Does elision account for molecular saturation: Case study based on mitochondrial ribosomal DNA among Characiform fishes (Teleostei: Ostariophysii)

Does elision account for molecular saturation: Case study based on mitochondrial ribosomal DNA... 1 <h5>Introduction</h5> Dealing with saturated data is a problem of major impact in phylogenetic studies using molecular data. Evolutionary trends and processes can distort phylogenetic information in sequences such that they do not reliably reflect the evolutionary process that generates them. The most direct effect of saturation concerns the initial step of phylogenetic analyses, the establishment of primary homology statements across taxa obtained during alignment ( Cerchio and Tucker, 1998; Geiger, 2002; Lutzoni et al., 2000 ). In a parsimony framework a logical means of assessing the quality of homology statements is cladistic character congruence ( Kluge, 1989 ). Character congruence argues that among all competing hypotheses, the one that is supported by the greatest number of independent congruent characters is best. The sine quae non of this paradigm is the maximization of homology during the alignment procedure ( Giribet et al., 2001; Phillips et al., 2000 ). When homology assignment is ambiguous, various alternative strategies may be considered: excluding the alignment-ambiguous sites as a way of minimizing non-homology (the exclusion method of Gatesy et al., 1994 ), generating multiple alignments and keeping only repeated clades across alignments (the multiple analysis method of Lee, 2001 ), treating the http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Molecular Phylogenetics and Evolution Elsevier

Does elision account for molecular saturation: Case study based on mitochondrial ribosomal DNA among Characiform fishes (Teleostei: Ostariophysii)

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Publisher
Elsevier
Copyright
Copyright © 2005 Elsevier Inc.
ISSN
1055-7903
eISSN
1095-9513
D.O.I.
10.1016/j.ympev.2005.01.010
Publisher site
See Article on Publisher Site

Abstract

1 <h5>Introduction</h5> Dealing with saturated data is a problem of major impact in phylogenetic studies using molecular data. Evolutionary trends and processes can distort phylogenetic information in sequences such that they do not reliably reflect the evolutionary process that generates them. The most direct effect of saturation concerns the initial step of phylogenetic analyses, the establishment of primary homology statements across taxa obtained during alignment ( Cerchio and Tucker, 1998; Geiger, 2002; Lutzoni et al., 2000 ). In a parsimony framework a logical means of assessing the quality of homology statements is cladistic character congruence ( Kluge, 1989 ). Character congruence argues that among all competing hypotheses, the one that is supported by the greatest number of independent congruent characters is best. The sine quae non of this paradigm is the maximization of homology during the alignment procedure ( Giribet et al., 2001; Phillips et al., 2000 ). When homology assignment is ambiguous, various alternative strategies may be considered: excluding the alignment-ambiguous sites as a way of minimizing non-homology (the exclusion method of Gatesy et al., 1994 ), generating multiple alignments and keeping only repeated clades across alignments (the multiple analysis method of Lee, 2001 ), treating the

Journal

Molecular Phylogenetics and EvolutionElsevier

Published: Apr 1, 2005

References

  • Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record
    Philippe, H.; Sorhannus, U.; Baroin, A.; Perasso, R.; Gasse, F.; Adoutte, A.
  • How good are deep phylogenetic trees?
    Philippe, H.; Laurent, J.
  • Multiple sequence alignment in phylogenetic analysis
    Phillips, A.; Janies, D.; Wheeler, W.
  • Noise
    Wenzel, J.W.; Siddall, M.E.
  • Elision : A method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites
    Wheeler, W.C.; Gatesy, J.; DeSalle, R.
  • Fixed character states and the optimization of molecular sequence data
    Wheeler, W.C.

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