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Citation for Study 10562

Citation title: "Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life".

Study name: "Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life".

This study is part of submission 10552 (Status: Published).

Citation

Parfrey L.W., Grant J.R., Tekle Y.I., Lasek-nesselquist E., Patterson D.J., Morrison H.G., Sogin M., & Katz L.A. 2010. Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life. Systematic Biology, .

Authors

• Parfrey L.W.
• Grant J.R.
• Tekle Y.I.
• Lasek-nesselquist E.
• Patterson D.J.
• Morrison H.G.
• Sogin M.
• Katz L.A.

Abstract

An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ?supergroups?, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ?Chromalveolata? is rejected. Further, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.

Keywords

Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10562
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref19001,
  	 author = {Laura Wegener Parfrey and Jessica R Grant and Yonas I Tekle  and Erica  Lasek-Nesselquist and David J Patterson and Hilary G Morrison and Mitchell  Sogin and Laura A Katz},
  	 title = {Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life},
  	 year = {2010},
  	 keywords = {Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes.  Previous work has divided eukaryotic diversity into a small number of high-level ?supergroups?, many of which receive strong support in phylogenomic analyses.  However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error.  Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses.  Here, we use a taxon-rich strategy to assess eukaryotic relationships.  We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life.  The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies.  The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses.  Several major groups are stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ?Chromalveolata? is rejected.  Further, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host.  Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes.  Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 19001
  AU  - Parfrey,Laura Wegener
  AU  - Grant,Jessica R
  AU  - Tekle ,Yonas I
  AU  - Lasek-Nesselquist,Erica 
  AU  - Patterson,David J
  AU  - Morrison,Hilary G
  AU  - Sogin,Mitchell 
  AU  - Katz,Laura A
  T1  - Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life
  PY  - 2010
  KW  - Keywords: Microbial eukaryotes
  KW  - supergroups
  KW  - taxon sampling
  KW  - Rhizaria
  KW  - systematic error
  UR  - http://dx.doi.org/
  N2  - An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes.  Previous work has divided eukaryotic diversity into a small number of high-level ?supergroups?, many of which receive strong support in phylogenomic analyses.  However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error.  Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses.  Here, we use a taxon-rich strategy to assess eukaryotic relationships.  We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life.  The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies.  The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses.  Several major groups are stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ?Chromalveolata? is rejected.  Further, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host.  Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes.  Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.
  L3  - 
  JF  - Systematic Biology
  VL  - 
  IS  - 
  ER  -