Noise and incongruence: Interpreting results of the incongruence length difference test

Incongruence between data sets is an important concept in molecular phyloge netics and is commonly measured by the incongruence length difference (ILD) test (J. S. Farris et al. Cladistics 10, 315-319). The ILD test has been u sed to infer specific evolutionary events and to determine whether to combi ne data sets for phylogenetic analysis. However, the interpretation in the literature of the test's results varies because authors have conflicting ex pectations of the effect that noise will have. Using simulations we demonst rate that noise can by itself generate highly significant results in the IL D test and demonstrate why this is the case. To clarify the interpretation of test results, we suggest an additional procedure in which the result is compared against a frequency distribution generated from completely shuffle d data. As examples, we apply this approach to two previous studies that ha ve reported incongruence. (C) 2000 Academic Press.