CiteULike CiteULike
Delicious Delicious
Connotea Connotea

Citation for Study 19270

Reviewer/Referee Access Agreement

You have reached this page using a special URL that is intended to be used by journal editors and reviewers or referees of a paper that is under consideration for publication. This URL gives you access to the submitted data and metadata associated with analyses and results presented in the paper under review. Please carefully examine the data paying special attention to the following:
  • The citation data (authors, year, citation, abstract) should be complete, except for information that is not yet known (e.g. volume or page numbers).
  • Verify that nexus files are error-free and executable by software programs (e.g. PAUP, Mesquite, MacClade, etc). Please make sure that the taxon labels for trees are identical, or a subset of, the taxon labels in data matrices connected by way of an analysis. If taxon labels in trees do not match with taxon labels in associated data matrices, the data will not be useful to the scientific community.
  • Verify that data are not missing and that opportunities to supply valuable metadata are not overlooked. For example, TreeBASE can store Genbank accession numbers, museum voucher IDs, latitude and longitudes for specimen localities, character names and character state names for morphological data, etc. Including these metadata are sometimes overlooked by submitting authors, yet sharing this metadata is extremely valuable to the scientific community. Please use your power as a reviewer to encourage the sharing of richly-annotated metadata.
  • Verify that analyses are not missing and that, where possible, analysis entries include software commands (e.g. the contents of a PAUP block or MrBayes block) so that analyses can be replicated easily (e.g. commands that describe substitution models, data partitions, and heuristic search parameters).
  • Verify that taxon labels are mapped against TreeBASE's taxonomic dictionary. Data in TreeBASE can only be found using a taxon name search if the taxon labels are properly mapped.
By clicking the 'OK' button below, you agree to keep these data confidential; you agree not to retain these data after completing your report to the journal editor; you agree not to use these data or knowledge of these data for the purposes of your research until and unless the paper under review has been published and the data have been made available to the general public; you agree to keep the URL confidential.
About Citation title: "Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)".
About Study name: "Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)".
About This study is part of submission 19270 (Status: Published).

Citation

Wei X., Mccune B., Lumbsch H.T., Li H., Leavitt S., Yamamoto Y., Tchabanenko S., & Wei J. 2016. Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota). PLoS ONE, 11(11): e0163664.

Authors

  • Wei X. (submitter) Phone 86-13651162596
  • Mccune B.
  • Lumbsch H.T.
  • Li H.
  • Leavitt S.
  • Yamamoto Y.
  • Tchabanenko S.
  • Wei J.

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.

External links

About this resource

  • Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S19270
  • Other versions: Download Reconstructed NEXUS File Nexus Download NeXML File NeXML
  • Show BibTeX reference
  • Show RIS reference