CiteULike

Delicious

Connotea

Citation for Study 12640

Citation title: "Separating the Wheat from the Chaff:: Mitigating the Effects of Noise in a Plastome Phylogenomic Data Set from Pinus L. (Pinaceae)".

Study name: "Separating the Wheat from the Chaff:: Mitigating the Effects of Noise in a Plastome Phylogenomic Data Set from Pinus L. (Pinaceae)".

This study is part of submission 12640 (Status: Published).

Citation

Parks M., Cronn R., & Liston A. 2012. Separating the Wheat from the Chaff:: Mitigating the Effects of Noise in a Plastome Phylogenomic Data Set from Pinus L. (Pinaceae). BMC Evolutionary Biology, .

Authors

• Parks M. (submitter) 541-737-5299
• Cronn R.
• Liston A.

Abstract

Background Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ?noisy? data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or elevated rates of evolution. Results We investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups. While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses. Close investigation of these nodes revealed dramatically different responses to data removal. Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included. Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear. When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set. Conclusions These results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies. For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses

Keywords

Pinus, phylogenomics, plastome, phylogenetic noise, chloroplast

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S12640
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref20643,
  	 author = {Matthew  Parks and Richard  Cronn and Aaron  Liston},
  	 title = {Separating the Wheat from the Chaff:: Mitigating the Effects of Noise in a Plastome Phylogenomic Data Set from Pinus L. (Pinaceae)},
  	 year = {2012},
  	 keywords = {Pinus, phylogenomics, plastome, phylogenetic noise, chloroplast},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Evolutionary Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Background
  Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ?noisy? data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or elevated rates of evolution.
  
  Results
  We investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups. While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses. Close investigation of these nodes revealed dramatically different responses to data removal. Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included. Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear. When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set.
  
  Conclusions
  These results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies. For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 20643
  AU  - Parks,Matthew 
  AU  - Cronn,Richard 
  AU  - Liston,Aaron 
  T1  - Separating the Wheat from the Chaff:: Mitigating the Effects of Noise in a Plastome Phylogenomic Data Set from Pinus L. (Pinaceae)
  PY  - 2012
  KW  - Pinus
  KW  - phylogenomics
  KW  - plastome
  KW  - phylogenetic noise
  KW  - chloroplast
  UR  - http://dx.doi.org/
  N2  - Background
  Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ?noisy? data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or elevated rates of evolution.
  
  Results
  We investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups. While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses. Close investigation of these nodes revealed dramatically different responses to data removal. Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included. Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear. When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set.
  
  Conclusions
  These results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies. For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses
  
  L3  - 
  JF  - BMC Evolutionary Biology
  VL  - 
  IS  - 
  ER  -