Is Congruence between Data Partitions a Reliable Predictor of Phylogenetic Accuracy? Empirically Testing an Iterative Procedure for Choosing among Phylogenetic Methods

The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence wer...

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Bibliographic Details
Published in:Systematic biology 1997-09, Vol.46 (3), p.464-478
Main Author: Cunningham, Clifford W.
Format: Article
Language:English
Subjects:
Animals
Biometry - methods
Codon - genetics
Codons
Congruence
Data Interpretation, Statistical
DNA, Mitochondrial - genetics
Evolution
incongruence tests
Likelihood Functions
Mathematical congruence
maximum likelihood
Models, Genetic
Muridae - classification
Muridae - genetics
Nucleotide sequences
Parsimony
Peromyscus - classification
Peromyscus - genetics
phylogenetic accuracy
Phylogenetics
Phylogeny
six-parameter parsimony
successive weighting
Taxa
Term weighting
transversion parsimony
Vertebrates
weighted parsimony
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Summary:The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.
ISSN:1063-5157
1076-836X
DOI:10.1093/sysbio/46.3.464