Abstract Detail

Sequence-based Identification of Fungi

Hibbett, David S. [1].

Challenges and opportunities in sequence-based identification and classification of fungi.

Ever since the advent of the PCR, molecular data have been routinely used to detect fungi in environmental samples and to reveal cryptic lineages within morphologically homogeneous groups. As early as 2009, the number of species-level entities discovered with molecular data approached (or exceeded) the magnitude of specimen-based taxon discovery, and the rate of molecular taxon discovery has only accelerated through the use of current-generation sequencing technologies. In parallel with advances in sequencing methods, there has been great progress in the development of tools and databases for sequence-based identification (and community comparison), some of which will be illustrated in this symposium. However, there are still no generally-accepted protocols for naming taxa based on sequence data (although clever, Code-compliant workarounds are available), or for integrating molecular OTUs into widely used taxonomic databases (e.g., GBIF). Consequently, the results of molecular environmental studies are not easily comparable, and traditional taxonomic resources fail to capture the diversity of fungi now being discovered with molecular tools. To integrate sequence-based taxa into mainstream fungal taxonomy, there are many questions that need to be addressed, such as “what is the optimal form for the names of sequence-based taxa (codes? binomials? with or without identifying pre- or suffixes?)” and “how can the rules of the ICNAFP be modified to allow sequence-based taxon description?” In contrast to these somewhat mundane operational considerations, there are other questions that, while intellectually appealing, may not actually help us design useful sequence-based classification systems. In particular, it is not very helpful to ask “what is the one best marker (and the appropriate sequence similarity value) for delimiting fungal species?” It is now painfully obvious that there is no one gene that “works” in all groups (the selection of ITS as The fungal barcode locus notwithstanding). Moreover, even with fully resolved phylogenies in hand, as well as morphological and physiological data, reasonable systematists (to say nothing of unreasonable ones) may have legitimate disagreements about species limits. Perhaps the least productive discussion we could entertain would center on the question “what is a species?” Any system of sequence-based classification that we devise and promote for general use must be adaptable for any gene or combination of genes, it must be compatible with the existing infrastructure of biodiversity informatics, and it must allow for differences in taxonomic opinion.

1 - Clark University, Biology Department, 950 Main street, Worcester, MA, 01610, USA

Keywords:
Systematics
bioinformatics
nomenclatures
phylogenetic species.

Presentation Type: Symposium or Colloquium Presentation
Session: SY8
Location: Room 103 AB/Kellogg Hotel and Conference Center
Date: Wednesday, June 11th, 2014
Time: 1:00 PM
Number: SY8001
Abstract ID:142
Candidate for Awards:None