Rooting molecular trees: problems and strategies

Rooting molecular trees: problems and strategies In constructing phylogenies from molecular data both the composition of the ingroup and the choice of outgroup can strongly affect the chances of obtaining the correct topology. This is because tree topology and uneven rates of molecular evolution affect the ability of tree‐building algorithms to find the correct tree. Outgroups can be added in one of two ways, either to a single sister clade (preferably the closest) or through addition of single taxa from different clades. On theoretical and empirical grounds the former strategy is shown to be much more beneficial, both in terms of redressing balance and reducing stemminess. For parsimony to perform well some selection of sequence data, through omission or weighting, is also often necessary to reduce levels of homoplasy. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Biological Journal of the Linnean Society Oxford University Press

Rooting molecular trees: problems and strategies

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Publisher
Oxford University Press
Copyright
Copyright © 1994 Wiley Subscription Services, Inc., A Wiley Company
ISSN
0024-4066
eISSN
1095-8312
DOI
10.1111/j.1095-8312.1994.tb00962.x
Publisher site
See Article on Publisher Site

Abstract

In constructing phylogenies from molecular data both the composition of the ingroup and the choice of outgroup can strongly affect the chances of obtaining the correct topology. This is because tree topology and uneven rates of molecular evolution affect the ability of tree‐building algorithms to find the correct tree. Outgroups can be added in one of two ways, either to a single sister clade (preferably the closest) or through addition of single taxa from different clades. On theoretical and empirical grounds the former strategy is shown to be much more beneficial, both in terms of redressing balance and reducing stemminess. For parsimony to perform well some selection of sequence data, through omission or weighting, is also often necessary to reduce levels of homoplasy.

Journal

Biological Journal of the Linnean SocietyOxford University Press

Published: Mar 1, 1994

References

  • Theories and methods in different approaches to phylogenetic systematics
    Brooks, Brooks; Wiley, Wiley
  • The importance of fossils in phylogeny reconstruction
    Donoghue, Donoghue; Doyle, Doyle; Gauthier, Gauthier; Kluge, Kluge; Rowe, Rowe
  • Phylogenies from molecular sequences: inference and reliability
    Felsenstein, Felsenstein
  • Amniote phylogeny and the importance of fossils
    Gauthier, Gauthier; Kluge, Kluge; Rowe, Rowe
  • Ontogeny and phylogenetic systematics
    Kluge, Kluge
  • Outgroups and ontogeny
    Nelson, Nelson
  • Nucleic acid sequence phylogeny and random outgroups
    Wheeler, Wheeler

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