When Does the Incongruence Length Difference Test Fail?

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 asymmetric. Finally, the comparison of the two data sets, simulated under contrasting tree structures (symmetric vs. asymmetric) but under the same evolutionary conditions, led us to reject the hypothesis of congruence, albeit weakly, particularly when the number of informative sites was low and among-site substitution rate heterogeneous. We conclude that the ILD test has only limited power to detect incongruence caused by differences in the evolutionary conditions or in the tree topology, except when numerous characters are present and the substitution rate is homogeneous from site to site.

Taxonomy and pathogenicity of two novel Chrysoporthe species from Eucalyptus grandis and Syzygium guineense in Zambia

“…This P-value was less than the conventionally accepted P-value of 0.05 required to combine data. However, several studies have accepted a Pvalue less than 0.05 and have further stated that the conventional P-value of 0.05 is conservative (Cunningham 1997;Darlu and Lecointre 2002;Dettman et al 2003). Furthermore, similar topology of the phylograms obtained from rDNA ITS and β-tubulin genes, and the increased bootstrap support for the groups obtained using the combined dataset, suggested that the data of these genes could be considered collectively.…”

Fourfold polyphyly of the genus formerly known as Upucerthia, with notes on the systematics and evolution of the avian subfamily Furnariinae

“…First, we calculated the significance of two-and three-partition versions of the ILD test. Although interpretation of this test's significance is problematic (Dolphin et al, 2000;Darlu and Lecointre, 2002;Barker and Lutzoni, 2002), it has been suggested that the test might serve as an initial screen for incongruence, given its propensity toward Type I rather than Type II error (Hipp et al, 2004). Second, we compared optimal trees from these gene regions under the ML criterion.…”

Multilocus sequence analysis of Fusarium pseudograminearum reveals a single phylogenetic species

“…All four loci were combined into the MLS, despite significant incongruence between genes as growing evidence indicates that combining all genes can improve the accuracy of phylogenies relative to individual gene phylogenies, or those based on only congruent gene sequences, even in the presence of significant incongruence (Cunningham 1997;Darlu & Lecointre 2002;Yoder et al 2001). Both BI and MP analysis of the MLS placed the species F. cerealis, F. culmorum, F. pseudograminearum and the Fg clade into separated clades with strong statistical support (PP ¼ 1.00, BS ¼ 100 %).…”