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Open Access Methodology article

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis

Véronique Campbell*, Pierre Legendre and François-Joseph Lapointe

Author Affiliations

Département de Sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada

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BMC Evolutionary Biology 2011, 11:64  doi:10.1186/1471-2148-11-64

Published: 9 March 2011

Abstract

Background

CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions.

Results

Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices.

Conclusions

Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously.