Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (<i>Bryoria</i> sect. <i>Implexae</i>, <i>Parmeliaceae</i>)

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach - including morphological, chemical, molecular, and distributional characters - to re-assess species boundaries in a traditionally speciose group of hair lichens, <i>Bryoria</i> sect. <i>Implexae</i>. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, <i>GAPDH</i>, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are <i>Bryoria fuscescens</i>, <i>B. glabra</i>, <i>B. kockiana</i>, and <i>B. pseudofuscescens</i>. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the <i>B. fuscescens</i> complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of <i>Bryoria</i> are outlined.