CAN 3 INCONGRUENCE TESTS PREDICT WHEN DATA SHOULD BE COMBINED

Advocates of conditional combination have argued that testing for inco ngruence between data partitions is an important step in data explorat ion. Unless the partitions have had distinct histories, as in horizont al gene transfer, incongruence means that one or more data partitions support the wrong phylogeny. This study examines the relationship betw een incongruence and phylogenetic accuracy using three statistical tes ts of incongruence. These tests were applied to pairs of mitochondrial DNA data partitions from two well-corroborated vertebrate phylogenies . Of the three tests, the most useful was the incongruence length diff erence test (ILD, also called the partition homogeneity test). This te st distinguished between cases in which combining the data generally i mproved phylogenetic accuracy (P > 0.01) and cases in which accuracy o f the combined data suffered relative to the individual partitions (P < 0.001). In contrast, in several cases, the Templeton and Rodrigo tes ts detected highly significant incongruence (P < 0.001) even though co mbining the incongruent partitions actually increased phylogenetic acc uracy. All three tests identified cases in which improving the reconst ruction model could improve the phylogenetic accuracy of the individua l partitions.