The utility of the incongruence length difference test.

Uninformative characters and apparent conflict between molecules and morphology.

Incongruence between different data sets remains one of the central issues in systematics. Numerous treebased and character-based tests to identify incongruence have been developed, and each has strengths and weaknesses (e.g., for reviews, see Cunningham 1997a; Johnson and Soltis 1998). Currently, one of the most widely used methods for evaluating incongruence within a parsimony framework is th...

Correcting the problem of false incongruence due to noise imbalance in the incongruence length difference (ILD) test.

The incongruence length difference (ILD) test is prone to suggesting significant conflict between character partitions when these differ only in the amount of undirected homoplasy (noise). This has been shown to be due to nonlinearity in the relationship between tree length and noise. Here we show that by standardizing either tree length or 1-retention index on a 0-to-1 scale, and then taking t...

Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test.

Can three incongruence tests predict when data should be combined?

Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one or more data support the wrong phylogeny. This study examines the relationship between incongruence and phylogenetic accuracy using three tes...

When does the incongruence length difference test fail?

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...

Escherichia coli molecular phylogeny using the incongruence length difference test.

Molecular phylogeny of the species Escherichia coli using the E. coli reference (ECOR) collection strains has been hampered by (1) the absence of rooting in the commonly used phenogram obtained from multilocus enzyme electrophoresis (MLEE) data and (2) the existence of recombination events between strains that scramble phylogenetic trees reconstructed from the nucleotide sequences of genes. We ...