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Missing data and the design of phylogenetic analyses.

John J Wiens1

  • 1Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA. wiensj@life.bio.sunysb.edu

Journal of Biomedical Informatics
|June 1, 2005
PubMed
Summary

Missing data in phylogenetic analyses does not always harm accuracy. Including incomplete taxa and characters can improve phylogenetic reconstructions, even subdividing misleading long branches.

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Phylogenetic analyses often exclude taxa or characters with missing data due to concerns about accuracy.
  • These exclusions may lack strong empirical support and can limit the scope of phylogenetic studies.
  • Missing data is a common challenge in molecular phylogenetics.

Purpose of the Study:

  • To review the impact of missing data on phylogenetic analyses.
  • To evaluate the effects of including incomplete taxa and characters in phylogenetic reconstructions.
  • To provide guidance on managing missing data in the design of phylogenetic studies.

Main Methods:

  • Review of existing literature and theoretical considerations.
  • Analysis of simulation studies investigating the effects of missing data.
  • Examination of how missing data influences phylogenetic accuracy and tree reconstruction.

Main Results:

  • Highly incomplete taxa can be accurately placed in phylogenies if sufficient characters are sampled overall.
  • Inclusion of incomplete taxa can improve phylogenetic accuracy by breaking up long branches.
  • Adding characters with missing data can enhance accuracy but carries a risk of long-branch attraction.

Conclusions:

  • Excluding taxa or characters solely due to missing data may be unwarranted.
  • Strategic inclusion of data with missing entries can lead to more accurate and efficient phylogenetic reconstructions.
  • Understanding the nuanced effects of missing data enables better study design for large-scale phylogenetics.

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