Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them.
Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them.
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DOI：
10.5598/imafungus.2018.09.01.09
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发表时间：
2018-06
期刊：
影响因子：
5.4
通讯作者：
Hawksworth DL
中科院分区：
文献类型：
--
作者：
Lücking R;Hawksworth DL
鉴于环境测序已经在Sequence Read Archive中积累了超过10亿个真菌ITS读数，大约是GenBank中真菌ITS序列的1000倍，因此迫切需要一个基于序列的、无凭证的真菌正式命名。这些未命名的真菌可能有助于弥合11.5万至14万个目前被接受的物种与220万至380万个预测物种之间的差距，这一缺口实际上无法通过标本或基于培养的清单来填补。该准则从来没有旨在对分类所选的字符的性质施加限制，而对物理类型的要求现在正在成为科学进步的制约因素。我们详细阐述了基于序列的命名的承诺和陷阱，并提供了潜在的解决方案的主要关切的真菌学社区。缺省情况下缺乏物理标本或培养物的基于序列的分类群的类型可以用四种替代方法来指定：(1)底层样本(‘袋’型)，(2)DNA提取物，(3)荧光原位杂交(FISH)，或(4)类型序列本身。只有第(4)项需要修改《规范》，而后者将是最直接的办法，符合五种主要功能中的三种类型，比实物标本更好。第五种方式，即在插图中表示序列，在《守则》中被裁定为不可接受。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，人工制品是可以管理的。概念性错误，如同质性、基因组内变异、基因复制、杂交和水平基因转移，适用于所有分子方法，不能用作反对基于序列的命名法的特定论点。这些现象的潜在影响是可控的，因为系统发育物种划分在真菌中起到了令人满意的作用。基于序列的命名法最严重的缺点是可能进行平行分类，要么通过描述已经具有基于物理类型的名称的分类单元，要么通过使用不同的标记来界定同一谱系内的物种。根据全球预测的真菌物种的数量，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。这与基于物理类型的约30%的历史错误率相比是有利的，通过在《守则》中对这一方法增加具体规定，可以将这一错误率降至几乎为零。为了避免基于不同标记的平行分类，基于序列的命名应限于单一标记，最好是真菌及其条形码标记；这是可能的，因为基于序列的命名不旨在准确地划分物种，而是命名谱系以生成一个参考数据库，而不管这些谱系代表的是物种、密切相关的物种复合体还是种下。我们认为，聚类法不适合于基于序列的命名法；相反，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、无凭证物种的更高水平系统发育的战略，包括系统发育分类、‘劫持’物种划界方法和时间带。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，能够显著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。
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.
影响因子：
1.4
作者：
von Konrat M;de Lange P;Greif M;Strozier L;Hentschel J;Heinrichs J
通讯作者：
Heinrichs J