Multigene Phylogenetic Analyses to Delimit New Species in Fungal Plant Pathogens

Abstract

Supporting the identification of unknown strains or specimens by sequencing a genetic marker commonly used for phylogenetics or DNA barcoding is now standard practice for mycologists and plant pathologists. Does one have a new species when a strain differs by a few base pairs when compared to reference sequences from taxonomically well-characterized species that do not differ morphologically from this new strain? If variation at the intra- and interspecific levels for the locus used for identification is already understood for all the closely related species, it is possible to make a reliable prediction of a new species status, but ultimately this question can only be properly addressed by determining the presence or absence of gene flow among a group of strains of the putative new species and strains of previously delimited species. The Phylogenetic Species Concept (PSC) and its assessment using multigene phylogeny and Genealogical Concordance Phylogenetic Species Recognition (GCPSR) are the basis for this chapter. The theoretical framework and a variety of tools to apply these concepts are explained, to assist in the assessment of whether a species is distinct or new when confronted with some sequence divergence from reference data.

Molecular markers delimit cryptic species in Ceratocystis sensu stricto

“…Furthermore, biological species recognition is not possible for all fungi and it can be unreliable and misleading in laboratory environments (Harrington 2000;Taylor et al 2000). During the course of the past 25 years, phylogenetic analysis and Genealogical Concordance Phylogenetic Species Recognition (GCPSR) has gained acceptance in the recognition of many new taxa that would not have been possible based on other criteria (Bridge et al 2005;Rintoul et al 2012;Taylor et al 2000).…”

Delimiting cryptic pathogen species causing apple Valsa canker with multilocus data

“…There are many cases where closely related species, even morphologically indistinguishable, can differ greatly in their virulence and host specificity, and thus the level of threat they pose to agriculture and forestry. Specific and precise species delimitation of these pathogens is essential for effective disease control and quarantine regulations, and for sustainable management practices in agriculture and forestry (Rintoul et al 2012). However, methods for species delimitation are very limited in many groups, often relying on very limited morphological and cultural characteristics that vary widely during life history and can be easily influenced by nonheritable factors such as environmental conditions and sexual forms.…”

“…Especially, due to stochastic lineage sorting across genomes and ongoing gene flow during speciation, for closely related fungi, one marker is definitely not enough (Dupuis et al 2012). As a consequence, multiple independent loci are required for reliable species delimitation (Rintoul et al 2012). Multilocus data have been successfully applied to delimitate several closely related plant pathogenic ascomycete fungi, for example, in Neurospora (Dettman et al 2003), Fusarium (O'Donnell et al 2004 and Septoria (Verkley et al 2013).…”

Blastomycosis

“…The identification of species by sequencing a genetic marker has become common practice among mycologists [14,16]. Genealogical concordance phylogenetic species recognition (GCPSR) techniques have been used to identify populations, delineate cryptic species, and document genetic recombination and gene flow in a number of fungal pathogens [9,11,[17][18][19][20].…”