Picking holes in traditional species delimitations: an integrative taxonomic reassessment of theParmotrema perforatumgroup (Parmeliaceae, Ascomycota)

Abstract

Accurate species delimitation is important as species are a fundamental unit in ecological, evolutionary and conservation biology research. In lichenized fungi, species delimitation has been difficult due to a lack of taxonomically important characteristics and due to the limits of traditional, morphology‐based species concepts. In this study we reassess the current taxonomy of the Parmotrema perforatum group, which recognizes six closely related species divided into three species pairs, each pair comprising one apotheciate (sexual) and one sorediate (asexual) species. Each pair is further characterized by a distinct combination of secondary metabolites. It was hypothesized that the three apotheciate species are reproductively isolated sibling species and that each sorediate species evolved once from the chemically identical apotheciate species. In this study, species boundaries were re‐examined using an integrative approach incorporating morphological, chemical and molecular sequence data to delimit species boundaries. Phylogenetic trees were inferred from a seven‐locus DNA sequence dataset using concatenated gene tree and coalescent‐based species‐tree inference methods. Furthermore, we employed a multi‐species coalescent method to validate candidate species. Micromorphological measurements of conidia were found to be congruent with phylogenetic clusters. Each approach that we applied to the P. perforatum group consistently recovered four of the currently circumscribed species (P. perforatum, P. hypotropum, P. subrigidum and P. louisianae), whereas P. preperforatum and P. hypoleucinum were consistently combined and are thus interpreted as conspecific.

Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus

“…Furthermore, Cryptococcus has a sexual cycle and clearly can reproduce both sexually and asexually. Moreover, the methods used have been applied to identify species-level lineages in asexual taxa ( 126 – 134 ). Methods using branch length differences to identify thresholds between intra- and interspecific distances (such as the coalescence-based general mixed Yule coalescent method) potentially underestimate species diversity in asexual species, since sexual species are separated by larger genetic gaps than asexual species ( 135 ).…”

Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra

“…The Parmotremaperforatum group was used as a model system of species delimitation based on the reproductive mode and secondary metabolites (Culberson and Culberson 1973). However, a recent study suggests that the phylogenetic relationships between sexual and asexual populations might be more complex (Widhelm et al 2016).…”

Elucidating species richness in lichen fungi: The genusSticta(Ascomycota: Peltigeraceae) in Puerto Rico

“…Species delimitation analyses have been amply used for exploring diversity patterns in lichenized fungi, particularly for assessing boundaries within species complexes and/or uncover instances of cryptic speciation (Parnmen & al., 2012; Kraichak & al., 2015; Alors & al., 2016; Widhelm & al., 2016; Zhao & al., 2017). In this work, these methods provided additional means of evaluating species boundaries, particularly in complex clades such as those containing strongly supported subclades (e.g., Sticta aff.…”