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Citation for Study 19270

Citation title: "Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)".

Study name: "Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)".

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) 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

• DOI: 10.1371/journal.pone.0163664

About this resource

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

  		@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. 
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 25870
  AU  - Wei,Xinli 
  AU  - McCune,Bruce 
  AU  - Lumbsch,H. Thorsten
  AU  - Li,Hui 
  AU  - Leavitt,Steve 
  AU  - Yamamoto,Yoshikazu  
  AU  - Tchabanenko,Svetlana  
  AU  - Wei,Jiangchun 
  T1  - Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota)
  PY  - 2016
  KW  - 
  UR  - http://dx.doi.org/10.1371/journal.pone.0163664
  N2  - 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. 
  
  L3  - 10.1371/journal.pone.0163664
  JF  - PLoS ONE
  VL  - 11
  IS  - 11
  ER  -