© 2004 Society of Systematic Biologists
The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated
Edited by Peter Lockhart: Associate Editor
1 School of Biological Sciences, University of Sydney NSW 2006 Australia; E-mail: lsj@bio.usyd.edu.au (L.S.J.)
2 Sydney University Biological Informatics and Technology Centre, University of Sydney NSW 2006 Australia
3 School of Mathematics and Statistics, University of Sydney NSW 2006 Australia
Received July 1, 2003; Revised September 14, 2003; Accepted March 26, 2004
| The first 150 words of the full text of this article appear below. |
The effect of compositional heterogeneity in sequence data on phylogenetic inference was first identified as a potential problem in the late 1980s and early 1990s (Chang and Campbell, 2000; Conant and Lewis, 2001; Foster and Hickey, 1999; Hasegawa et al., 1993; Klenk et al., 1994; Lockhart et al., 1992a, 1992b; Loomis and Smith, 1990; Olsen and Woese, 1993; Penny et al., 1990; Sogin et al., 1993; Tarrío et al., 2001; Van Den Bussche et al., 1998; Weisburg et al., 1989), and by 1993 the first methods had been developed to measure the extent of the problem (Lockhart et al., 1993, 1994; Steel et al., 1993, 1995) or to overcome it (Foster, 2004; Galtier and Gouy, 1995, 1998; Galtier et al., 1999; Gu and Li, 1996
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Materials and Methods |
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Sequence Data
Phylogenetic Analyses
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Results and Discussion |
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Phylogenetic Results Inferred Assuming Compositional Homogeneity
Phylogenetic Results Inferred Assuming a General Model of Nucleotide Substitution
Implications and Consequences of the Results
Methods for Assessing Compositional Heterogeneity
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Concluding Remarks and Recommendations |
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