Discovering cryptic species in the Aspiciliella intermutans complex (Megasporaceae, Ascomycota) – First results using gene concatenation and coalescent-based species tree approaches

Abstract

Taxonomic identifications in some groups of lichen-forming fungi have been challenge largely due to the scarcity of taxonomically relevant features and limitations of morphological and chemical characters traditionally used to distinguish closely related taxa. Delineating species boundaries in closely related species or species complexes often requires a range of multisource data sets and comprehensive analytical methods. Here we aim to examine species boundaries in a group of saxicolous lichen forming fungi, the Aspiciliella intermutans complex ( Megasporaceae ), widespread mainly in the Mediterranean. We gathered DNA sequences of the nuclear ribosomal internal transcribed spacer (nuITS), the nuclear large subunit (nuLSU), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the DNA replication licensing factor MCM7 from 80 samples mostly from Iran, Caucasia, Greece and eastern Europe. We used a combination of phylogenetic strategies and a variety of empirical, sequence-based species delimitation approaches to infer species boundaries in this group. The latter included: the automatic barcode gap discovery (ABGD), the multispecies coalescent approach *BEAST and Bayesian Phylogenetics and Phylogeography (BPP) program. Different species delimitation scenarios were compared using Bayes factors species delimitation analysis. Furthermore, morphological, chemical, ecological and geographical features of the sampled specimens were examined. Our study uncovered cryptic species diversity in A . intermutans and showed that morphology-based taxonomy may be unreliable, underestimating species diversity in this group of lichens. We identified a total of six species-level lineages in the A . intermutans complex using inferences from multiple empirical operational criteria. We found little corroboration between morphological and ecological features with our proposed candidate species, while secondary metabolite data do not corroborate tree topology. The present study on the A . intermutans species-complex indicates that the genus Aspiciliella , as currently circumscribed, is more diverse in Eurasia than previously expected.

Taxonomic recognition of some species-level lineages circumscribed in nominal Rhizoplaca subdiscrepans s. lat. (Lecanoraceae, Ascomycota)

“…Chemical characters that are widely used for species delimitation in lichenology are not always good taxonomic indicators, especially when they do not correspond with molecular data ( Hawksworth, 1976 ; Culberson, 1986 ; Ryan & Nash, 1997 ; Divakar et al, 2010 ; Thell et al, 2017 ; Ossowska et al, 2018 ; Zakeri et al, 2019 ). This fact may apply among others to the genus Rhizoplaca for which high chemical variability has been shown ( Wei & Wei, 2005 ; Zhou et al, 2006 ; Leavitt et al, 2013a ).…”

Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

“…Indeed, cryptic speciation is a matter of perception, and often there are subtle (or simply overlooked) characters that eventually separate phylogenetically distinct lineages (Molina et al 2011;Nuñez-Zapata et al 2011;Frolov et al 2016;Santos et al 2019). Sometimes, such characters may be difficult to discern or are only unveiled as statistically supported differences in morphometrics, not useful in the field or in keys (Altermann et al 2014(Altermann et al , 2016Schneider et al 2016;Zahradníková et al 2018;Zakeri et al 2019). For such cases, "near-cryptic" may be a better term.…”

Lichen cell factories: methods for the isolation of photobiont and mycobiont partners for defined pure and co-cultivation

“…DNA was extracted from the fresh lichen material and the isolated fungal and algae subcultures from it, which were dried and grinded with a mill MM301 (Retsch GmbH, Germany). The grinded material was processed as described in Zakeri et al [ 38 , 39 ].…”