Increased Congruence Does Not Necessarily Indicate Increased Phylogenetic Accuracy—The Behavior of the Incongruence Length Difference Test in Mixed-Model Analyses

Comprehensive phylogenetic analyses utilize data from distinct sources, including nuclear, mitochondrial, and plastid molecular sequences and morphology. Such heterogeneous datasets are likely to require distinct models of analysis, given the different histories of mutational biases operating on the...

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Bibliographic Details
Published in:Systematic biology 2002-01, Vol.51 (1), p.19-31
Main Authors: Dowton, Mark, Austin, Andrew D.
Format: Article
Language:English
Subjects:
Accuracy
Analysis
Analytical estimating
Animals
Cost efficiency
Cost estimation models
Data Interpretation, Statistical
Databases, Nucleic Acid
Datasets
DNA, Ribosomal - genetics
Electron Transport Complex IV - genetics
Evolution
Genes, Insect
Hymenoptera - classification
Hymenoptera - enzymology
Hymenoptera - genetics
Incongruence
Modeling
Models, Genetic
Parsimony
partition homogeneity
Phylogenetics
Phylogeny
sensitivity analysis
simulated dataset
six-parameter parsimony
Term weighting
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Summary:Comprehensive phylogenetic analyses utilize data from distinct sources, including nuclear, mitochondrial, and plastid molecular sequences and morphology. Such heterogeneous datasets are likely to require distinct models of analysis, given the different histories of mutational biases operating on these characters. The incongruence length difference (ILD) test is increasingly being used to arbitrate between competing models of phylogenetic analysis in cases where multiple data partitions have been collected. Our work suggests that the ILD test is unlikely to be an effective measure of congruence when two datasets differ markedly in size. We show that models that increase the contribution of one data partition over another are likely to increase congruence, as measured by this test. More alarmingly, for many bipartition comparisons, character congruence increases bimodally—either increasing or decreasing the contribution of one data partition will increase congruence—making it impossible to arrive at a single optimally congruent model of analysis.
ISSN:1063-5157
1076-836X
DOI:10.1080/106351502753475853