CiteULike

Delicious

Connotea

Citation for Study 15699

Citation title: "Molecular phylogeny of the Cymbellales (Heterokontophyta: Bacillariophyceae) with a comparison of models for accommodating rate-variation across sites".

Study name: "Molecular phylogeny of the Cymbellales (Heterokontophyta: Bacillariophyceae) with a comparison of models for accommodating rate-variation across sites".

This study is part of submission 15699 (Status: Published).

Citation

Nakov T., Ruck E.C., Galachyants Y., Spaulding S., & Theriot E.C. 2014. Molecular phylogeny of the Cymbellales (Heterokontophyta: Bacillariophyceae) with a comparison of models for accommodating rate-variation across sites. Phycologia, .

Authors

• Nakov T. (submitter) 512-471-4997
• Ruck E.C. 512-471-4997
• Galachyants Y.
• Spaulding S.
• Theriot E.C. 512-983-4205

Abstract

We reconstructed the phylogeny of representatives from nine genera and three families of the Cymbellales using two nuclear and three chloroplast genes. After rooting with Anomoeoneis, Placoneis was found as sister to a clade composed of Cymbella, Cymbopleura, Encyonema, Gomphonema, and Gomphoneis. The latter group was divided into lineages with mainly heteropolar and dorsiventral valve symmetry. The data and chloroplast morphology also supported a close relationship between Geissleria decussis and Placoneis. Expectedly, the sequenced genes exhibited substantial across-site rate variation (ASRV) that prompted us to assess the stability of the inferred relationships in the face of different approaches for modeling ASRV. While the overall topology remained stable across analyses, relationships between Cymbella and Cymbopleura and within one clade of Gomphonema varied dependent on the employed model. In some cases a strongly supported relationship in one analysis was not recovered by another that differed solely in how the data were partitioned. These topological fluctuations appeared in areas of the tree with the least balanced taxon sampling and they altered the outcomes of phylogenetic hypotheses tests of monophyly. Assessing how different models for ASRV affect tree topology and clade support values therefore seems important in cases of sparse or unbalanced taxon sampling or when assessing the phylogenetic affinity of previously unsampled taxa when lineage-specific biases in base composition or evolutionary rate are more difficult to detect.

Keywords

Alignment partitioning, Across-site rate variation, Cymbella, Cymbopleura, Diatoms, Geissleria, Gomphonema, Phylogeny, Placoneis.

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S15699
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref23119,
  	 author = {Teofil  Nakov and Elizabeth Clare Ruck and Yuri  Galachyants and Sarah  Spaulding and Edward Claiborne Theriot},
  	 title = {Molecular phylogeny of the Cymbellales (Heterokontophyta: Bacillariophyceae) with a comparison of models for accommodating rate-variation across sites},
  	 year = {2014},
  	 keywords = {Alignment partitioning, Across-site rate variation, Cymbella, Cymbopleura, Diatoms, Geissleria, Gomphonema, Phylogeny, Placoneis.},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Phycologia},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {We reconstructed the phylogeny of representatives from nine genera and three families of the Cymbellales using two nuclear and three chloroplast genes. After rooting with Anomoeoneis, Placoneis was found as sister to a clade composed of Cymbella, Cymbopleura, Encyonema, Gomphonema, and Gomphoneis. The latter group was divided into lineages with mainly heteropolar and dorsiventral valve symmetry. The data and chloroplast morphology also supported a close relationship between Geissleria decussis and Placoneis. Expectedly, the sequenced genes exhibited substantial across-site rate variation (ASRV) that prompted us to assess the stability of the inferred relationships in the face of different approaches for modeling ASRV. While the overall topology remained stable across analyses, relationships between Cymbella and Cymbopleura and within one clade of Gomphonema varied dependent on the employed model. In some cases a strongly supported relationship in one analysis was not recovered by another that differed solely in how the data were partitioned. These topological fluctuations appeared in areas of the tree with the least balanced taxon sampling and they altered the outcomes of phylogenetic hypotheses tests of monophyly. Assessing how different models for ASRV affect tree topology and clade support values therefore seems important in cases of sparse or unbalanced taxon sampling or when assessing the phylogenetic affinity of previously unsampled taxa when lineage-specific biases in base composition or evolutionary rate are more difficult to detect.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 23119
  AU  - Nakov,Teofil 
  AU  - Ruck,Elizabeth Clare
  AU  - Galachyants,Yuri 
  AU  - Spaulding,Sarah 
  AU  - Theriot,Edward Claiborne
  T1  - Molecular phylogeny of the Cymbellales (Heterokontophyta: Bacillariophyceae) with a comparison of models for accommodating rate-variation across sites
  PY  - 2014
  KW  - Alignment partitioning
  KW  - Across-site rate variation
  KW  - Cymbella
  KW  - Cymbopleura
  KW  - Diatoms
  KW  - Geissleria
  KW  - Gomphonema
  KW  - Phylogeny
  KW  - Placoneis.
  UR  - http://dx.doi.org/
  N2  - We reconstructed the phylogeny of representatives from nine genera and three families of the Cymbellales using two nuclear and three chloroplast genes. After rooting with Anomoeoneis, Placoneis was found as sister to a clade composed of Cymbella, Cymbopleura, Encyonema, Gomphonema, and Gomphoneis. The latter group was divided into lineages with mainly heteropolar and dorsiventral valve symmetry. The data and chloroplast morphology also supported a close relationship between Geissleria decussis and Placoneis. Expectedly, the sequenced genes exhibited substantial across-site rate variation (ASRV) that prompted us to assess the stability of the inferred relationships in the face of different approaches for modeling ASRV. While the overall topology remained stable across analyses, relationships between Cymbella and Cymbopleura and within one clade of Gomphonema varied dependent on the employed model. In some cases a strongly supported relationship in one analysis was not recovered by another that differed solely in how the data were partitioned. These topological fluctuations appeared in areas of the tree with the least balanced taxon sampling and they altered the outcomes of phylogenetic hypotheses tests of monophyly. Assessing how different models for ASRV affect tree topology and clade support values therefore seems important in cases of sparse or unbalanced taxon sampling or when assessing the phylogenetic affinity of previously unsampled taxa when lineage-specific biases in base composition or evolutionary rate are more difficult to detect.
  
  L3  - 
  JF  - Phycologia
  VL  - 
  IS  - 
  ER  -