Molecular Biology and Evolution, Vol 14, 733-740, Copyright © 1997 by Society for Molecular Biology and Evolution
CW Cunningham
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 tests 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 difference test (ILD, also called the
partition homogeneity test). This test distinguished between cases in which
combining the data generally improved phylogenetic accuracy (P > 0.01)
and cases in which accuracy of the combined data suffered relative to the
individual partitions (P < 0.001). In contrast, in several cases, the
Templeton and Rodrigo tests detected highly significant incongruence (P
< 0.001) even though combining the incongruent partitions actually
increased phylogenetic accuracy. All three tests identified cases in which
improving the reconstruction model would improve the phylogenetic accuracy
of the individual partitions.
ORIGINAL ARTICLE
Can three incongruence tests predict when data should be combined?
Zoology Department, Duke University, Durham, North Carolina 27705, USA. cliff@acpub.duke.edu
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