Intraspecific <i>ITS</i> Variability in the Kingdom <i>Fungi</i> as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

TLDR

The ITS region is widely used for fungal species identification, yet its intraspecific variability—often presumed to be limited—is actually variable and its separation from interspecific differences is contested. The study estimates intraspecific ITS variability across all fungi represented in international sequence databases. The authors quantify this variability by analyzing ITS sequences retrieved from global databases. They found substantial intraspecific ITS variation across fungi, with no universal 3 % threshold, indicating that automated species delimitation is unreliable and expert taxonomic input remains essential.

Abstract

The internal transcribed spacer ( ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra- and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3% threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.