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Updated: May 10, 2026

Detection of Architectural Distortion in Prior Mammograms via Analysis of Oriented Patterns
Published on: August 30, 2013
An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters
Mark P Simmons1, Pablo A Goloboff
1Department of Biology, Colorado State University, Fort Collins, CO 80523, USA. psimmons@lamar.colostate.edu
Abstract:
Empirical and simulated examples are used to demonstrate an artifact caused by undersampling optimal trees in data matrices that consist mostly or entirely of locally sampled (as opposed to globally, for most or all terminals) characters. The artifact is that unsupported clades consisting entirely of terminals scored for the same locally sampled partition may be resolved and assigned high resampling support-despite their being properly unsupported (i.e., not resolved in the strict consensus of all optimal trees). This artifact occurs despite application of random-addition sequences for stepwise terminal addition. The artifact is not necessarily obviated with thorough conventional branch swapping methods (even tree-bisection-reconnection) when just a single tree is held, as is sometimes implemented in parsimony bootstrap pseudoreplicates, and in every GARLI, PhyML, and RAxML pseudoreplicate and search for the most likely tree for the matrix as a whole. Hence GARLI, RAxML, and PhyML-based likelihood results require extra scrutiny, particularly when they provide high resolution and support for clades that are entirely unsupported by methods that perform more thorough searches, as in most parsimony analyses.
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