Correction: Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.

[This corrects the article DOI: 10.1371/journal.pone.0237507.].

Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera.

DNA barcoding can identify biological species and provides an important tool in diverse applications, such as conserving species and identifying pathogens, among many others. If combined with statistical tests, DNA barcoding can focus taxonomic scrutiny onto anomalous species identifications based on morphological features. Accordingly, we put nonparametric tests into a taxonomic context to answer questions about our sequence dataset of the formal fungal barcode, the nuclear ribosomal internal transcribed spacer (ITS). For example, does DNA barcoding concur with annotated species identifications significantly better if expert taxonomists produced the annotations? Does species assignment improve significantly if sequences are restricted to lengths greater than 500 bp? Both questions require a figure of merit to measure of the accuracy of species identification, typically provided by the probability of correct identification (PCI). Many articles on DNA barcoding use variants of PCI to measure the accuracy of species identification, but do not provide the variants with names, and the absence of explicit names hinders the recognition that the different variants are not comparable from study to study. We provide four variant PCIs with a name and show that for fixed data they follow systematic inequalities. Despite custom, therefore, their comparison is at a minimum problematic. Some popular PCI variants are particularly vulnerable to errors in species annotation, insensitive to improvements in a barcoding pipeline, and unable to predict identification accuracy as a database grows, making them unsuitable for many purposes. Generally, the Fractional PCI has the best properties as a figure of merit for species identification. The fungal genus Ramaria provides unusual taxonomic difficulties. As a case study, it shows that a good taxonomic background can be combined with the pertinent summary statistics of molecular results to improve the identification of doubtful samples, linking both disciplines synergistically.

Taxonomy and phylogeny of yellow Clavaria species with clamped basidia-Clavaria flavostellifera sp. nov. and the typification of C. argillacea, C. flavipes and C. sphagnicola.

This study explores species limits of a group of Clavaria species with taxonomic and nomenclatural problems and discusses the phylogeny and circumscription of the genus. The nuc 28S rDNA (28S) and internal transcribed spacer region phylogenies resolve species relationships, and the ITS is shown to be an adequate barcode marker for Clavaria. Yellow, clamped species of Clavaria are distributed in two clades, (i) C. flavostellifera, sister to C. incarnata and C. asterospora in ITS analyses, characterized by producing ornamented spores, and (ii) C. argillacea-C. citrinorubra-C. flavipes-C. sphagnicola, with smooth spores. Clavaria flavostellifera is described as new species based on morphological and molecular characters. Molecular evidence that supports C. sphagnicola as distinct from C. argillacea is provided. The usefulness of spore ornamentation as a taxonomic character is discussed; it is present only in some taxa and then only on spores trapped in the hymenium. Descriptions of C. argillacea, C. flavipes and C. sphagnicola are provided, along with color photographs and a key to yellow species of Clavaria with clamped basidia. Camarophyllopsis and Clavicorona are recovered within a paraphyletic Clavaria in our 28S phylogeny. Clampless contextual hyphae and narrow, slightly thick-walled mycelial hyphae are proposed as synapomorphies of Camarophyllopsis and Clavaria.