高技能水平。