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Citation for Study 10454

Citation title: "The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Datasets".

Study name: "The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Datasets".

This study is part of submission 10444 (Status: Published).

Citation

Evans N.M., & Cartwright P. 2010. The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Datasets. Molecular Biology and Evolution, .

Authors

• Evans N.M.
• Cartwright P.

Abstract

Myxozoans are a diverse group of microscopic endoparasites that have been the focus of much controversy regarding their phylogenetic position. Two dramatically different hypotheses have been put forward regarding the placement of Myxozoa within Metazoa. One hypothesis, supported by rDNA data, place Myxozoa as a sister taxon to Bilateria. The alternative hypothesis, supported by phylogenomic data and morphology, place Myxozoa within Cnidaria. Here we investigate these conflicting hypotheses and explore the effects of missing data, model choice, and inference methods, all of which can have an effect in placing highly divergent taxa. In addition, we identify subsets of the data that most influence the placement of Myxozoa and explore their effects by removing them from the datasets. Assembling the largest taxonomic sampling of myxozoans and cnidarians to date, with a comprehensive sampling of other metazoans for 18S and 28S nuclear ribosomal DNA sequences, we recover a well-supported placement of Myxozoa as an early diverging clade of Bilateria. By conducting parametric bootstrapping, we find that the bilaterian placement of Buddenbrockia could not alone, be explained by long-branch attraction. After trimming a published phylogenomic dataset, to circumvent problems of missing data, we recover the myxozoan Buddenbrockia plumatellae as a medusozoan cnidarian. In further explorations of these datasets, we find that removal of just a few identified sites under a maximum likelihood criterion employing the WAG amino acid substitution model, changes the placement of Buddenbrockia from within Cnidaria to the alternative hypothesis at the base of Bilateria. Under a Bayesian criterion employing the CAT model, the cnidarian placement is more resilient to data removal, but under one test, a well-supported early diverging bilaterian position for Buddenbrockia is recovered. Our results confirm the existence of two relatively stable placements for myxozoans and demonstrate that conflicting signal exists not only between the two types of data but also within the phylogenomic dataset. These analyses underscore the importance of careful model selection, taxon and data sampling, and in-depth data exploration, when investigating the phylogenetic placement of highly divergent taxa.

Keywords

phylogenomic, ribosomal, CAT model, Myxozoa

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10454
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref18929,
  	 author = {Nathaniel M Evans and Paulyn  Cartwright},
  	 title = {The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal  Datasets},
  	 year = {2010},
  	 keywords = {phylogenomic, ribosomal, CAT model, Myxozoa },
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Biology and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Myxozoans are a diverse group of microscopic endoparasites that have been the focus of much controversy regarding their phylogenetic position. Two dramatically different hypotheses have been put forward regarding the placement of Myxozoa within Metazoa. One hypothesis, supported by rDNA data, place Myxozoa as a sister taxon to Bilateria. The alternative hypothesis, supported by phylogenomic data and morphology, place Myxozoa within Cnidaria.  Here we investigate these conflicting hypotheses and explore the effects of missing data, model choice, and inference methods, all of which can have an effect in placing highly divergent taxa.  In addition, we identify subsets of the data that most influence the placement of Myxozoa and explore their effects by removing them from the datasets. Assembling the largest taxonomic sampling of myxozoans and cnidarians to date, with a comprehensive sampling of other metazoans for 18S and 28S nuclear ribosomal DNA sequences, we recover a well-supported placement of Myxozoa as an early diverging clade of Bilateria.  By conducting parametric bootstrapping, we find that the bilaterian placement of Buddenbrockia could not alone, be explained by long-branch attraction.  After trimming a published phylogenomic dataset, to circumvent problems of missing data, we recover the myxozoan Buddenbrockia plumatellae as a medusozoan cnidarian.  In further explorations of these datasets, we find that removal of just a few identified sites under a maximum likelihood criterion employing the WAG amino acid substitution model, changes the placement of Buddenbrockia from within Cnidaria to the alternative hypothesis at the base of Bilateria.   Under a Bayesian criterion employing the CAT model, the cnidarian placement is more resilient to data removal, but under one test, a well-supported early diverging bilaterian position for Buddenbrockia is recovered.  Our results confirm the existence of two relatively stable placements for myxozoans and demonstrate that conflicting signal exists not only between the two types of data but also within the phylogenomic dataset.  These analyses underscore the importance of careful model selection, taxon and data sampling, and in-depth data exploration, when investigating the phylogenetic placement of highly divergent taxa.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 18929
  AU  - Evans,Nathaniel M
  AU  - Cartwright,Paulyn 
  T1  - The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal  Datasets
  PY  - 2010
  KW  - phylogenomic
  KW  - ribosomal
  KW  - CAT model
  KW  - Myxozoa 
  UR  - http://dx.doi.org/
  N2  - Myxozoans are a diverse group of microscopic endoparasites that have been the focus of much controversy regarding their phylogenetic position. Two dramatically different hypotheses have been put forward regarding the placement of Myxozoa within Metazoa. One hypothesis, supported by rDNA data, place Myxozoa as a sister taxon to Bilateria. The alternative hypothesis, supported by phylogenomic data and morphology, place Myxozoa within Cnidaria.  Here we investigate these conflicting hypotheses and explore the effects of missing data, model choice, and inference methods, all of which can have an effect in placing highly divergent taxa.  In addition, we identify subsets of the data that most influence the placement of Myxozoa and explore their effects by removing them from the datasets. Assembling the largest taxonomic sampling of myxozoans and cnidarians to date, with a comprehensive sampling of other metazoans for 18S and 28S nuclear ribosomal DNA sequences, we recover a well-supported placement of Myxozoa as an early diverging clade of Bilateria.  By conducting parametric bootstrapping, we find that the bilaterian placement of Buddenbrockia could not alone, be explained by long-branch attraction.  After trimming a published phylogenomic dataset, to circumvent problems of missing data, we recover the myxozoan Buddenbrockia plumatellae as a medusozoan cnidarian.  In further explorations of these datasets, we find that removal of just a few identified sites under a maximum likelihood criterion employing the WAG amino acid substitution model, changes the placement of Buddenbrockia from within Cnidaria to the alternative hypothesis at the base of Bilateria.   Under a Bayesian criterion employing the CAT model, the cnidarian placement is more resilient to data removal, but under one test, a well-supported early diverging bilaterian position for Buddenbrockia is recovered.  Our results confirm the existence of two relatively stable placements for myxozoans and demonstrate that conflicting signal exists not only between the two types of data but also within the phylogenomic dataset.  These analyses underscore the importance of careful model selection, taxon and data sampling, and in-depth data exploration, when investigating the phylogenetic placement of highly divergent taxa.
  L3  - 
  JF  - Molecular Biology and Evolution
  VL  - 
  IS  - 
  ER  -