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
Molecular Phylogenetics and Evolution – Elsevier
Published: Apr 1, 2005
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