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

Abstract

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.

Phylogeny, Taxonomy and Evolutionary Trade-Offs in Reproductive Traits of Gomphoid Fungi (Gomphaceae, Gomphales)

“…This classification is consistent with some previous studies [ 1 , 3 ]. Our phylogenetic analysis supports a sister relationship between Gomphus and Turbinellus , contrasting with those studies in which Turbinellus , together with two or more genera of Gomphaceae, were found to be sisters to either Gomphus alone or Gomphus together with several species of Ramaria [ 2 , 63 , 64 , 65 ]. The previous definition of gomphoid fungi [ 1 ], including Gloeocantharellus , turned out to be unnatural.…”

“…Gomphus harbors conspicuous members of Gomphaceae and are often confused with other genera in the family. Recent analyses [ 3 , 63 , 64 , 65 ] indicated that Gomphus, in its broader sense, constitutes a paraphyletic group of fungi with Ramaria sensu lato. To maintain the monophyly of Gomphus , some species were transferred to Gloeocantharellus , and Turbinellus was resurrected [ 1 , 3 ].…”

Ramaria barenthalensis a new record from western Himalayas, Azad Jammu and Kashmir, Pakistan

“…Morpho-anatomical features are insufficient to identify a mushroom species. Fifteen species of Ramaria were identified and characterized by Martin et al (2020) using combined morphological and molecular data. In conclusion, R. barenthalensis is recorded as a new coralloid fungus to the state of Jammu and Kashmir, Pakistan based on morpho-anatomical and molecular characterization.…”

“…Quél., are common edible coralloid fungi (Krupodorova and Sevindik 2020). Ramaria species have been identified through scanning electron microscopy and molecular techniques by Martin et al (2020). Internal transcribed spacer (ITS) restriction length polymorphism was observed among Ramaria species and used as a diagnostic tool for characterization (Nouhra et al 2005).…”

Molecular Isolation, Screening and Identification of Hydrocarbon Degrading Fungi from Oil Contaminated Soils, Iraq

“…The findings revealed that both morphometric data and molecular methods were effective in the identification of A. fumigatus (GenBank accession KU321562.1), A. flavus (GenBank accession MH270609.1), A. niger (GenBank accession MK452260.1), and P. chrysogenum (GenBank accession MK696383.1). Utilizing ITS rDNA sequence similarity (95%) to establish species boundaries operationally, a total of 277 fungal species were identified from 1,403 endophytic strains isolated from various common plants across arctic, boreal, temperate, and tropical regions, representing a wide range of phylogenetically diverse plant taxa [37].…”