Reference-based RADseq for species delineation in a recently diverged asexually reproducing species complex (Parmeliaceae, Ascomycota)

Cryptic species are common in lichen-forming fungi and have been reported from different genera in the most speciose family, Parmeliaceae. We here address the species delimitation in a group of mainly asexually reproducing Parmelina species. The morphologically distinct P. pastillifera was previously found nested within a morphologically circumscribed P. tiliacea based on several loci. However, these studies demonstrated a relatively high genetic diversity within P. tiliacea sensu lato. Here, we revisit the species delimitation in the group by analyzing single nucleotide polymorphisms (SNPs) through genome-wide assessment using RAD sequencing and population genomic methods. Our data support previous studies and provide further insight into the phylogenetic relationships of the four clades found within the complex. Based on the evidence suggesting a lack of gene flow among the clades, we recognize the four clades as distinct species: P. pastillifera, P. tiliacea sensu stricto, and two new species: P. clandestina sp. nov. and P. mediterranea sp. nov.