When does the incongruence length difference test fail?

Molecular Biology and Evolution
Pierre Darlu, Guillaume Lecointre

Abstract

This paper examines the efficiency of the incongruence length difference test (ILD) proposed by Farris et al. (1994) for assessing the incongruence between sets of characters. DNA sequences were simulated under various evolutionary conditions: (1) following symmetric or asymmetric trees, (2) with various mutation rates, (3) with constant or variable evolutionary rates along the branches, and (4) with different among-site substitution rates. We first compared two sets of sequences generated along the same tree and under the same evolutionary conditions. The probability of a Type-I error (wrongly rejecting the true hypothesis of congruence) was substantially below the standard 5% level of significance given by the ILD test; this finding indicates that the choice of the 5% level is rather conservative in this case. We then compared two data sets, still generated along the same tree, but under different evolutionary conditions (constant vs. variable evolutionary rate, homogeneity vs. heterogeneity rate of substitution). Under these conditions, the probability of rejecting the true hypothesis of congruence was greater than the 5% given by the ILD test and increased with the number of sites and the degree to which the tree was asymme...Continue Reading

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Citations

Feb 17, 2009·Journal of Plant Research·Izu A Fijridiyanto, Noriaki Murakami
Jul 16, 2010·Journal of Plant Research·Atsuko Takano, Hiroshi Okada
Jun 10, 2004·Molecular Phylogenetics and Evolution·Phillip Q SpinksWilliam P McCord
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Mar 17, 2004·Molecular Phylogenetics and Evolution·Patricia Escobar-PáramoGuillaume Lecointre
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