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Citation for Study 1486

Citation title: "An empirical Assessment of Long Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics.".

This study was previously identified under the legacy study ID S1430 (Status: Published).

Citation

Brinkmann H., Giezen M., Zhou Y., Raucourt G., & Philippe H. 2005. An empirical Assessment of Long Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics. Systematic Biology, 54(5): 743-757.

Authors

• Brinkmann H. 514-343-6111 Ext.5091
• Giezen M.
• Zhou Y.
• Raucourt G.
• Philippe H.

Abstract

In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene datasets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long branch attraction artefact (LBA) using real instead of simulated sequences. Two fast evolving eukaryotic lineages, whose evolutionary positions are well-established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large dataset was assembled (44 species, 133 genes and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the non-phylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.

External links

• DOI: 10.1080/10635150500234609

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1486
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref14836,
  	 author = {Henner  Brinkmann and M. v. d.  Giezen and Yan  Zhou and G. P. d.  Raucourt and Herv?  Philippe},
  	 title = {An empirical Assessment of Long Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics.},
  	 year = {2005},
  	 keywords = {},
  	 doi = {10.1080/10635150500234609},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {54},
  	 number = {5},
  	 pages = {743--757},
  	 abstract = {In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene datasets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long branch attraction artefact (LBA) using real instead of simulated sequences. Two fast evolving eukaryotic lineages, whose evolutionary positions are well-established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large dataset was assembled (44 species, 133 genes and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the non-phylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 14836
  AU  - Brinkmann,Henner 
  AU  - Giezen,M. v. d. 
  AU  - Zhou,Yan 
  AU  - Raucourt,G. P. d. 
  AU  - Philippe,Herv? 
  T1  - An empirical Assessment of Long Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics.
  PY  - 2005
  KW  - 
  UR  - http://dx.doi.org/10.1080/10635150500234609
  N2  - In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene datasets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long branch attraction artefact (LBA) using real instead of simulated sequences. Two fast evolving eukaryotic lineages, whose evolutionary positions are well-established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large dataset was assembled (44 species, 133 genes and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the non-phylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.
  L3  - 10.1080/10635150500234609
  JF  - Systematic Biology
  VL  - 54
  IS  - 5
  SP  - 743
  EP  - 757
  ER  -