@ARTICLE{TreeBASE2Ref25870, author = {Xinli Wei and Bruce McCune and H. Thorsten Lumbsch and Hui Li and Steve Leavitt and Yoshikazu Yamamoto and Svetlana Tchabanenko and Jiangchun Wei}, title = {Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)}, year = {2016}, keywords = {}, doi = {10.1371/journal.pone.0163664}, url = {http://}, pmid = {}, journal = {PLoS ONE}, volume = {11}, number = {11}, pages = {e0163664}, abstract = {Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in closely related fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we implemented a variety of empirical sequence-based species delimitation approaches, including the ?Automatic Barcode Gap Discovery? (ABGD), the Poisson tree process model (PTP), and the multispecies coalescent approach BPP. Comparisons of pairwise genetic distances, pairwise fixation indices (FST) were also employed to elucidate insight into species boundaries in this group. The majority of the species delimitation analyses methods implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages. However, strong support from the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP, and genetic clusters in this group generally corresponded to the distinct reproductive strategies. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories. } }

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