Rota, J. & Wahlberg, N. (2012). Exploration of data partitioning in an eight-gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae). —Zoologica Scripta, 41, 536–546. (Link)
Unintended disagreements occur when a parent (B) is
thinned by swapping a child (E) to another part of the
taxonomic tree, resulting in existing IDs of the parent being interpreted
as disagreements with existing IDs of the swapped child.
Identification
ID 2 of taxon E will be an unintended disagreement with ID 1 of taxon B after the taxon swap
If thinning a parent results in more than 10 unintended disagreements, you
should split the parent after swapping the child to replace existing IDs
of the parent (B) with IDs that don't disagree.
